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WO2025122500A1 - Fusions de gènes esr1 et leurs utilisations - Google Patents

Fusions de gènes esr1 et leurs utilisations Download PDF

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Publication number
WO2025122500A1
WO2025122500A1 PCT/US2024/058267 US2024058267W WO2025122500A1 WO 2025122500 A1 WO2025122500 A1 WO 2025122500A1 US 2024058267 W US2024058267 W US 2024058267W WO 2025122500 A1 WO2025122500 A1 WO 2025122500A1
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Prior art keywords
esri
nucleic acid
fusion
acid molecule
gene
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English (en)
Inventor
Hanna TUKACHINSKY
Sally TRABUCCO
Christine Anna PARACHONIAK
Samantha MORLEY
Mark Rosenzweig
Pierre VANDEN BORRE
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Foundation Medicine Inc
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Foundation Medicine Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • ESRE estrogen receptor 1
  • Endocrine therapy has been highly successful in targeted treatment for cancers such as estrogen receptor-positive (ER+) breast cancer, including selective ER modulators or degraders that inhibit estradiol-ER binding and aromatase inhibitors that reduce estradiol production.
  • ESRI mutations (ESR 1 mut) are an established biomarker of ET resistance in patients (pts) with hormone receptor positive (HR+) MBC.
  • ES'/?/mut acquired in response to standard-of-care ET now confer access to novel ET recently approved by health authorities.
  • ESRI mutations and fusions have been described in breast cancer and associated with resistance to ET (see, e.g., Hartmaier, R.J. et al. (2016) Ann Oncol.
  • a method of selecting a therapy for an individual having breast cancer or for identifying an individual having breast cancer who may benefit from a treatment comprising an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor comprising detecting in a sample from the individual an estrogen receptor 1 (ESRI) fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ES
  • a method of identifying one or more treatment options for an individual having breast cancer comprising detecting or acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and generating a report comprising one or more treatment options identified for the individual based, at least in part, on detection or on acquiring knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule,
  • a method of selecting a treatment for an individual having breast cancer comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI00422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein responsive to the acquisition of said knowledge: (i) the individual is classified as a candidate to receive a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an anti-cancer agent other than a
  • a method of predicting survival of an individual having breast cancer, or an individual having breast cancer treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof; wherein responsive to the acquisition of said knowledge, the individual is predicted to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase
  • a method of treating or delaying progression of breast cancer comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual having breast cancer, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and responsive to said knowledge, administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • a method of treating or delaying progression of breast cancer comprising administering to an individual having breast cancer an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor, wherein the anti-cancer agent is administered responsive to acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • a method of treating or delaying progression of breast cancer comprising detecting an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual having breast cancer, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof; and administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • a method of monitoring, evaluating or screening an individual having breast cancer comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein responsive to the acquisition of said knowledge, the individual is predicted to benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor and/or to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as
  • a method of detecting an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide in breast cancer comprising detecting an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual having breast cancer, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2. IYD, IMPG1, STAG2. TNRC6B. or C6orfl5, or a portion thereof.
  • a method of detecting the presence or absence of breast cancer in an individual comprising detecting the presence or absence of breast cancer in a sample from the individual; and detecting an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI 00422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the method further comprises detecting the presence of breast cancer in a sample from the individual; and/or detecting the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual.
  • a method of monitoring progression or recurrence of breast cancer in an individual comprising detecting, in a first sample obtained from the individual at a first time point, the presence or absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; detecting, in a second sample obtained from the individual at a second time point after the first time point, the presence or absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; and providing an assessment of breast cancer progression or breast cancer recurrence in the individual based, at least in part, on the presence or absence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample; wherein the ES
  • the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample identifies the individual as having decreased risk of breast cancer progression or breast cancer recurrence when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the method further comprises selecting a treatment, administering a treatment, adjusting a treatment, adjusting a dose of a treatment, or applying a treatment to the individual based, at least in part, on detecting the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample, wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • a method of monitoring resistance to endocrine therapy in an individual with breast cancer comprising detecting, in a sample obtained from the individual during or after treatment with an endocrine therapy, an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; and providing an assessment of resistance to endocrine therapy in the individual based, at least in part, on the detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample; wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2.
  • the method further comprises after providing the assessment of resistance to endocrine therapy, administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor; wherein optionally the method further comprises halting administration of an endocrine therapy to the individual based, at least in part, on the detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • a method of monitoring sensitivity to endocrine therapy in an individual with breast cancer comprising detecting, in a sample obtained from the individual before, during, or after treatment with an endocrine therapy, absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; and providing an assessment of sensitivity to endocrine therapy in the individual based, at least in part, on the detection of the absence of an ESRI fusion nucleic acid molecule, or ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample; wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPGI, STAG2, TNRC6
  • the method further comprises, prior to the detection or acquisition of knowledge, administering to the individual an effective amount of an endocrine therapy.
  • the individual has previously been treated with an endocrine therapy.
  • the endocrine therapy comprises treatment with a SERM or an aromatase inhibitor.
  • a method of detecting an ESRI fusion nucleic acid molecule comprising providing a plurality of nucleic acid molecules obtained from a sample from an individual having breast cancer, wherein the plurality of nucleic acid molecules comprises nucleic acid molecules corresponding to an ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI 00422737, SNAP9I, ZBTB2, IYD, IMPGI, STAG2, TNRC6B, or C6orfl5, or a portion thereof; optionally, ligating one or more adapters onto one or more nucleic acid molecules from the plurality of nucleic acid molecules; optionally, amplifying the one or more ligated nucleic acid molecules from the plurality of nucleic acid molecules; optionally, capturing ampl
  • a method of detecting an ESRI fusion nucleic acid molecule comprising providing a sample from an individual having breast cancer, wherein the sample comprises a plurality of nucleic acid molecules; preparing a nucleic acid sequencing library from the plurality of nucleic acid molecules in the sample; amplifying said library; selectively enriching for one or more nucleic acid molecules comprising nucleotide sequences corresponding to an ESRI fusion nucleic acid molecule in said library to produce an enriched sample, wherein the an ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; sequencing the enriched sample, thereby producing a plurality of sequence reads; analyzing the
  • the one or more adapters comprise amplification primers, flow cell adapter sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the library, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule, and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the amplified nucleic acid molecules are captured by hybridization with one or more bait molecules.
  • the amplifying comprises performing a polymerase chain reaction (PCR) amplification technique, a non-PCR amplification technique, or an isothermal amplification technique.
  • PCR polymerase chain reaction
  • the methods further comprise selectively enriching for one or more nucleic acid molecules in the sample comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule; wherein the selectively enriching produces an enriched sample.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the sample, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules in the sample comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the one or more bait molecules comprise a capture nucleic acid molecule configured to hybridize to a nucleotide sequence corresponding to the ESRI fusion nucleic acid molecule.
  • the capture nucleic acid molecule comprises between about 10 and about 30 nucleotides, between about 50 and about 1000 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, or between about 100 and about 200 nucleotides.
  • the one or more bait molecules are conjugated to an affinity reagent or to a detection reagent.
  • the affinity reagent is an antibody, an antibody fragment, or biotin, or wherein the detection reagent is a fluorescent marker.
  • the capture nucleic acid molecule comprises a DNA, RNA, or mixed DNA/RNA molecule.
  • the selectively enriching comprises amplifying the one or more nucleic acid molecules comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule using a polymerase chain reaction (PCR) to produce an enriched sample.
  • the methods further comprise sequencing the enriched sample.
  • the plurality of nucleic acid molecules comprises a mixture of cancer nucleic acid molecules and non-cancer nucleic acid molecules.
  • the cancer nucleic acid molecules are derived from a tumor portion of a heterogeneous tissue biopsy sample, and the non-cancer nucleic acid molecules are derived from a normal portion of the heterogeneous tissue biopsy sample.
  • the sample comprises a liquid biopsy sample, and wherein the cancer nucleic acid molecules are derived from a circulating tumor DNA (ctDNA) fraction of the liquid biopsy sample, and the non-cancer nucleic acid molecules are derived from a nontumor fraction of the liquid biopsy sample.
  • the ctDNA fraction of the liquid biopsy sample comprises at least 1% of nucleic acid molecules in the liquid biopsy sample.
  • the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the sequencing comprises a massively parallel sequencing technique, and the massively parallel sequencing technique comprises next- generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next- generation sequencing
  • a method of identifying a candidate treatment for breast cancer in an individual in need thereof comprising: performing DNA sequencing on a sample obtained from the individual to determine a sequencing mutation profile, wherein the sequencing mutation profile identifies presence of an ESRI fusion nucleic acid molecule in the sample, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the presence of the ESRI fusion nucleic acid molecule in the sample identifies the individual as one who may benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or predicts the individual to have longer survival when treated with a treatment comprising an anti- cancer agent other than a SERM or an aromatase inhibitor, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the sequencing comprises a massively parallel sequencing technique, and the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next generation sequencing
  • the sequencing mutation profile identifies a fragment of the ESRI fusion nucleic acid molecule comprising a breakpoint or fusion junction.
  • the methods further comprise generating a molecular profile for the individual, based, at least in part, on detecting or acquiring knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample from the individual.
  • the molecular profile for the individual further comprises results from a comprehensive genomic profiling (CGP) test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP genomic profiling
  • the molecular profile for the individual further comprises results from a nucleic acid sequencingbased test.
  • the methods further comprise selecting a treatment, administering a treatment, or applying a treatment to the individual based on the generated molecular profile, wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the methods further comprise generating a report, wherein the report comprises the molecular profile for the individual.
  • the report further comprises information on a treatment or one or more treatment options identified or selected for the individual based, at least in part, on the molecular profile for the individual, wherein the treatment or one or more treatment options comprise an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the methods further comprise providing the report to the individual, a caregiver, a healthcare provider, a physician, an oncologist, an electronic medical record system, a hospital, a clinic, a third-party payer, an insurance company, or a government office.
  • the individual is a human.
  • the methods further comprise obtaining the sample from the individual.
  • the sample is obtained or derived from the breast cancer.
  • the sample comprises a tissue biopsy sample, a liquid biopsy sample, or a normal control.
  • the sample is from a tumor biopsy, tumor specimen, or circulating tumor cell.
  • the sample is a liquid biopsy sample comprising blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the sample comprises cells and/or nucleic acids from the breast cancer.
  • the sample comprises mRNA, DNA, circulating tumor DNA (ctDNA), cell-free DNA, or cell-free RNA from the breast cancer.
  • the sample is a liquid biopsy sample comprising circulating tumor cells (CTCs).
  • the sample is a liquid biopsy sample comprising cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), or any combination thereof.
  • the acquiring knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises detecting the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • detecting the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample comprises detecting a fragment of the ESRI fusion nucleic acid molecule, or of the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, comprising a breakpoint or fusion junction.
  • the ESRI fusion nucleic acid molecule is detected in the sample by one or more of: a nucleic acid hybridization assay, an amplification-based assay, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, real-time PCR, a screening analysis, fluorescence in situ hybridization (FISH), spectral karyotyping, multicolor FISH (mFISH), comparative genomic hybridization, in situ hybridization, sequence-specific priming (SSP) PCR, high-performance liquid chromatography (HPEC), mass-spectrometric genotyping, or sequencing.
  • a nucleic acid hybridization assay an amplification-based assay, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, real-time PCR, a screening analysis, fluorescence in situ hybridization (FISH), spectral karyotyping, multicolor FISH (mFISH), comparative genomic hybridization, in situ hybrid
  • the sequencing comprises a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the massively parallel sequencing (MPS) technique comprises next-generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next-generation sequencing
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule is detected in the sample by one or more of: immunoblotting, enzyme linked immunosorbent assay (ELISA), immunohistochemistry, or mass spectrometry.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule is oncogenic; optionally wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule promotes cancer cell survival, angiogenesis, cancer cell proliferation, and any combination thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule confers resistance to an endocrine therapy.
  • the anti-cancer agent comprises one or more of a small molecule inhibitor, an antibody, a cellular therapy, a nucleic acid, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), a treatment for cancer comprising an ESRI gene fusion or rearrangement, an anti-cancer agent being tested in a clinical trial, a treatment for cancer comprising an ESRI gene fusion or rearrangement being tested in a clinical trial, or any combination thereof.
  • PROTAC PROteolysis-TArgeting Chimera
  • the anticancer agent comprises a selective estrogen receptor covalent antagonist (SERCA).
  • the anti-cancer agent is H3B-5942 or H3B-6545.
  • the anti-cancer agent comprises a selective estrogen receptor degrader (SERD).
  • SESD selective estrogen receptor degrader
  • the anti-cancer agent is fulvestrant, elacestrant, amcenestrant, camizestrant, giredestrant, rintodestrant, imlunestrant, ZB-716, Zn-c5, LSZ102, LY3484356, or D-0502, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent comprises a PROTAC.
  • the PROTAC is ARV-471.
  • the anti-cancer agent comprises a CDK4/6 inhibitor.
  • the CDK4/6 inhibitor is palbociclib, abemaciclib, ribociclib, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent comprises treatment with a SERD and a CDK4/6 inhibitor.
  • the anti-cancer agent comprises a PI3K inhibitor.
  • the PI3K inhibitor is GSK2636771, buparlisib, AZD8186, copanlisib, LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib, pictilisib, GDC0032, IPI145, INK1117, SAR260301, KIN-193, duvelisib, GS-9820, GSK2636771, GDC-0980, AMG319, paxalisib, or alpelisib, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent comprises an mTOR inhibitor.
  • the mTOR inhibitor is temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, or OSI027, or a pharmaceutically acceptable salt thereof.
  • the nucleic acid inhibits the expression of an ESRI nucleic acid molecule, or an ESRI polypeptide encoded by the ESRI nucleic acid molecule.
  • the nucleic acid is a double-stranded RNA (dsRNA), a small interfering RNA (siRNA), or a small hairpin RNA (shRNA).
  • the cellular therapy is an adoptive therapy, a T cell-based therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR)-T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, a macrophage-based therapy, an induced pluripotent stem cell-based therapy, a B cell-based therapy, or a dendritic cell (DC)-based therapy.
  • the treatment or the one or more treatment options further comprise an additional anti-cancer therapy.
  • the additional anti-cancer therapy comprises one or more of a small molecule inhibitor, a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti- angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy, an anti-neoplastic agent, a growth inhibitory agent, a cytotoxic agent, a vaccine, a small molecule agonist, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), or any combination thereof.
  • the anti-cancer agent comprises a SERD
  • the additional anti-cancer therapy comprises a CDK4/6 inhibitor.
  • the SERM is tamoxifen, raloxifene, EM652, GW7604, keoxifene, toremifene, kaledoxifene, broparestrol, clomifene, cyclofenil, lasofoxifene, ormeloxifene, or ospemifene.
  • the aromatase inhibitor is aminoglutethimide, testolactone, anastrozole, letrozole, exemestane, vorozole, formestane, fadrozole, 4-hydroxy androstenedione, 1,4,6- androstatrien-3, 17-dione (ATD), 4- Androstene-3, 6, 17-trione (“6-OXO”), or a pharmaceutically acceptable salt thereof.
  • an endocrine therapy comprises a SERM or an aromatase inhibitor.
  • the breast cancer is advanced or metastatic. In some embodiments, the breast cancer is hormone receptor positive (HR+) breast cancer. In some embodiments, the cancer is endometrial cancer.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, encoding an ESRI DNA binding domain, or a portion thereof, to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI DNA binding domain, or a portion thereof, fused to a polypeptide encoded by any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exon 2 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exons 1-2 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a EOC100422737 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a EOC 100422737 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a EOC100422737 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the IMPG1 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the IMPG1 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IMPG1 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IMPG1 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C- terminus direction, an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof.
  • a system for detecting an ESRI fusion nucleic acid molecule e.g., according to any one of the embodiments disclosed herein.
  • the system comprises a memory configured to store one or more program instructions; and one or more processors configured to execute the one or more program instructions, the one or more program instructions when executed by the one or more processors are configured to perform the method according to any one of the embodiments disclosed herein.
  • the system comprises a memory configured to store one or more program instructions; and one or more processors configured to execute the one or more program instructions, the one or more program instructions when executed by the one or more processors are configured to obtain a plurality of sequence reads of one or more nucleic acid molecules, wherein the one or more nucleic acid molecules are derived from a sample obtained from an individual having breast cancer; analyze the plurality of sequence reads for presence of an ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and detect, based on the analyzing, the ESRI fusion nucleic acid molecule in the sample.
  • the one or more processors configured to execute the one or more program
  • a non-transitory computer readable storage medium comprising one or more programs executable by one or more computer processors for detecting an ESRI fusion nucleic acid molecule, e.g., according to any one of the embodiments disclosed herein.
  • the method comprises obtaining, using the one or more processors, a plurality of sequence reads of one or more nucleic acid molecules, wherein the one or more nucleic acid molecules are derived from a sample obtained from an individual having breast cancer; analyzing, using the one or more processors, the plurality of sequence reads for presence of an ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and detecting, using the one or more processors and based on the analyzing, the ESRI fusion nucleic acid molecule in the sample.
  • the method further comprises generating, using the one or more processors, a genomic profile for the sample.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule confers resistance to an endocrine therapy.
  • the plurality of sequence reads is obtained by sequencing; optionally wherein the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; and optionally wherein the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • the individual is administered a treatment based at least in part on the genomic profile; optionally wherein the treatment comprises an anticancer agent other than a SERM or an aromatase inhibitor.
  • the genomic profile further comprises results from a comprehensive genomic profiling (CGP) test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP genomic profiling
  • the genomic profile further comprises results from a nucleic acid sequencingbased test.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, encoding an ESRI DNA binding domain, or a portion thereof, to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI DNA binding domain, or a portion thereof, fused to a polypeptide encoded by any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exon 2 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exons 1-2 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a EOC100422737 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a EOC 100422737 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a EOC100422737 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the IMPG1 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the IMPG1 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IMPG1 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IMPG1 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C- terminus direction, an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof.
  • FIGS. 1 & 2 show the ESRI mutational landscape observed in liquid and tissue biopsies from patients with metastatic breast cancer (MBC). Shown are ESRI fusions (arrow) detected in liquid and tissue biopsies (as indicated) relative to other ESRI mutations (FIG. 1) or relative to rare ESRI mutations (FIG. 2). Graphs show raw count (n) observed for each mutation or fusion, as indicated.
  • FIG. 3A shows variant allele frequency of ESRI fusions (x) in liquid biopsies with highly polyclonal ESRI resistance. Shown are percent tumor fraction and variant allele frequency for 77 liquid biopsies with 4 or more ESRI mutations or fusions. Data for ESRI fusions are circled.
  • FIG. 3B shows fusion junctions of ESRI fusions observed in tissue or liquid biopsies.
  • FIG. 4 shows ESRI co-occurring mutations in liquid biopsies. ESRI fusions indicated with arrows.
  • FIG. 5 shows ESRI co-occurring mutations in tissue biopsies. ESRI fusions indicated with arrows.
  • FIG. 6 depicts an exemplary device, in accordance with some embodiments.
  • FIG. 7 depicts an exemplary system, in accordance with some embodiments.
  • FIG. 8 depicts a block diagram of an exemplary process for detecting an ESRI fusion nucleic acid molecule of the present disclosure, in accordance with some embodiments.
  • the present disclosure relates generally to detecting ESRI gene fusions in cancer, as well as methods of treatment, and uses related thereto.
  • the present disclosure describes the results of comprehensive genomic profiling (CGP) of tissue and liquid biopsies from patients with metastatic breast cancer (MBC), which identified 28 fusions of the ESRI DNA binding domain to 13 unique gene partners.
  • CGP genomic profiling
  • MSC metastatic breast cancer
  • SERM selective estrogen receptor modulator
  • aromatase inhibitor to which an ESRI gene fusion may confer resistance.
  • cancer and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Included in this definition are benign and malignant cancers.
  • ESRl refers to a gene encoding an estrogen receptor 1 polypeptide.
  • the human ESRI gene is located on chromosome 6q25.1-q25.2.
  • ESRI is also known as ER, ESR, Era, ESRA, ESTRR, and NR3AL
  • an ESRI gene is a human ESRI gene.
  • An exemplary ESRI amino acid sequence is provided below.
  • references to a specific ESRI mutation by amino acid position refer to amino acid numbering according to SEQ ID NO:1.
  • the DNA-binding domain of ESRI is made up of amino acids 180-261 according to SEQ ID NO:1.
  • nucleic acid refers to polymers of nucleotides of any length, and include DNA and RNA.
  • the nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction.
  • polynucleotides as defined herein include, without limitation, single- and double- stranded DNA, DNA including single- and double- stranded regions, single- and double- stranded RNA, and RNA including single- and double- stranded regions, hybrid molecules comprising DNA and RNA that may be single- stranded or, more typically, double-stranded or include single- and double- stranded regions.
  • polynucleotide refers to triple- stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules.
  • the regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules.
  • One of the molecules of a triple-helical region often is an oligonucleotide.
  • the term “polynucleotide” specifically includes cDNAs.
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer.
  • the sequence of nucleotides may be interrupted by nonnucleotide components.
  • a polynucleotide may be further modified after synthesis, such as by conjugation with a label.
  • modifications include, for example, “caps,” substitution of one or more of the naturally-occurring nucleotides with an analog, intemucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, and the like) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, and the like), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, and the like), those with intercalators (e.g., acridine, psoralen, and the like), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, and the like), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acid,
  • any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports.
  • the 5' and 3' terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms.
  • Other hydroxyls may also be derivatized to standard protecting groups.
  • Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2'-0-methyl-, 2'-0-allyl-, 2'-fluoro-, or 2'- azido-ribose, carbocyclic sugar analogs, a-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs, and abasic nucleoside analogs such as methyl riboside.
  • One or more phosphodiester linkages may be replaced by alternative linking groups.
  • linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(0)S ("thioate”), P(S)S ("dithioate”), "(0)NR 2 ("amidate”), P(0)R, P(0)OR', CO or
  • each R or R' is independently H or substituted or unsubstituted alkyl (1 -20 C) optionally containing an ether (-0-) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical.
  • a polynucleotide can contain one or more different types of modifications as described herein and/or multiple modifications of the same type. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.
  • Oligonucleotide generally refers to short, single stranded, polynucleotides that are, but not necessarily, less than about 250 nucleotides in length. Oligonucleotides may be synthetic. The terms “oligonucleotide” and “polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.
  • antibody herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
  • Antibody fragments comprise a portion of an intact antibody comprising the antigen-binding region thereof.
  • the antibody fragment described herein is an antigen-binding fragment.
  • Examples of antibody fragments include Fab, Fab', F(ab')2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multispecific antibodies formed from antibody fragments.
  • the term “detection” includes any means of detecting, including direct and indirect detection.
  • biomarker refers to an indicator, e.g., predictive, diagnostic, and/or prognostic, which can be detected in a sample.
  • the biomarker may serve as an indicator of a particular subtype of a disease or disorder (e.g., cancer) characterized by certain, molecular, pathological, histological, and/or clinical features (e.g., responsiveness to therapy including an immunotherapy, such as a checkpoint inhibitor).
  • a biomarker is a collection of genes and/or a collective number of mutations/alterations (e.g., somatic mutations) in a collection of genes, for example, a biomarker may comprise an ESRI gene fusion, fusion nucleic acid molecule, or fusion polypeptide.
  • Biomarkers include, but are not limited to, polynucleotides (e.g., DNA and/or RNA), polynucleotide alterations (e.g., polynucleotide copy number alterations, e.g., DNA copy number alterations), polypeptides, polypeptide and polynucleotide modifications (e.g., post-translational modifications), carbohydrates, and/or glycolipid-based molecular markers.
  • polynucleotides e.g., DNA and/or RNA
  • polynucleotide alterations e.g., polynucleotide copy number alterations, e.g., DNA copy number alterations
  • polypeptides e.g., polypeptide and polynucleotide modifications (e.g., post-translational modifications)
  • carbohydrates e.g., glycolipid-based molecular markers.
  • “Amplification,” as used herein generally refers to the process of producing multiple copies of a desired sequence. “Multiple copies” mean at least two copies. A “copy” does not necessarily mean perfect sequence complementarity or identity to the template sequence. For example, copies can include nucleotide analogs such as deoxyinosine, intentional sequence alterations (such as sequence alterations introduced through a primer comprising a sequence that is hybridizable, but not complementary, to the template), and/or sequence errors that occur during amplification.
  • PCR polymerase chain reaction
  • sequence information from the ends of the region of interest or beyond needs to be available, such that oligonucleotide primers can be designed; these primers will be identical or similar in sequence to opposite strands of the template to be amplified.
  • the 5' terminal nucleotides of the two primers may coincide with the ends of the amplified material.
  • PCR can be used to amplify specific RNA sequences, specific DNA sequences from total genomic DNA, and cDNA transcribed from total cellular RNA, bacteriophage, or plasmid sequences, etc. See generally Mullis et al., Cold Spring Harbor Symp. Quant. Biol. 51:263 (1987) and Erlich, ed., PCR Technology (Stockton Press, NY, 1989).
  • PCR is considered to be one, but not the only, example of a nucleic acid polymerase reaction method for amplifying a nucleic acid test sample, comprising the use of a known nucleic acid (DNA or RNA) as a primer and utilizes a nucleic acid polymerase to amplify or generate a specific piece of nucleic acid or to amplify or generate a specific piece of nucleic acid which is complementary to a particular nucleic acid.
  • DNA or RNA DNA or RNA
  • diagnosis is used herein to refer to the identification or classification of a molecular or pathological state, disease or condition (e.g., cancer).
  • diagnosis may refer to identification of a particular type of cancer.
  • Diagnosis may also refer to the classification of a particular subtype of cancer, for instance, by histopathological criteria, or by molecular features (e.g., a subtype characterized by expression of one or a combination of biomarkers (e.g., particular genes or proteins encoded by said genes)).
  • a method of aiding diagnosis of a disease or condition can comprise measuring certain somatic mutations in a biological sample from an individual.
  • sample refers to a composition that is obtained or derived from a subject and/or individual of interest that contains a cellular and/or other molecular entity that is to be characterized and/or identified, for example, based on physical, biochemical, chemical, and/or physiological characteristics.
  • disease sample and variations thereof refers to any sample obtained from a subject of interest that would be expected or is known to contain the cellular and/or molecular entity that is to be characterized.
  • Samples include, but are not limited to, tissue samples, primary or cultured cells or cell lines, cell supernatants, cell lysates, platelets, serum, plasma, vitreous fluid, lymph fluid, synovial fluid, follicular fluid, seminal fluid, amniotic fluid, milk, whole blood, plasma, serum, blood-derived cells, urine, cerebro- spinal fluid, saliva, sputum, tears, perspiration, mucus, tumor lysates, and tissue culture medium, tissue extracts such as homogenized tissue, tumor tissue, cellular extracts, and combinations thereof.
  • the sample is a whole blood sample, a plasma sample, a serum sample, or a combination thereof.
  • the sample is from a tumor (e.g., a “tumor sample”), such as from a biopsy.
  • the sample is a formalin-fixed paraffin-embedded (FFPE) sample.
  • FFPE formalin-fixed paraffin-embedded
  • a “tumor cell” as used herein refers to any tumor cell present in a tumor or a sample thereof. Tumor cells may be distinguished from other cells that may be present in a tumor sample, for example, stromal cells and tumor-infiltrating immune cells, using methods known in the art and/or described herein.
  • segmentation refers to a process for partitioning of sequence read data into a number of non-overlapping segments that cover all sequence read data points, such that each segment of a plurality of segments is as homogeneous as possible and all sequence reads associated with a given segment have the same copy number.
  • segmentation may be performed by processing aligned sequence read data (or other sequencing-related data, e.g., coverage data, allele frequency data, etc., derived from the sequence read data) using any of a variety of methods known to those of skill in the art (see., e.g., Braun and Miller (1998), “Statistical methods for DNA sequence segmentation”, Statistical Science 13(2): 142-162).
  • segmentation methods include, but are not limited to, circular binary segmentation (CBS) methods, maximum likelihood methods, hidden Markov chain methods, walking Markov methods, Bayesian methods, long-range correlation methods, change point methods, or any combination thereof.
  • CBS circular binary segmentation
  • a “reference sample,” “reference cell,” “reference tissue,” “control sample,” “control cell,” or “control tissue,” as used herein, refer to a sample, cell, tissue, standard, or level that is used for comparison purposes.
  • correlate or “correlating” is meant comparing, in any way, the performance and/or results of a first analysis or protocol with the performance and/or results of a second analysis or protocol. For example, one may use the results of a first analysis or protocol in carrying out a second protocol and/or one may use the results of a first analysis or protocol to determine whether a second analysis or protocol should be performed. With respect to the embodiment of polypeptide analysis or protocol, one may use the results of the polypeptide expression analysis or protocol to determine whether a specific therapeutic regimen should be performed. With respect to the embodiment of polynucleotide analysis or protocol, one may use the results of the polynucleotide expression analysis or protocol to determine whether a specific therapeutic regimen should be performed.
  • ‘Individual response” or “response” can be assessed using any endpoint indicating a benefit to the individual, including, without limitation, (1) inhibition, to some extent, of disease progression (e.g., cancer progression), including slowing down or complete arrest; (2) a reduction in tumor size; (3) inhibition (i.e., reduction, slowing down, or complete stopping) of cancer cell infiltration into adjacent peripheral organs and/or tissues; (4) inhibition (i.e.
  • metastasis a condition in which metastasis is reduced or complete stopping.
  • relief, to some extent, of one or more symptoms associated with the disease or disorder e.g., cancer
  • increase or extension in the length of survival, including overall survival and progression free survival e.g., decreased mortality at a given point of time following treatment.
  • an “effective response” of a patient or a patient's “responsiveness” to treatment with a medicament and similar wording refers to the clinical or therapeutic benefit imparted to a patient at risk for, or suffering from, a disease or disorder, such as cancer.
  • a disease or disorder such as cancer.
  • such benefit includes any one or more of: extending survival (including overall survival and/or progression-free survival); resulting in an objective response (including a complete response or a partial response); or improving signs or symptoms of cancer.
  • an “effective amount” refers to an amount of a therapeutic agent to treat or prevent a disease or disorder in a mammal.
  • the therapeutically effective amount of the therapeutic agent may reduce the number of cancer cells; reduce the primary tumor size; inhibit (i.e., slow to some extent, and in some embodiments stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent, and in some embodiments stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the disorder.
  • the drug may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic.
  • efficacy in vivo can, for example, be measured by assessing the duration of survival, time to disease progression (TTP), response rates (e.g., CR and PR), duration of response, and/or quality of life.
  • pharmaceutical formulation refers to a preparation which is in such form as to permit the biological activity of an active ingredient contained therein to be effective, and which contains no additional components which are unacceptably toxic to a subject to which the formulation would be administered.
  • a “pharmaceutically acceptable carrier” refers to an ingredient in a pharmaceutical formulation, other than an active ingredient, which is nontoxic to a subject.
  • a pharmaceutically acceptable carrier includes, but is not limited to, a buffer, excipient, stabilizer, or preservative.
  • treatment refers to clinical intervention in an attempt to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastasis, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • the terms “individual,” “patient,” or “subject” are used interchangeably and refer to any single animal, e.g., a mammal (including such non-human animals as, for example, dogs, cats, horses, rabbits, zoo animals, cows, pigs, sheep, and non- human primates) for which treatment is desired.
  • a mammal including such non-human animals as, for example, dogs, cats, horses, rabbits, zoo animals, cows, pigs, sheep, and non- human primates
  • the patient, individual or subject herein is a human.
  • administering refers to a method of giving a dosage of an agent or a pharmaceutical composition (e.g., a pharmaceutical composition including the agent) to a subject (e.g., a patient).
  • Administering can be by any suitable means, including parenteral, intrapulmonary, and intranasal, and, if desired for local treatment, intralesional administration.
  • Parenteral infusions include, for example, intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration.
  • Dosing can be by any suitable route, e.g., by injections, such as intravenous or subcutaneous injections, depending in part on whether the administration is brief or chronic.
  • Various dosing schedules including, but not limited to, single or multiple administrations over various time-points, bolus administration, and pulse infusion are contemplated herein.
  • concurrent administration includes a dosing regimen wherein the administration of one or more agent(s) continues after discontinuing the administration of one or more other agent(s).
  • package insert is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, combination therapy, contraindications, and/or warnings concerning the use of such therapeutic products.
  • An “article of manufacture” is any manufacture (e.g., a package or container) or kit comprising at least one reagent, e.g., a medicament for treatment of a disease or disorder (e.g., cancer), or a reagent for specifically detecting a biomarker described herein.
  • the manufacture or kit is promoted, distributed, or sold as a unit for performing the methods described herein.
  • the phrase “based on” when used herein means that the information about one or more biomarkers is used to inform a treatment decision, information provided on a package insert, or marketing/promotional guidance, etc.
  • provided herein are methods for selecting a therapy for an individual having cancer.
  • SERM selective estrogen receptor modulator
  • provided herein are methods for identifying one or more treatment options for an individual having cancer.
  • methods for selecting a treatment for an individual having cancer are methods for predicting survival of an individual having cancer.
  • provided herein are methods for treating or delaying progression of cancer.
  • methods for monitoring, evaluating or screening an individual having cancer are provided herein.
  • provided herein are methods for assessing an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide, in cancer in an individual. In some aspects, provided herein are methods for detecting an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide in cancer, or in a sample obtained from a cancer or from an individual diagnosed with, suspected to have, or being screen for cancer. In some aspects, provided herein are methods for detecting the presence or absence of cancer in an individual. In some aspects, provided herein are methods for monitoring progression or recurrence of breast cancer in an individual. In some aspects, provided herein are methods for monitoring resistance to endocrine therapy in an individual with cancer. In some aspects, provided herein are methods for monitoring sensitivity or responsiveness to endocrine therapy in an individual with cancer.
  • the methods comprise detecting e.g., in a sample from the individual) an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the methods provided herein comprise detecting in a sample from an individual, e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer, an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule.
  • detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide, in the sample identifies the individual as one who may benefit from a treatment comprising an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor.
  • SERM selective estrogen receptor modulator
  • the methods comprise selecting an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor as a treatment for an individual having cancer, e.g., responsive to detection of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual, e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer.
  • SERM selective estrogen receptor modulator
  • the methods comprise generating a report comprising one or more treatment options identified for an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) based at least in part on detection of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • detection of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide, in the sample identifies the individual as one who may benefit from a treatment comprising an endocrine therapy.
  • the methods comprise selecting an endocrine therapy as a treatment for an individual having cancer, e.g., responsive to detection of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual, e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer.
  • the methods comprise generating a report comprising one or more treatment options identified for an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) based at least in part on detection of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • the one or more treatment options comprise an endocrine therapy.
  • the methods comprise administering to an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) an effective amount of a treatment that comprises an anti-cancer therapy, such as an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor, responsive to detecting an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • an anti-cancer therapy such as an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor
  • the methods comprise administering to an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) an effective amount of a treatment that comprises an endocrine therapy, responsive to detecting the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • an individual e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer
  • an effective amount of a treatment that comprises an endocrine therapy responsive to detecting the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer)
  • the individual is predicted to have longer survival when treated with a treatment comprising an anti-cancer therapy, such as an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • an anti-cancer therapy such as an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor
  • the methods comprise providing an assessment of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, e.g., responsive to detecting the presence or absence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide, in a sample.
  • responsive to detection of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer), the individual is predicted to be resistant to an endocrine therapy.
  • the methods comprise detecting or acquiring knowledge of the presence or absence of a cancer in a sample from the individual.
  • the methods comprise detecting, in a first sample obtained from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) at a first time point, the presence or absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; detecting, in a second sample obtained from the individual at a second time point after the first time point, the presence or absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; and providing an assessment of cancer progression or cancer recurrence in the individual based, at least in part, on the presence or absence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample.
  • an individual e.g., an
  • the methods comprise detecting, in a first sample obtained from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) at a first time point, the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; detecting, in a second sample obtained from the individual at a second time point after the first time point, the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; and providing an assessment of resistance to endocrine therapy in the individual based, at least in part, on the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the second sample.
  • a first sample obtained from an individual e.g., an individual having cancer, suspected of having cancer,
  • the methods comprise detecting, in a first sample obtained from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) at a first time point, the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; detecting, in a second sample obtained from the individual at a second time point after the first time point, the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule; and providing an assessment of sensitivity or responsiveness to endocrine therapy in the individual based, at least in part, on the absence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the second sample.
  • a first sample obtained from an individual e.g., an individual having cancer, suspected
  • the methods comprise performing DNA sequencing on a sample obtained from an individual to determine a sequencing mutation profile, wherein the sequencing mutation profile identifies the presence or absence of an ESRI fusion nucleic acid molecule.
  • the methods comprise identifying a candidate treatment based, at least in part, on the sequencing mutation profile.
  • the candidate treatment comprises an anti-cancer therapy described herein, such as an anticancer agent other than a SERM or an aromatase inhibitor or an endocrine therapy.
  • the candidate treatment is an anti-cancer agent other than a SERM or an aromatase inhibitor and identified based, at least in part, on the presence of an ESRI fusion nucleic acid molecule as identified in the sequencing mutation profile.
  • the candidate treatment is an endocrine therapy and identified based, at least in part, on the absence of an ESRI fusion nucleic acid molecule as identified in the sequencing mutation profile.
  • the methods comprise detecting, in a sample obtained from the individual during or after treatment with an endocrine therapy, an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; and providing an assessment of resistance to endocrine therapy in the individual based, at least in part, on the detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • the methods comprise detecting, in a sample obtained from the individual before, during, or after treatment with an endocrine therapy, absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule; and providing an assessment of sensitivity or responsiveness to endocrine therapy in the individual based, at least in part, on the detection of the absence of an ESRI fusion nucleic acid molecule, or ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • the methods provided herein comprise acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual, e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer.
  • knowledge of the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual identifies the individual as one who may benefit from a treatment comprising an anti-cancer therapy, such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • an anti-cancer therapy such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the methods comprise selecting an anti-cancer therapy, such as an anti-cancer agent other than a SERM or an aromatase inhibitor, as a treatment for an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer), e.g., responsive to knowledge of the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from the individual.
  • an anti-cancer therapy such as an anti-cancer agent other than a SERM or an aromatase inhibitor
  • the methods comprise generating a report comprising one or more treatment options identified for an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) based at least in part on knowledge of the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule in sample from the individual.
  • the one or more treatment options comprise an anti-cancer therapy described herein, such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the methods comprise generating a report comprising one or more treatment options identified for an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer) based at least in part on knowledge of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule in sample from the individual.
  • the one or more treatment options comprise an endocrine therapy.
  • an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer)
  • the individual is classified as a candidate to receive a treatment comprising an anti-cancer therapy, e.g., such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • an anti-cancer therapy e.g., such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the individual responsive to acquisition of knowledge of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer), the individual is classified as a candidate to receive a treatment comprising an endocrine therapy.
  • an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer)
  • the individual is identified as likely to respond to a treatment that comprises an anti-cancer therapy, such as an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • an individual responsive to acquisition of knowledge of the absence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual (e.g., an individual having cancer, suspected of having cancer, being treated for cancer, or being tested for cancer), the individual is identified as likely to respond to a treatment that comprises an endocrine therapy.
  • the individual responsive to acquisition of knowledge of the presence of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule, in a sample from an individual, the individual is predicted to have longer survival when treated with a treatment comprising an an anti-cancer agent other than a SERM or an aromatase inhibitor, e.g., as compared to survival an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • systems and non-transitory computer readable storage media are for (e.g., are configured for) performing a method according to any one of the embodiments disclosed herein.
  • the systems and non-transitory computer readable storage media provided herein are for (e.g., are configured for) detecting (e.g., in a sample from the individual) an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the cancer is breast cancer (e.g., HR+ breast cancer).
  • the cancer is endometrial cancer.
  • the individual is a human.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Certain aspects of the present disclosure relate to genomic rearrangements involving an ESRI gene.
  • An ESRI rearrangement of the present disclosure may relate to any chromosomal translocation, fusion, or rearrangement involving the locus of an ESRI gene.
  • the rearrangements of the disclosure result in an ESRI fusion nucleic acid molecule that comprises at least a portion of an ESRI gene fused to at least a portion of another gene, e.g., CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5.
  • certain aspects of the present disclosure relate to ESRI fusion nucleic acid molecules, as well as to ESRI fusion polypeptides encoded by such ESRI fusion nucleic acid molecules.
  • ESRl refers to a gene encoding an ESRI mRNA or ESRI polypeptide.
  • ESRI is also known as ER, ESR, Era, ESRA, ESTRR, and NR3A1.
  • an ESRI gene is a human ESRI gene.
  • An exemplary ESRI gene is represented by NCBI Gene ID No. 2099.
  • an ESRI gene is located at chromosomal coordinates chr6:151, 656, 691-152, 129, 619 forward strand.
  • the ESRI gene encodes 22 exons; additional information about the structure of ESRI and its exons and splice variants can be found under Ensembl Gene Accession ENSG00000091831.
  • An exemplary ESRI mRNA sequence is represented by NCBI Ref. Seq. NM_000125.4, provided below as SEQ ID NO: 2:
  • references to a specific ESRI mutation, rearrangement, or gene fusion by amino acid position refer to amino acid numbering according to SEQ ID NO:1.
  • the DNA- binding domain of ESRI is made up of amino acids 180-261 according to SEQ ID NO:1.
  • an ESRI rearrangement results in a gene fusion, resulting in a fusion nucleic acid molecule comprising at least a portion of an ESRI gene, and at least a portion of another gene. Accordingly, in some aspects, provided herein are ESRI fusion nucleic acid molecules comprising at least a portion of an ESRI gene and at least a portion of another gene.
  • an ESRI fusion nucleic acid molecule of the disclosure comprises at least a portion of an ESRI gene and at least a portion of a CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5 gene.
  • an ESRI fusion nucleic acid molecule of the disclosure comprises at least a portion of an ESRI gene and at least a portion of a fusion partner gene as provided in Table A or FIG. 3B herein.
  • CCDC170 refers to a gene encoding a CCDC170 mRNA or polypeptide.
  • the CCDC170 gene encodes the coiled-coil domain containing 170 polypeptide.
  • CCDC170 is also known as C6orf97 or bA282Pl l.l.
  • a CCDC170 gene according to the present disclosure is a human CCDC170 gene.
  • An exemplary CCDC170 gene is represented by NCBI Gene ID No. 80129.
  • SMAD4 refers to a gene encoding a SMAD4 mRNA or polypeptide.
  • the SMAD4 gene encodes the Smad family 4 (SMAD4) polypeptide.
  • SMAD4 is also known as JIP, DPC4, MADH4, or MYHRS.
  • a SMAD4 gene according to the present disclosure is a human SMAD4 gene.
  • An exemplary SMAD4 gene is represented by NCBI Gene ID No. 4089.
  • LOC100422737'' refers to a gene encoding a LOC100422737 RNA or polypeptide.
  • the LOC100422737 gene encodes the long intergenic non-protein coding RNA 2532.
  • a LOC100422737 gene according to the present disclosure is a human LOC100422737 gene.
  • An exemplary LOC100422737 gene is represented by NCBI Gene ID No. 100422737.
  • SNAP91 refers to a gene encoding a SNAP91 mRNA or polypeptide.
  • the SNAP91 gene encodes the synaptosome associated protein 91.
  • SNAP91 is also known as CALM or API 80.
  • a SNAP91 gene according to the present disclosure is a human SNAP91 gene.
  • An exemplary SNAP91 gene is represented by NCBI Gene ID No. 9892.
  • ZBTB2 refers to a gene encoding a ZBTB2 mRNA or polypeptide.
  • the ZBTB2 gene encodes the zinc finger and BTB domain containing 2 protein (ZBTB2).
  • ZBTB2 is also known as ZNF437.
  • a ZBTB2 gene according to the present disclosure is a human ZBTB2 gene.
  • An exemplary ZBTB2 gene is represented by NCBI Gene ID No. 57621.
  • IYD refers to a gene encoding an IYD mRNA or polypeptide.
  • the IYD gene encodes the iodotyrosine deiodinase. IYD is also known as TDH4, IYD-1, DEHAL1, or C6orf71.
  • an IYD gene according to the present disclosure is a human IYD gene.
  • An exemplary IYD gene is represented by NCBI Gene ID No. 389434.
  • IIMPG1 refers to a gene encoding an 1MPG1 mRNA or polypeptide.
  • the 1MPG1 gene encodes the interphotoreceptor matrix proteoglycan 1.
  • 1MPG1 is also known as RP91, VMD4, GP147, SPACR, or IPM150.
  • an IMPG1 gene according to the present disclosure is a human 1MPG1 gene.
  • An exemplary 1MPG1 gene is represented by NCBI Gene ID No. 3617.
  • S7AG2 refers to a gene encoding a STAG2 mRNA or polypeptide.
  • the STAG2 gene encodes the STAG2 cohesin complex component.
  • STAG2 is also known as SA2, MKMS, SA-2, HPE13, SCC3B, NEDXCF, or bA51701.1.
  • a STAG2 gene according to the present disclosure is a human STAG2 gene.
  • An exemplary STAG2 gene is represented by NCBI Gene ID No. 10735.
  • TNRC6B refers to a gene encoding a TNRC6B mRNA or polypeptide.
  • the TNRC6B gene encodes the trinucleotide repeat containing adaptor 6B protein.
  • TNRC6B is also known as GDSBA.
  • a TNRC6B gene according to the present disclosure is a human TNRC6B gene.
  • An exemplary TNRC6B gene is represented by NCBI Gene ID No. 23112.
  • C6orfl5 refers to a gene encoding a C6orfl5 mRNA or polypeptide.
  • the C6orfl5 gene encodes the chromosome 6 open reading frame 15.
  • C6orfl5 is also known as STG.
  • a C6orfl5 gene according to the present disclosure is a human C6orfl5 gene.
  • An exemplary C6orfl5 gene is represented by NCBI Gene ID No. 29113.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, encoding an ESRI DNA binding domain, or a portion thereof, to any one of genes CCDC170, SMAD4, LOCI 00422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI DNA binding domain, or a portion thereof, fused to a polypeptide encoded by any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exon 2 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exons 1-2 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the EOC100422737 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a EOC 100422737 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C- terminus direction, an ESRI polypeptide, or a portion thereof, fused to a EOC 100422737 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the IMPG1 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the 1MPG1 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an 1MPG1 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an 1MPG1 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a C6orfl 5 gene, or a portion thereof.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof.
  • an ESRI fusion polypeptide of the disclosure is a fusion polypeptide encoded by any of the ESRI fusion nucleic acid molecules provided herein, or a portion thereof, e.g., as described above.
  • Certain aspects of the present disclosure relate to methods for selecting a therapy for an individual having breast cancer or for identifying an individual having breast cancer who may benefit from a treatment comprising an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor; identifying one or more treatment options for an individual having breast cancer; selecting a treatment for an individual having breast cancer; predicting survival of an individual having breast cancer; treating or delaying progression of breast cancer; monitoring, evaluating or screening an individual having breast cancer; monitoring progression or recurrence of breast cancer in an individual; and/or monitoring resistance to endocrine therapy in an individual with breast cancer.
  • SERM selective estrogen receptor modulator
  • detection or acquisition of knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule identifies the individual as one who may benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, or as one who may be resistant to a treatment comprising an endocrine therapy.
  • Certain aspects of the present disclosure relate to methods for selecting a therapy for an individual having breast cancer or for identifying an individual having breast cancer who may benefit from a treatment comprising an endocrine therapy; and/or monitoring sensitivity or responsiveness to endocrine therapy.
  • detection or acquisition of knowledge of absence of an ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule identifies the individual as one who may benefit from a treatment comprising an endocrine therapy, or as one who may be sensitive to a treatment comprising an endocrine therapy.
  • the methods comprise acquiring knowledge of or detecting in a sample from an individual having a cancer an ESRI fusion nucleic acid molecule of the disclosure, e.g., any of the ESRI fusion nucleic acid molecules described above and/or in the Examples herein.
  • the methods comprise acquiring knowledge of or detecting in a sample from an individual having a cancer an ESRI fusion polypeptide of the disclosure, e.g., any of the ESRI fusion polypeptides described above and/or in the Examples herein.
  • the methods comprise performing DNA sequencing on a sample obtained from the individual to determine a sequencing mutation profile on a group of genes, wherein the sequencing mutation profile identifies the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure.
  • the methods further comprise identifying a candidate treatment for a cancer in an individual, based at least in part on the sequencing mutation profile.
  • the candidate treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor (e.g., when the sequencing mutation profile identifies the presence of an ESRI fusion nucleic acid molecule of the disclosure).
  • the candidate treatment comprises an endocrine therapy (e.g., when the sequencing mutation profile identifies the absence of an ESRI fusion nucleic acid molecule of the disclosure).
  • the sequencing mutation profile identifies the presence or absence of a fragment of the ESRI fusion nucleic acid molecule comprising a breakpoint or fusion junction, e.g., one or more of the corresponding breakpoints described herein.
  • the methods further comprise generating a report comprising one or more treatment options identified for an individual (e.g., an individual having cancer) based at least in part on detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from the individual.
  • the treatment options comprise an anti-cancer agent other than a SERM or an aromatase inhibitor (e.g., when the report identifies the presence of an ESRI fusion nucleic acid molecule of the disclosure).
  • the treatment options comprise an endocrine therapy (e.g., when the report identifies the absence of an ESRI fusion nucleic acid molecule of the disclosure).
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer): (i) the individual is classified as a candidate to receive a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the individual responsive to acquisition of knowledge of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • the methods comprise administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the individual responsive to acquisition of knowledge of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor and/or to have longer survival when treated with a treatment comprising an anticancer agent other than a SERM or an aromatase inhibitor, as compared to an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • an individual responsive to acquisition of knowledge of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), an individual is predicted to be resistant to a treatment comprising an endocrine therapy.
  • an individual responsive to detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer): (i) the individual is classified as a candidate to receive a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the individual responsive to detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • the methods comprise administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • the individual responsive to detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor and/or to have longer survival when treated with a treatment comprising an anticancer agent other than a SERM or an aromatase inhibitor, as compared to an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • an individual responsive to detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), an individual is predicted to be resistant to a treatment comprising an endocrine therapy.
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer): (i) the individual is classified as a candidate to receive a treatment comprising an endocrine therapy; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an endocrine therapy.
  • the individual responsive to acquisition of knowledge of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to have longer survival when treated with a treatment comprising an endocrine therapy, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising an endocrine therapy.
  • the methods comprise administering to the individual an effective amount of a treatment that comprises an endocrine therapy.
  • the individual responsive to acquisition of knowledge of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to benefit from a treatment comprising an endocrine therapy and/or to have longer survival when treated with a treatment comprising an endocrine therapy, as compared to an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising an endocrine therapy.
  • an individual responsive to acquisition of knowledge of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), an individual is predicted to be sensitive to a treatment comprising an endocrine therapy.
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure responsive to detection of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer): (i) the individual is classified as a candidate to receive a treatment comprising an an endocrine therapy; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an endocrine therapy.
  • the individual responsive to detection of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to have longer survival when treated with a treatment comprising an endocrine therapy, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising an endocrine therapy.
  • the methods comprise administering to the individual an effective amount of a treatment that comprises an endocrine therapy.
  • the individual responsive to detection of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), the individual is predicted to benefit from a treatment comprising an endocrine therapy and/or to have longer survival when treated with a treatment comprising an endocrine therapy, as compared to an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide when treated with a treatment comprising an endocrine therapy.
  • an individual responsive to detection of the absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample from an individual (e.g., an individual having cancer), an individual is predicted to be sensitive to a treatment comprising an endocrine therapy.
  • the endocrine therapy comprises a SERM or an aromatase inhibitor.
  • SERMs include, without limitation, tamoxifen (NOLVADEX®, SOLTAMOX®, GENOX), raloxifene (EVISTA®, OPTRUMA), EM652, GW7604, keoxifene, toremifene (FARESTON®), apeledoxifene, broparestrol, clomifene, cyclofenil, lasofoxifene, ormeloxifene, ospemifene, or pharmaceutically acceptable salts thereof.
  • aromatase inhibitors include, without limitation, aminoglutethimide, testolactone (TESLAC®), anastrozole (ARIMIDEX®), letrozole (FEMARA®), exemestane (AROMASIN®), vorozole (RIVIZOR), formestane (LENT ARON®), fadrozole (AFEMA), 4-hydroxyandrostenedione, 1, 4, 6-androstatrien-3, 17-dione (ATD), 4-Androstene-3, 6, 17- trione (“6-OXO”), or pharmaceutically acceptable salts thereof.
  • the anti-cancer agent is approved or tested for use in E.S7?/mut cancer.
  • the anti-cancer agent comprises one or more of a small molecule inhibitor, an antibody, a cellular therapy, a nucleic acid, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), a treatment for cancer comprising an ESRI mutation, an anti-cancer agent being tested in a clinical trial, a treatment for cancer comprising an ESRI mutation being tested in a clinical trial, or any combination thereof.
  • PROTAC PROteolysis-TArgeting Chimera
  • the anti-cancer agent comprises a selective estrogen receptor covalent antagonist (SERCA), including without limitation H3B-5942, H3B-6545, or a pharmaceutically acceptable salt thereof (see, e.g., Wang, Y. et al. (2023) Acta Pharmaceutica Sinica B 13( 12):4963-4982).
  • SERCA selective estrogen receptor covalent antagonist
  • the anti-cancer agent comprises a selective estrogen receptor degrader (SERD), including without limitation fulvestrant (FASLODEX®), elacestrant (ORSERDUTM), amcenestrant, camizestrant, giredestrant, rintodestrant, imlunestrant, ZB-716, Zn-c5, LSZ102, LY3484356, or D-0502, or a pharmaceutically acceptable salt thereof see, e.g., Patel, R. et al. (2023) NPJ Breast Cancer 9(l):20).
  • the anti-cancer agent comprises a PROTAC, including without limitation ARV-471.
  • the anti-cancer agent comprises a CDK4/6 inhibitor, including without limitation palbociclib, abemaciclib, ribociclib, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent comprises treatment with a SERD and a CDK4/6 inhibitor (see, e.g., Brett, J.O. et al. (2023) Oncologist 28(2): 172- 179).
  • the anti-cancer agent comprises a PI3K inhibitor, including without limitation GSK2636771, buparlisib, AZD8186, copanlisib, LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib, pictilisib, GDC0032, IPI145, INK1117, SAR260301, KIN-193, duvelisib, GS-9820, GSK2636771, GDC-0980, AMG319, paxalisib, or alpelisib, or a pharmaceutically acceptable salt thereof.
  • a PI3K inhibitor including without limitation GSK2636771, buparlisib, AZD8186, copanlisib, LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib, pictilisib, GDC0032, IPI145,
  • the anti-cancer agent comprises an mTOR inhibitor, including without limitation temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, or OSI027, or a pharmaceutically acceptable salt thereof.
  • an mTOR inhibitor including without limitation temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, or OSI027, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent is a nucleic acid that inhibits the expression of an ESRI nucleic acid molecule (e.g., bearing an ESRI mutation), or an ESRI polypeptide encoded by the ESRI nucleic acid molecule, including without limitation a double- stranded RNA (dsRNA), a small interfering RNA (siRNA), or a small hairpin RNA (shRNA).
  • dsRNA double- stranded RNA
  • siRNA small interfering RNA
  • shRNA small hairpin RNA
  • the anti-cancer agent is a cellular therapy that is an adoptive therapy, a T cellbased therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR)-T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, a macrophage-based therapy, an induced pluripotent stem cell-based therapy, a B cell-based therapy, or a dendritic cell (DC)-based therapy.
  • the anti-cancer agent can be a targeted therapy that targets, or is otherwise approved for use in treating a cancer comprising a mutation in, one or more oncogenic or tumor suppressor mutations, e.g., detected in a liquid biopsy sample as disclosed herein.
  • the anti-cancer agent other than a SERM or aromatase inhibitor is a targeted therapy targeting one of the one or more oncogenic or tumor suppressor mutations.
  • an anti-cancer therapy of the disclosure is a small molecule inhibitor; an antibody; a cellular therapy; a nucleic acid; a virus-based therapy; an antibodydrug conjugate; a recombinant protein; a fusion protein; a natural compound; a peptide; a PROteolysis-TArgeting Chimera (PROTAC); a targeted therapy; or any combination thereof, e.g., a described in further detail below.
  • the anti-cancer therapy is an immunotherapy, such as any immunotherapy known in the art or described herein (e.g., a checkpoint inhibitor, cancer vaccine, cell-based therapy, T cell receptor (TCR)-based therapy, adjuvant immunotherapy, cytokine immunotherapy, or oncolytic virus therapy).
  • the anti-cancer therapy is an immune checkpoint inhibitor, such as any immune checkpoint inhibitor described herein or known in the art.
  • the anti-cancer therapy comprises an immunotherapy (i.e., a cancer immunotherapy), such as a checkpoint inhibitor, cancer vaccine, cell-based therapy, T cell receptor (TCR)-based therapy, adjuvant immunotherapy, cytokine immunotherapy, and oncolytic virus therapy, as well as any combination thereof.
  • a cancer immunotherapy i.e., a checkpoint inhibitor, cancer vaccine, cell-based therapy, T cell receptor (TCR)-based therapy, adjuvant immunotherapy, cytokine immunotherapy, and oncolytic virus therapy, as well as any combination thereof.
  • the cancer immunotherapy comprises a small molecule, nucleic acid, polypeptide, carbohydrate, toxin, cell-based agent, or cell-binding agent. Examples of cancer immunotherapies are described in greater detail herein but are not intended to be limiting.
  • the cancer immunotherapy activates one or more aspects of the immune system to attack a cell (e.g., a tumor cell) that expresses a neoantigen.
  • a cell e.g., a tumor cell
  • the cancer immunotherapies of the present disclosure are contemplated for use as monotherapies, or in combination approaches comprising two or more in any combination or number, subject to medical judgement. Any of the cancer immunotherapies (optionally as monotherapies or in combination with another cancer immunotherapy or other therapeutic agent described herein) may find use in any of the methods described herein.
  • the cancer immunotherapy comprises a cancer vaccine.
  • a range of cancer vaccines have been tested that employ different approaches to promoting an immune response against a cancer (see, e.g., Emens L A, Expert Opin Emerg Drugs 13(2): 295-308 (2008) and US20190367613). Approaches have been designed to enhance the response of B cells, T cells, or professional antigen-presenting cells against tumors.
  • Exemplary types of cancer vaccines include, but are not limited to, DNA-based vaccines, RNA-based vaccines, virus transduced vaccines, peptide-based vaccines, dendritic cell vaccines, oncolytic viruses, whole tumor cell vaccines, tumor antigen vaccines, etc.
  • the cancer vaccine can be prophylactic or therapeutic.
  • the cancer vaccine is formulated as a peptide-based vaccine, a nucleic acid-based vaccine, an antibody-based vaccine, or a cell-based vaccine.
  • a vaccine composition can include naked cDNA in cationic lipid formulations; lipopeptides (e.g., Vitiello, A. et al, J. Clin. Invest. 95:341, 1995); naked cDNA or peptides encapsulated, e.g., in poly(DL-lactide- co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et ah, Molec. Immunol.
  • PLG poly(DL-lactide- co-glycolide)
  • a cancer vaccine is formulated as a peptide-based vaccine, or nucleic acidbased vaccine in which the nucleic acid encodes the polypeptides.
  • a cancer vaccine is formulated as an antibody-based vaccine.
  • a cancer vaccine is formulated as a cell-based vaccine.
  • the cancer vaccine is a peptide cancer vaccine, which in some embodiments is a personalized peptide vaccine.
  • the cancer vaccine is a multivalent long peptide, a multiple peptide, a peptide mixture, a hybrid peptide, or a peptide pulsed dendritic cell vaccine (see, e.g., Yamada et al, Cancer Sci, 104: 14-21, 2013). In some embodiments, such cancer vaccines augment an anti-cancer response.
  • the cancer vaccine comprises a polynucleotide that encodes a neoantigen, e.g., neoantigen(s) expressed by a cancer of the disclosure, such as a cancer in an individual.
  • the cancer vaccine comprises DNA that encodes the neoantigen(s).
  • the cancer vaccine comprises RNA that encodes the neoantigen(s).
  • the cancer vaccine comprises a polynucleotide that encodes the neoantigen(s).
  • the cancer vaccine further comprises one or more additional antigens, neoantigens, or other sequences that promote antigen presentation and/or an immune response.
  • the polynucleotide is complexed with one or more additional agents, such as a liposome or lipoplex.
  • the polynucleotide(s) are taken up and translated by antigen presenting cells (APCs), which then present the neoantigen(s) via MHC class I on the APC cell surface.
  • APCs antigen presenting cells
  • the cancer vaccine is selected from sipuleucel-T (e.g., Provenge®, Dendreon/V aleant Pharmaceuticals), which has been approved for treatment of asymptomatic, or minimally symptomatic metastatic castrate -resistant (hormone-refractory) prostate cancer; and talimogene laherparepvec (e.g., Imlygic®, BioVex/ Amgen, previously known as T-VEC), a genetically modified oncolytic viral therapy approved for treatment of unresectable cutaneous, subcutaneous and nodal lesions in melanoma.
  • sipuleucel-T e.g., Provenge®, Dendreon/V aleant Pharmaceuticals
  • talimogene laherparepvec e.g., Imlygic®, BioVex/ Amgen, previously known as T-VEC
  • the cancer vaccine is selected from an oncolytic viral therapy such as pexastimogene devacirepvec (PexaVec/JX-594, SillaJen/formerly Jennerex Biotherapeutics), a thymidine kinase- (TK-) deficient vaccinia virus engineered to express GM-CSF, for hepatocellular carcinoma (NCT02562755) and melanoma (NCT00429312); pelareorep (e.g., Reolysin®, Oncolytics Biotech), a variant of respiratory enteric orphan virus (reovirus) which does not replicate in cells that are not RAS-activated, in numerous cancers, including colorectal cancer (NCT01622543), prostate cancer (NCT01619813), head and neck squamous cell cancer (NCT01166542), pancreatic adenocarcinoma (NCT00998322), and non-small cell lung cancer (NSCLC)
  • the cancer vaccine is selected from JX-929 (SillaJen/formerly Jennerex Biotherapeutics), a TK- and vaccinia growth factor-deficient vaccinia virus engineered to express cytosine deaminase, which is able to convert the prodrug 5-fluorocytosine to the cytotoxic drug 5-fluorouracil; TGO1 and TG02 (Targovax/formerly Oncos), peptide-based immunotherapy agents targeted for difficult-to-treat RAS mutations; and TILT- 123 (TILT Biotherapeutics), an engineered adenovirus designated: Ad5/3-E2F-delta24-hTNFa-IRES-hIL20; and VSV-GP (ViraTherapeutics) a vesicular stomatitis virus (VSV) engineered to express the glycoprotein (GP) of lymphocytic choriomeningitis virus (LCMV), which can be further engineered to express antigens
  • the cancer vaccine comprises a vector-based tumor antigen vaccine.
  • Vectorbased tumor antigen vaccines can be used as a way to provide a steady supply of antigens to stimulate an anti-tumor immune response.
  • vectors encoding for tumor antigens are injected into an individual (possibly with pro-inflammatory or other attractants such as GM-CSF), taken up by cells in vivo to make the specific antigens, which then provoke the desired immune response.
  • vectors may be used to deliver more than one tumor antigen at a time, to increase the immune response.
  • recombinant virus, bacteria or yeast vectors can trigger their own immune responses, which may also enhance the overall immune response.
  • the cancer vaccine comprises a DNA-based vaccine.
  • DNA-based vaccines can be employed to stimulate an anti-tumor response.
  • the ability of directly injected DNA that encodes an antigenic protein, to elicit a protective immune response has been demonstrated in numerous experimental systems. Vaccination through directly injecting DNA that encodes an antigenic protein, to elicit a protective immune response often produces both cell-mediated and humoral responses.
  • reproducible immune responses to DNA encoding various antigens have been reported in mice that last essentially for the lifetime of the animal (see, e.g., Yankauckas et al.
  • plasmid (or other vector) DNA that includes a sequence encoding a protein operably linked to regulatory elements required for gene expression is administered to individuals (e.g. human patients, non-human mammals, etc.).
  • individuals e.g. human patients, non-human mammals, etc.
  • the cells of the individual take up the administered DNA and the coding sequence is expressed.
  • the antigen so produced becomes a target against which an immune response is directed.
  • the cancer vaccine comprises an RNA-based vaccine.
  • RNA-based vaccines can be employed to stimulate an anti-tumor response.
  • RNA-based vaccines comprise a self-replicating RNA molecule.
  • the self-replicating RNA molecule may be an alphavirus-derived RNA replicon.
  • Self-replicating RNA (or "SAM") molecules are well known in the art and can be produced by using replication elements derived from, e.g., alphaviruses, and substituting the structural viral proteins with a nucleotide sequence encoding a protein of interest.
  • a selfreplicating RNA molecule is typically a +-strand molecule which can be directly translated after delivery to a cell, and this translation provides a RNA-dependent RNA polymerase which then produces both antisense and sense transcripts from the delivered RNA.
  • the delivered RNA leads to the production of multiple daughter RNAs.
  • These daughter RNAs, as well as collinear subgenomic transcripts, may be translated themselves to provide in situ expression of an encoded polypeptide, or may be transcribed to provide further transcripts with the same sense as the delivered RNA which are translated to provide in situ expression of the antigen.
  • the cancer immunotherapy comprises a cell-based therapy. In some embodiments, the cancer immunotherapy comprises a T cell-based therapy. In some embodiments, the cancer immunotherapy comprises an adoptive therapy, e.g., an adoptive T cell-based therapy. In some embodiments, the T cells are autologous or allogeneic to the recipient. In some embodiments, the T cells are CD 8+ T cells. In some embodiments, the T cells are CD4+ T cells.
  • Adoptive immunotherapy refers to a therapeutic approach for treating cancer or infectious diseases in which immune cells are administered to a host with the aim that the cells mediate either directly or indirectly specific immunity to (i.e., mount an immune response directed against) cancer cells.
  • the immune response results in inhibition of tumor and/or metastatic cell growth and/or proliferation, and in related embodiments, results in neoplastic cell death and/or resorption.
  • the immune cells can be derived from a different organism/host (exogenous immune cells) or can be cells obtained from the subject organism (autologous immune cells).
  • the immune cells e.g., autologous or allogeneic T cells (e.g., regulatory T cells, CD4+ T cells, CD8+ T cells, or gamma-delta T cells), NK cells, invariant NK cells, or NKT cells) can be genetically engineered to express antigen receptors such as engineered TCRs and/or chimeric antigen receptors (CARs).
  • the host cells e.g., autologous or allogeneic T-cells
  • TCR T cell receptor
  • NK cells are engineered to express a TCR.
  • the NK cells may be further engineered to express a CAR.
  • Multiple CARs and/or TCRs, such as to different antigens, may be added to a single cell type, such as T cells or NK cells.
  • the cells comprise one or more nucleic acids/expression constructs/vectors introduced via genetic engineering that encode one or more antigen receptors, and genetically engineered products of such nucleic acids.
  • the nucleic acids are heterologous, i.e., normally not present in a cell or sample obtained from the cell, such as one obtained from another organism or cell, which for example, is not ordinarily found in the cell being engineered and/or an organism from which such cell is derived.
  • the nucleic acids are not naturally occurring, such as a nucleic acid not found in nature (e.g. chimeric).
  • a population of immune cells can be obtained from a subject in need of therapy or suffering from a disease associated with reduced immune cell activity. Thus, the cells will be autologous to the subject in need of therapy.
  • a population of immune cells can be obtained from a donor, such as a histocompatibility-matched donor.
  • the immune cell population can be harvested from the peripheral blood, cord blood, bone marrow, spleen, or any other organ/tissue in which immune cells reside in said subject or donor.
  • the immune cells can be isolated from a pool of subjects and/or donors, such as from pooled cord blood.
  • the donor when the population of immune cells is obtained from a donor distinct from the subject, the donor may be allogeneic, provided the cells obtained are subject-compatible, in that they can be introduced into the subject.
  • allogeneic donor cells may or may not be human-leukocyte-antigen (HLA)-compatible.
  • HLA human-leukocyte-antigen
  • the cell-based therapy comprises a T cell-based therapy, such as autologous cells, e.g., tumor-infiltrating lymphocytes (TILs); T cells activated ex-vivo using autologous DCs, lymphocytes, artificial antigen-presenting cells (APCs) or beads coated with T cell ligands and activating antibodies, or cells isolated by virtue of capturing target cell membrane; allogeneic cells naturally expressing anti-host tumor T cell receptor (TCR); and non-tumor- specific autologous or allogeneic cells genetically reprogrammed or "redirected" to express tumor-reactive TCR or chimeric TCR molecules displaying antibodylike tumor recognition capacity known as "T- bodies”.
  • TILs tumor-infiltrating lymphocytes
  • APCs artificial antigen-presenting cells
  • TCR non-tumor-specific autologous or allogeneic cells genetically reprogrammed or "redirected" to express tumor-reactive TCR or chimeric TCR molecules displaying antibodylike tumor recognition capacity
  • the T cells are derived from the blood, bone marrow, lymph, umbilical cord, or lymphoid organs.
  • the cells are human cells.
  • the cells are primary cells, such as those isolated directly from a subject and/or isolated from a subject and frozen.
  • the cells include one or more subsets of T cells or other cell types, such as whole T cell populations, CD4+ cells, CD8+ cells, and subpopulations thereof, such as those defined by function, activation state, maturity, potential for differentiation, expansion, recirculation, localization, and/or persistence capacities, antigen- specificity, type of antigen receptor, presence in a particular organ or compartment, marker or cytokine secretion profile, and/or degree of differentiation.
  • the cells may be allogeneic and/or autologous.
  • the cells are pluripotent and/or multipotent, such as stem cells, such as induced pluripotent stem cells (iPSCs).
  • the T cell-based therapy comprises a chimeric antigen receptor (CAR)-T cell-based therapy.
  • CAR chimeric antigen receptor
  • This approach involves engineering a CAR that specifically binds to an antigen of interest and comprises one or more intracellular signaling domains for T cell activation.
  • the CAR is then expressed on the surface of engineered T cells (CAR-T) and administered to a patient, leading to a T-cell-specific immune response against cancer cells expressing the antigen.
  • the CAR specifically binds a neoantigen, such as a neoantigen expressed in a cancer of a disclosure, e.g., in an individual.
  • the T cell-based therapy comprises T cells expressing a recombinant T cell receptor (TCR).
  • TCR recombinant T cell receptor
  • This approach involves identifying a TCR that specifically binds to an antigen of interest, which is then used to replace the endogenous or native TCR on the surface of engineered T cells that are administered to a patient, leading to a T-cell-specific immune response against cancer cells expressing the antigen.
  • the recombinant TCR specifically binds a neoantigen expressed in a cancer of a disclosure, e.g., in an individual.
  • the T cell-based therapy comprises tumor-infiltrating lymphocytes (TILs).
  • TILs can be isolated from a tumor or cancer of the present disclosure, then isolated and expanded in vitro. Some or all of these TILs may specifically recognize an antigen expressed by the tumor or cancer of the present disclosure.
  • the TILs are exposed to one or more neoantigens, e.g., expressed in a cancer of a disclosure, in vitro after isolation. TILs are then administered to the patient (optionally in combination with one or more cytokines or other immune-stimulating substances).
  • the cell-based therapy comprises a natural killer (NK) cellbased therapy.
  • Natural killer (NK) cells are a subpopulation of lymphocytes that have spontaneous cytotoxicity against a variety of tumor cells, virus-infected cells, and some normal cells in the bone marrow and thymus. NK cells are critical effectors of the early innate immune response toward transformed and virus-infected cells. NK cells can be detected by specific surface markers, such as CD16, CD56, and CD8 in humans. NK cells do not express T-cell antigen receptors, the pan T marker CD3, or surface immunoglobulin B cell receptors.
  • NK cells are derived from human peripheral blood mononuclear cells (PBMC), unstimulated leukapheresis products (PBSC), human embryonic stem cells (hESCs), induced pluripotent stem cells (iPSCs), bone marrow, or umbilical cord blood by methods well known in the art.
  • PBMC peripheral blood mononuclear cells
  • hESCs human embryonic stem cells
  • iPSCs induced pluripotent stem cells
  • bone marrow or umbilical cord blood by methods well known in the art.
  • the cell-based therapy comprises a dendritic cell (DC)-based therapy, e.g., a dendritic cell vaccine.
  • DC dendritic cell
  • the DC vaccine comprises antigen-presenting cells that are able to induce specific T cell immunity, which are harvested from the patient or from a donor.
  • the DC vaccine can then be exposed in vitro to a peptide antigen, for which T cells are to be generated in the patient.
  • dendritic cells loaded with the antigen are then injected back into the patient.
  • immunization may be repeated multiple times if desired.
  • Dendritic cell vaccines are vaccines that involve administration of dendritic cells that act as APCs to present one or more cancer- specific antigens to the patient’s immune system.
  • the dendritic cells are autologous or allogeneic to the recipient.
  • the cancer immunotherapy comprises a TCR-based therapy.
  • the cancer immunotherapy comprises administration of one or more TCRs or TCR-based therapeutics that specifically bind an antigen expressed by a cancer of the present disclosure, e.g., a neoantigen expressed in a cancer of a disclosure, e.g., in an individual.
  • the TCR-based therapeutic may further include a moiety that binds an immune cell (e.g., a T cell), such as an antibody or antibody fragment that specifically binds a T cell surface protein or receptor (e.g., an anti-CD3 antibody or antibody fragment).
  • the immunotherapy comprises adjuvant immunotherapy.
  • Adjuvant immunotherapy comprises the use of one or more agents that activate components of the innate immune system, e.g., HILTONOL® (imiquimod), which targets the TLR7 pathway.
  • the immunotherapy comprises cytokine immunotherapy.
  • Cytokine immunotherapy comprises the use of one or more cytokines that activate components of the immune system. Examples include, but are not limited to, aldesleukin (e.g., PROLEUKIN®; interleukin-2), interferon alfa-2a (e.g., ROFERON®-A), interferon alfa-2b (e.g., INTRON®-A), and peginterferon alfa-2b (e.g., PEGINTRON®).
  • aldesleukin e.g., PROLEUKIN®
  • interleukin-2 interferon alfa-2a
  • interferon alfa-2b e.g., INTRON®-A
  • peginterferon alfa-2b e.g., PEGINTRON®
  • the immunotherapy comprises oncolytic virus therapy.
  • Oncolytic virus therapy uses genetically modified viruses to replicate in and kill cancer cells, leading to the release of antigens that stimulate an immune response.
  • replication-competent oncolytic viruses expressing a tumor antigen comprise any naturally occurring (e.g., from a “field source”) or modified replication-competent oncolytic virus.
  • the oncolytic virus, in addition to expressing a tumor antigen may be modified to increase selectivity of the virus for cancer cells.
  • replication-competent oncolytic viruses include, but are not limited to, oncolytic viruses that are a member in the family of myoviridae, siphoviridae, podpviridae, teciviridae, corticoviridae, plasmaviridae, lipothrixviridae, fuselloviridae, poxyiridae, iridoviridae, phycodnaviridae, baculoviridae, herpesviridae, adnoviridae, papovaviridae, polydnaviridae, inoviridae, microviridae, geminiviridae, circoviridae, parvoviridae, hcpadnaviridae, retroviridae, cyctoviridae, reoviridae, birnaviridae, paramyxoviridae, rhabdoviridae, filoviridae,
  • replication-competent oncolytic viruses include adenovirus, retrovirus, reovirus, rhabdovirus, Newcastle Disease virus (NDV), polyoma virus, vaccinia virus (VacV), herpes simplex virus, picomavirus, coxsackie virus and parvovirus.
  • a replicative oncolytic vaccinia virus expressing a tumor antigen may be engineered to lack one or more functional genes in order to increase the cancer selectivity of the virus.
  • an oncolytic vaccinia virus is engineered to lack thymidine kinase (TK) activity.
  • the oncolytic vaccinia virus may be engineered to lack vaccinia virus growth factor (VGF). In some embodiments, an oncolytic vaccinia virus may be engineered to lack both VGF and TK activity. In some embodiments, an oncolytic vaccinia virus may be engineered to lack one or more genes involved in evading host interferon (IFN) response such as E3L, K3L, B18R, or B8R. In some embodiments, a replicative oncolytic vaccinia virus is a Western Reserve, Copenhagen, Lister or Wyeth strain and lacks a functional TK gene.
  • VGF vaccinia virus growth factor
  • an oncolytic vaccinia virus may be engineered to lack both VGF and TK activity.
  • an oncolytic vaccinia virus may be engineered to lack one or more genes involved in evading host interferon (IFN) response such as E3L, K3L, B18R, or B8R.
  • IFN evading host
  • the oncolytic vaccinia virus is a Western Reserve, Copenhagen, Lister or Wyeth strain lacking a functional B18R and/or B8R gene.
  • a replicative oncolytic vaccinia virus expressing a tumor antigen may be locally or systemically administered to a subject, e.g. via intratumoral, intraperitoneal, intravenous, intra-arterial, intramuscular, intradermal, intracranial, subcutaneous, or intranasal administration.
  • the anti-cancer therapy comprises an immune checkpoint inhibitor.
  • the methods provided herein comprise administering to an individual an effective amount of an immune checkpoint inhibitor.
  • a checkpoint inhibitor targets at least one immune checkpoint protein to alter the regulation of an immune response.
  • Immune checkpoint proteins include, e.g., CTLA4, PD-L1, PD-1, PD- L2, VISTA, B7-H2, B7-H3, B7-H4, B7-H6, 2B4, ICOS, HVEM, CEACAM, LAIR1, CD80, CD86, CD276, VTCN1, MHC class I, MHC class II, GALS, adenosine, TGFR, CSF1R, MICA/B, arginase, CD160, gp49B, PIR-B, KIR family receptors, TIM-1, TIM-3, TIM-4, LAG-3, BTLA, SIRPalpha (CD47), CD48, 2B4 (CD244), B7.1, B7.2, ILT-2, ILT-4, TIGIT, LAG-3, BTLA, IDO, 0X40, and A2aR.
  • molecules involved in regulating immune checkpoints include, but are not limited to: PD-1 (CD279), PD-L1 (B7- Hl, CD274), PD-L2 (B7-CD, CD273), CTLA-4 (CD152), HVEM, BTLA (CD272), a killercell immunoglobulin-like receptor (KIR), LAG-3 (CD223), TIM-3 (HAVCR2), CEACAM, CEACAM-1, CEACAM-3, CEACAM-5, GAL9, VISTA (PD-1H), TIGIT, LAIR1, CD160, 2B4, TGFRbeta, A2AR, GITR (CD357), CD80 (B7-1), CD86 (B7-2), CD276 (B7-H3), VTCNI (B7-H4), MHC class I, MHC class II, GALS, adenosine, TGFR, B7-H1, 0X40 (CD134), CD94 (KLRD1), CD
  • an immune checkpoint inhibitor decreases the activity of a checkpoint protein that negatively regulates immune cell function, e.g., in order to enhance T cell activation and/or an anti-cancer immune response.
  • a checkpoint inhibitor increases the activity of a checkpoint protein that positively regulates immune cell function, e.g., in order to enhance T cell activation and/or an anti-cancer immune response.
  • the checkpoint inhibitor is an antibody.
  • checkpoint inhibitors include, without limitation, a PD- 1 axis binding antagonist, a PD-L1 axis binding antagonist (e.g., an anti-PD-Ll antibody, e.g., atezolizumab (MPDL3280A)), an antagonist directed against a co-inhibitory molecule (e.g., a CTLA4 antagonist (e.g., an anti-CTLA4 antibody), a TIM-3 antagonist (e.g., an anti- TIM-3 antibody), or a LAG-3 antagonist (e.g., an anti-LAG-3 antibody)), or any combination thereof.
  • a CTLA4 antagonist e.g., an anti-CTLA4 antibody
  • a TIM-3 antagonist e.g., an anti- TIM-3 antibody
  • LAG-3 antagonist e.g., an anti-LAG-3 antibody
  • the immune checkpoint inhibitors comprise drugs such as small molecules, recombinant forms of ligand or receptors, or antibodies, such as human antibodies (see, e.g., International Patent Publication W02015016718; Pardoll, Nat Rev Cancer, 12(4): 252-64, 2012; both incorporated herein by reference).
  • known inhibitors of immune checkpoint proteins or analogs thereof may be used, in particular chimerized, humanized or human forms of antibodies may be used.
  • the checkpoint inhibitor is a PD-L1 axis binding antagonist.
  • PD-1 programmed death 1
  • PDCD1, programmed cell death 1
  • CD279 CD279
  • SEB2 programmed cell death 1
  • An exemplary human PD-1 is shown in UniProtKB/Swiss-Prot Accession No. Q15116.
  • PD-L1 (programmed death ligand 1) is also referred to in the art as “programmed cell death 1 ligand 1,” “PDCD1 LG1,” “CD274,” “B7- H,” and “PDL1.”
  • An exemplary human PD-L1 is shown in UniProtKB/Swiss-Prot Accession No.Q9NZQ7.1.
  • PD-L2 (programmed death ligand 2) is also referred to in the art as “programmed cell death 1 ligand 2,” “PDCD1 LG2,” “CD273,” “B7-DC,” “Btdc,” and “PDL2.”
  • An exemplary human PD-L2 is shown in UniProtKB/Swiss-Prot Accession No.
  • the checkpoint inhibitor is a PD-1 binding antagonist/inhibitor.
  • the PD-1 binding antagonist/inhibitor is a molecule that inhibits the binding of PD-1 to its ligand binding partners.
  • the PD-1 ligand binding partners are PD-L1 and/or PD-L2.
  • the checkpoint inhibitor is a PD-L1 binding antagonist/inhibitor.
  • a PD-L1 binding antagonist/inhibitor is a molecule that inhibits the binding of PD-L1 to its binding ligands.
  • PD-L1 binding partners are PD-1 and/or B7-1.
  • the checkpoint inhibitor is a PD-L2 binding antagonist/inhibitor.
  • the PD-L2 binding antagonist/inhibitor is a molecule that inhibits the binding of PD-L2 to its ligand binding partners.
  • the PD-L2 binding ligand partner is PD- 1.
  • the antagonist or inhibitor may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or an oligopeptide.
  • the PD-1, PD-L1, or PD-L1 binding antagonist or inhibitor is a small molecule, a nucleic acid, a polypeptide (e.g., antibody), a carbohydrate, a lipid, a metal, or a toxin.
  • the PD-1 binding antagonist or inhibitor is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), for example, as described below.
  • the anti-PD-1 antibody is one or more of MDX-1 106 (nivolumab), MK-3475 (pembrolizumab, e.g., Keytruda®), MEDI-0680 (AMP-514), PDR001, REGN2810, MGA-012, JNJ-63723283, BI 754091, BGB-108, BGB-A317, JS-001, STI-Al l 10, INCSHR-1210, PF-06801591, TSR-042, AM0001, ENUM 244C8, ENUM 388D4, cemiplimab, or dostarlimab.
  • MDX-1 106 nivolumab
  • MK-3475 pembrolizumab, e.g., Keytruda®
  • the PD-1 binding antagonist or inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PD-L1 or PD-L2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence)).
  • the PD-1 binding antagonist or inhibitor is AMP- 224.
  • Other examples of anti-PD-1 antibodies include, but are not limited to, MEDI- 0680 (AMP-514; AstraZeneca), PDR001 (CAS Registry No.
  • REGN2810 e.g., LIBTAYO® or cemiplimab-rwlc; Regeneron
  • BGB-108 BeiGene
  • BGB- A317 BeiGene
  • BI 754091 JS-001 (Shanghai Junshi)
  • STI-Al l 10 Sorrento
  • INCSHR- 1210 Incyte
  • PF-06801591 Pfizer
  • TSR-042 also known as ANB011;
  • the PD-1 axis binding antagonist or inhibitor comprises tislelizumab (BGB-A317), BGB-108, STI-Al l 10, AM0001, BI 754091, sintilimab (IBI308), cetrelimab (JNJ-63723283), toripalimab (JS-001), camrelizumab (SHR-1210, INCSHR-1210, HR-301210), MEDI-0680 (AMP-514), MGA-012 (INCMGA 0012), nivolumab (BMS-936558, MDX1106, ONO-
  • spartalizumab PDR001
  • pembrolizumab MK-3475, SCH 900475, e.g., Keytruda®
  • PF-06801591 cemiplimab
  • dostarlimab TSR-042, ANB011
  • FITC-YT-16 PD-1 binding peptide
  • APL-501 or CBT-501 or genolimzumab G-226
  • AGEN-2034 GLS-010, budigalimab (ABBV-181)
  • AK-103, BAT-1306, CS-1003 AM- 0001, TILT-123, BH-2922, BH-29
  • the PD-L1 binding antagonist or inhibitor is a small molecule that inhibits PD-1. In some embodiments, the PD-L1 binding antagonist or inhibitor is a small molecule that inhibits PD-L1. In some embodiments, the PD-L1 binding antagonist or inhibitor is a small molecule that inhibits PD-L1 and VISTA or PD-L1 and TIM3. In some embodiments, the PD-L1 binding antagonist or inhibitor is CA-170 (also known as AUPM- 170). In some embodiments, the PD-L1 binding antagonist or inhibitor is an anti-PD-Ll antibody.
  • the anti-PD-Ll antibody can bind to a human PD-L1, for example a human PD-L1 as described above herein and/or as shown in UniProtKB/Swiss- Prot Accession No.Q9NZQ7.1, or a variant thereof.
  • the PD-L1 binding antagonist or inhibitor is a small molecule, a nucleic acid, a polypeptide (e.g., antibody), a carbohydrate, a lipid, a metal, or a toxin.
  • the PD-L1 binding antagonist or inhibitor is an anti-PD-Ll antibody, for example, as described below.
  • the anti-PD-Ll antibody is capable of inhibiting the binding between PD-L1 and PD-1, and/or between PD-L1 and B7-1.
  • the anti-PD-Ll antibody is a monoclonal antibody.
  • the anti-PD-Ll antibody is an antibody fragment selected from a Lab, Eab'-SH, Ev, scEv, or (Eab')2 fragment.
  • the anti-PD-Ll antibody is a humanized antibody. In some instances, the anti-PD-Ll antibody is a human antibody.
  • the anti- PD-Ll antibody is selected from YW243.55.S70, MPDL3280A (atezolizumab), MDX-1 105, MEDI4736 (durvalumab), MSB0010718C (avelumab), LY3300054, STI-A1014, KN035, EAZ053, or CX-072.
  • the PD-L1 axis binding antagonist or inhibitor comprises atezolizumab, avelumab, durvalumab (imfinzi), BGB-A333, SHR-1316 (HTI- 1088), CK-301, BMS-936559, envafolimab (KN035, ASC22), CS1001, MDX-1105 (BMS- 936559), LY3300054, STI-A1014, FAZ053, CX-072, INCB086550, GNS-1480, CA-170, CK-301, M-7824, HTI-1088 (HTI-131, SHR-1316), MSB-2311, AK- 106, AVA-004, BBI- 801, CA-327, CBA-0710, CBT-502, FPT-155, IKT-201, IKT-703, 10-103, JS-003, KD-033, KY-1003, MCLA-145, MT-5050, SNA-02, BCD-135, A
  • the checkpoint inhibitor is an antagonist or inhibitor of CTLA4. In some embodiments, the checkpoint inhibitor is a small molecule antagonist or inhibitor of CTLA4. In some embodiments, the checkpoint inhibitor is an anti-CTLA4 antibody.
  • CTLA4 is part of the CD28-B7 immunoglobulin superfamily of immune checkpoint molecules that acts to negatively regulate T cell activation, particularly CD28- dependent T cell responses. CTLA4 competes for binding to common ligands with CD28, such as CD80 (B7-1) and CD86 (B7-2), and binds to these ligands with higher affinity than CD28.
  • CTLA4 activity is thought to enhance CD28-mediated costimulation (leading to increased T cell activation/priming), affect T cell development, and/or deplete Tregs (such as intratumoral Tregs).
  • the CTLA4 antagonist or inhibitor is a small molecule, a nucleic acid, a polypeptide (e.g., antibody), a carbohydrate, a lipid, a metal, or a toxin.
  • the CTLA-4 antagonist or inhibitor comprises ipilimumab (IBB 10, BMS-734016, MDX010, MDX- CTLA4, MEDI4736), tremelimumab (CP-675, CP-675,206), APL-509, AGEN1884, CS1002, AGEN1181, Abatacept (Orencia, BMS-188667, RG2077), BCD-145, ONC-392, ADU-1604, REGN4659, ADG116, KN044, KN046, or a derivative thereof, or an antibody that competes with any of the preceding.
  • the immune checkpoint inhibitor comprises a LAG-3 antagonist or inhibitor (e.g., an antibody, an antibody conjugate, or an antigenbinding fragment thereof).
  • the LAG-3 antagonist or inhibitor comprises a small molecule, a nucleic acid, a polypeptide (e.g., an antibody), a carbohydrate, a lipid, a metal, or a toxin.
  • the LAG-3 antagonist or inhibitor comprises a small molecule.
  • the LAG-3 antagonist or inhibitor comprises a LAG-3 binding agent.
  • the LAG-3 antagonist or inhibitor comprises an antibody, an antibody conjugate, or an antigen-binding fragment thereof.
  • the LAG-3 antagonist or inhibitor comprises eftilagimod alpha (IMP321, IMP-321, EDDP-202, EOC-202), relatlimab (BMS-986016), GSK2831781 (IMP-731), LAG525 (IMP701), TSR-033, EVIP321 (soluble LAG-3 protein), BI 754111, IMP761, REGN3767, MK-4280, MGD-013, XmAb22841, INCAGN-2385, ENUM-006, AVA-017, AM-0003, iOnctura anti-LAG-3 antibody, Arcus Biosciences LAG-3 antibody, Sym022, a derivative thereof, or an antibody that competes with any of the preceding.
  • eftilagimod alpha IMP321, IMP-321, EDDP-202, EOC-202
  • relatlimab BMS-986016
  • GSK2831781 IMP-731
  • LAG525 IMP701
  • the immune checkpoint inhibitor is monovalent and/or monospecific. In some embodiments, the immune checkpoint inhibitor is multivalent and/or multispecific.
  • an anti-cancer therapy of the disclosure e.g., an immunotherapy
  • an additional anti-cancer therapy is any anti-cancer therapy known in the art or described herein.
  • the additional anti-cancer therapy comprises one or more of a small molecule inhibitor, a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy, an anti- neoplastic agent, a growth inhibitory agent, a cytotoxic agent, a vaccine, a small molecule agonist, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), or any combination thereof.
  • a small molecule inhibitor e.g., a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-
  • an anti-cancer therapy of the disclosure comprises a cyclin- dependent kinase (CDK) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • CDK cyclin- dependent kinase
  • the CDK inhibitor inhibits CDK4.
  • the CDK inhibitor inhibits Cyclin D/CDK4.
  • the CDK inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of CDK4, (b) an antibody that inhibits one or more activities of CDK4 (e.g., by binding to and inhibiting one or more activities of CDK4, binding to and inhibiting expression of CDK4, and/or binding to and inhibiting one or more activities of a cell expressing CDK4, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of CDK4 (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • an antisense oligonucleotide miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like.
  • the CDK inhibitor inhibits CDK4 and CDK6.
  • the CDK inhibitor is a small molecule inhibitor of CDK4 (e.g., a competitive or non-competitive inhibitor).
  • CDK inhibitors include palbociclib, ribociclib, and abemaciclib, as well as pharmaceutically acceptable salts thereof.
  • an anti-cancer therapy of the disclosure comprises a murine double minute 2 homolog (MDM2) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • MDM2 murine double minute 2 homolog
  • the MDM2 inhibitor is (a) a small molecule that inhibits one or more activities of MDM2 (e.g., binding to p53), (b) an antibody that inhibits one or more activities of MDM2 (e.g., by binding to and inhibiting one or more activities of MDM2, binding to and inhibiting expression of MDM2, and/or binding to and inhibiting one or more activities of a cell expressing MDM2, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of MDM2 (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • a nucleic acid that inhibits expression of MDM2 (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • the MDM2 inhibitor is a small molecule inhibitor of MDM2 (e.g., a competitive or noncompetitive inhibitor).
  • MDM2 inhibitors include nutlin-3a, RG7112, idasanutlin (RG7388), AMG-232, MI-63, MI-291, MI-391, MI-77301 (SAR405838), APG-115, DS-3032b, NVP-CGM097, and HDM-201 (siremadlin), as well as pharmaceutically acceptable salts thereof.
  • the MDM2 inhibitor inhibits or disrupts interaction between MDM2 and p53.
  • an anti-cancer therapy of the disclosure comprises (alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor) one or more of an antimetabolite, DNA-damaging agent, or platinum-containing therapeutic (e.g., 5- azacitadine, 5-fluorouracil, acadesine, busulfan, carboplatin, cisplatin, chlorambucil, CPT-11, cytarabine, daunorubicin, decitabine, doxorubicin, etoposide, fludarabine, gemcitabine, idarubicin, radiation, oxaliplatin, temozolomide, topotecan, trabectedin, GSK2830371, or rucaparib); a pro-apoptotic agent (e.g., a BCL2 inhibitor or downregulator, SMAC mimetic, or TRAIL agonist such as ABT-263, ABT-737, oridonin, venetoclax,
  • an antimetabolite
  • the anti-cancer therapy comprises an immunoregulatory molecule or a cytokine, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • An immunoregulatory profile is required to trigger an efficient immune response and balance the immunity in a subject.
  • immunoregulatory cytokines include, but are not limited to, interferons (e.g., IFNa, IFNP and IFNy), interleukins (e.g., IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL- 10, IL- 12 and IL-20), tumor necrosis factors (e.g., TNFa and TNFP), erythropoietin (EPO), FLT-3 ligand, glplO, TCA-3, MCP-1, MIF, MIP-la, MIP-ip, Rantes, macrophage colony stimulating factor (M-CSF), granulocyte colony stimulating factor (G-CSF), or granulocyte-macrophage colony stimulating factor (GM-CSF), as well as functional fragments thereof.
  • interferons e.g., IFNa, IFNP and IFNy
  • interleukins
  • any immunomodulatory chemokine that binds to a chemokine receptor i.e., a CXC, CC, C, or CX3C chemokine receptor
  • chemokines include, but are not limited to, MIP-3a (Lax), MIP-3P, Hcc-1, MPIF-1, MPIF- 2, MCP-2, MCP-3, MCP-4, MCP-5, Eotaxin, Tare, Elc, 1309, IL-8, GCP-2 Groa, Gro-P, Nap-2, Ena-78, Ip-10, MIG, LTac, SDF-1, or BCA-1 (Bic), as well as functional fragments thereof.
  • the immunoregulatory molecule is included with any of the treatments provided herein.
  • an anti-cancer therapy of the disclosure comprises a tyrosine kinase inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the tyrosine kinase inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of a tyrosine kinase, (b) an antibody that inhibits one or more activities of a tyrosine kinase (e.g., by binding to and inhibiting one or more activities of the tyrosine kinase, binding to and inhibiting expression, such as cell surface expression, of the tyrosine kinase, and/or binding to and inhibiting one or more activities of a cell expressing the tyrosine kinase, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic
  • the tyrosine kinase inhibitor is a small molecule inhibitor of a tyrosine kinase (e.g., a competitive or noncompetitive inhibitor).
  • tyrosine kinase inhibitors include imatinib, crenolanib, linifanib, ninetedanib, axitinib, dasatinib, imetelstat, midostaurin, pazopanib, sorafenib, sunitinb, motesanib, masitinib, vatalanib, cabozanitinib, tivozanib, OSL930, K18751, telatinib, dovitinib, tyrphostin AG 1296, and amuvatinib, as well as pharmaceutically acceptable salts thereof.
  • an anti-cancer therapy of the disclosure comprises a mitogen- activated protein kinase (MEK) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • MEK mitogen- activated protein kinase
  • the MEK inhibitor inhibits one or more activities of MEK1 and/or MEK2.
  • the anti-cancer therapy/MEK inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of MEK, (b) an antibody that inhibits one or more activities of MEK (e.g., by binding to and inhibiting one or more activities of MEK, binding to and inhibiting expression of MEK, and/or binding to and inhibiting one or more activities of a cell expressing MEK, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of MEK (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • an antisense oligonucleotide miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like.
  • the MEK inhibitor is a small molecule inhibitor of MEK (e.g., a competitive or non-competitive inhibitor).
  • MEK inhibitors include trametinib, cobimetinib, binimetinib, CI-1040, PD0325901, selumetinib, AZD8330, TAK- 733, GDC-0623, refametinib, pimasertib, RO4987655, RO5126766, WX-544, and HL-085, as well as pharmaceutically acceptable salts thereof.
  • the anti-cancer therapy inhibits one or more activities of the Raf/MEK/ERK pathway, including inhibitors of Raf, MEK, and/or ERK.
  • an anti-cancer therapy of the disclosure comprises a mammalian target of rapamycin (mTOR) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the mTOR inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of mTOR, (b) an antibody that inhibits one or more activities of mTOR (e.g., by binding to and inhibiting one or more activities of mTOR, binding to and inhibiting expression of mTOR, and/or binding to and inhibiting one or more activities of a cell expressing mTOR, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of mTOR (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • the mTOR inhibitor is a small molecule inhibitor of mTOR (e.g., a competitive inhibitor, such as an ATP-competitive inhibitor, or a non-competitive inhibitor, such as a rapamycin analog).
  • mTOR inhibitors include temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, and OSI027, as well as pharmaceutically acceptable salts thereof.
  • the anti-cancer therapy inhibits one or more activities of the Akt/mTOR pathway, including inhibitors of Akt and/or mTOR.
  • an anti-cancer therapy of the disclosure comprises a PI3K inhibitor or Akt inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the PI3K inhibitor inhibits one or more activities of PI3K.
  • the anti-cancer therapy/ PI3K inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of PI3K, (b) an antibody that inhibits one or more activities of PI3K (e.g., by binding to and inhibiting one or more activities of PI3K, binding to and inhibiting expression of PI3K, and/or binding to and inhibiting one or more activities of a cell expressing PI3K, such as by inducing antibodydependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of PI3K (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • an antisense oligonucleotide miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like.
  • the PI3K inhibitor is a small molecule inhibitor of PI3K (e.g., a competitive or non-competitive inhibitor).
  • PI3K inhibitors include GSK2636771, buparlisib (BKM120), AZD8186, copanlisib (BAY80-6946), LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib (GS-1101, CAL-101), pictilisib (GDC-094), GDC0032, IPI145, INK1117 (MLN1117), SAR260301, KIN-193 (AZD6482), duvelisib, GS-9820, GSK2636771, GDC- 0980, AMG319, paxalisib, and alpelisib (BYL719, Piqray), as well as pharmaceutically acceptable salts thereof.
  • the AKT inhibitor inhibits one or more activities of AKT (e.g., AKT1).
  • the AKT inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of AKT1, (b) an antibody that inhibits one or more activities of AKT1 (e.g., by binding to and inhibiting one or more activities of AKT1, binding to and inhibiting expression of AKT1, and/or binding to and inhibiting one or more activities of a cell expressing AKT1, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of AKT1 (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • the AKT1 inhibitor is a small molecule inhibitor of AKT1 (e.g., a competitive or non-competitive inhibitor).
  • AKT1 inhibitors include GSK690693, GSK2141795 (uprosertib), GSK2110183 (afuresertib), AZD5363, GDC-0068 (ipatasertib), AT7867, CCT128930, MK-2206, BAY 1125976, AKT1 and AKT2-IN-1, perifosine, and VIII, as well as pharmaceutically acceptable salts thereof.
  • the AKT1 inhibitor is a pan-Akt inhibitor.
  • an anti-cancer therapy of the disclosure comprises a hedgehog (Hh) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the Hh inhibitor is (a) a small molecule that inhibits one or more enzymatic activities of Hh, (b) an antibody that inhibits one or more activities of Hh (e.g., by binding to and inhibiting one or more activities of Hh, binding to and inhibiting expression of Hh, and/or binding to and inhibiting one or more activities of a cell expressing Hh, such as by inducing antibody-dependent cellular cytotoxicity, ADCC, or phagocytosis, ADCP), or (c) a nucleic acid that inhibits expression of Hh (e.g., an antisense oligonucleotide, miRNA, siRNA, morpholino, CRISPR-based therapeutic, and the like).
  • the Hh inhibitor is a small molecule inhibitor of Hh (e.g., a competitive or non-competitive inhibitor).
  • Hh inhibitors include sonidegib, vismodegib, erismodegib, saridegib, BMS833923, PF-04449913, and LY2940680, as well as pharmaceutically acceptable salts thereof.
  • an anti-cancer therapy of the disclosure comprises a heat shock protein (HSP) inhibitor, a MYC inhibitor, an HD AC inhibitor, an immunotherapy, a neoantigen, a vaccine, or a cellular therapy, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • HSP heat shock protein
  • the anti-cancer therapy comprises one or more of a chemotherapy, a VEGF inhibitor, an Integrin P3 inhibitor, a statin, an EGFR inhibitor, an mTOR inhibitor, a PI3K inhibitor, a MAPK inhibitor, or a CDK4/6 inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the anti-cancer therapy comprises a kinase inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the kinase inhibitor is crizotinib, alectinib, ceritinib, lorlatinib, brigatinib, ensartinib (X-396), repotrectinib (TPX-005), entrectinib (RXDX-101), AZD3463, CEP- 37440, belizatinib (TSR-011), ASP3026, KRCA-0008, TQ-B3139, TPX-0131, or TAE684 (NVP-TAE684).
  • the kinase inhibitor is an ALK kinase inhibitor, e.g., as described herein and/or in examples 3-39 of W02005016894.
  • the anti-cancer therapy comprises a heat shock protein (HSP) inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • HSP heat shock protein
  • the HSP inhibitor is a Pan-HSP inhibitor, such as KNK423.
  • the HSP inhibitor is an HSP70 inhibitor, such as cmHsp70.1, quercetin, VER155008, or 17-AAD.
  • the HSP inhibitor is a HSP90 inhibitor.
  • the HSP90 inhibitor is 17-AAD, Debio0932, ganetespib (STA-9090), retaspimycin hydrochloride (retaspimycin, IPI-504), AUY922, alvespimycin (KOS- 1022, 17-DMAG), tanespimycin (KOS-953, 17-AAG), DS 2248, or AT13387 (onalespib).
  • the HSP inhibitor is an HSP27 inhibitor, such as Apatorsen (OGX-427).
  • the anti-cancer therapy comprises a MYC inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the MYC inhibitor is MYCi361 (NUCC-0196361), MYCi975 (NUCC- 0200975), Omomyc (dominant negative peptide), ZINC16293153 (Min9), 10058-F4, JKY-2- 169, 7594-0035, or inhibitors of MYC/MAX dimerization and/or MYC/MAX/DNA complex formation.
  • the anti-cancer therapy comprises a histone deacetylase
  • the HDAC inhibitor is belinostat (PXD101, e.g., Beleodaq®), SAHA (vorinostat, suberoylanilide hydroxamine, e.g., Zolinza®), panobinostat (LBH589, LAQ-824), ACY1215 (Rocilinostat), quisinostat (JNJ-26481585), abexinostat (PCI-24781), pracinostat (SB939), givinostat (ITF2357), resminostat (4SC-201), trichostatin A (TSA), MS-275 (etinostat), Romidepsin (depsipeptide, FK228), MGCD0103 (mocetinostat), BML-210, CAY10603, valproic acid, MC1568, CUDC
  • the anti-cancer therapy comprises a VEGF inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the VEGF inhibitor is Bevacizumab (e.g., Avastin®), BMS-690514, or aflibercept.
  • the anti-cancer therapy comprises a VEGFR inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the VEGFR inhibitor is ramucirumab, pazopanib, sorafenib, sunitinib, golvatinib, vandetanib, cabozantinib, levantinib, axitinib, cediranib, tivozanib, lucitanib, semaxanib, nindentanib, or regorafenib.
  • the anti-cancer therapy comprises an integrin P3 inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the integrin P3 inhibitor is anti-avb3 (clone LM609), cilengitide (EMD121974, NSC, 707544), an siRNA, GLPG0187, MK-0429, CNTO95, TN-161, etaracizumab (MEDI-522), intetumumab (CNTO95) (anti-alphaV subunit antibody), abituzumab (EMD 525797/DI17E6) (anti-alphaV subunit antibody), JSM6427, SJ749, BCH- 15046, SCH221153, or SC56631.
  • the anti-cancer therapy comprises an allbp3 integrin inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the allbp3 integrin inhibitor is abciximab, eptifibatide (e.g., Integrilin®), or tirofiban (e.g., Aggrastat®).
  • the anti-cancer therapy comprises an mTOR inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the mTOR inhibitor is temsirolimus (CCI-779), KU-006379, PP242, Torinl, Torin2, ICSN3250, Rapalink-1, CC-223, sirolimus (rapamycin), everolimus (RAD001), dactosilib (NVP-BEZ235), GSK2126458, WAY-001, WAY-600, WYE-687, WYE-354, SF1126, XL765, INK128 (MLN012), AZD8055, OSI027, AZD2014, or AP- 23573.
  • the anti-cancer therapy comprises a statin or a statin-based agent, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the statin or statin-based agent is simvastatin, atorvastatin, fluvastatin, pitavastatin, pravastatin, rosuvastatin, or cerivastatin.
  • the anti-cancer therapy comprises a MAPK inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the MAPK inhibitor is SB203580, SKF-86002, BIRB-796, SC-409, RJW-67657, BIRB-796, VX-745, RO3201195, SB-242235, or MW181.
  • the anti-cancer therapy comprises an EGFR inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the EGFR inhibitor is cetuximab, panitumumab, lapatinib, gefitinib, vandetanib, dacomitinib, icotinib, osimertinib (AZD9291), afatanib, olmutinib, EGF816 (nazartinib), avitinib (AC0010), rociletinib (CO-1686), BMS-690514, YH5448, PF- 06747775, ASP8273, PF299804, AP26113, necitumumab (e.g., Portrazza®), BLU-945, amivantamab, or erlotinib.
  • the EGFR inhibitor is gefitinib or
  • the anti-cancer therapy comprises a nucleic acid molecule, such as a dsRNA, an siRNA, or an shRNA, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • dsRNAs having a duplex structure are effective at inducing RNA interference (RNAi).
  • the anti-cancer therapy comprises a small interfering RNA molecule (siRNA). dsRNAs and siRNAs can be used to silence gene expression in mammalian cells (e.g., human cells).
  • a dsRNA of the disclosure comprises any of between about 5 and about 10 base pairs, between about 10 and about 12 base pairs, between about 12 and about 15 base pairs, between about 15 and about 20 base pairs, between about 20 and 23 base pairs, between about 23 and about 25 base pairs, between about 25 and about 27 base pairs, or between about 27 and about 30 base pairs.
  • siRNAs are small dsRNAs that optionally include overhangs.
  • the duplex region of an siRNA is between about 18 and 25 nucleotides, e.g., any of 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides.
  • siRNAs may also include short hairpin RNAs (shRNAs), e.g., with approximately 29-base-pair stems and 2-nucleotide 3’ overhangs.
  • shRNAs short hairpin RNAs
  • Methods for designing, optimizing, producing, and using dsRNAs, siRNAs, or shRNAs, are known in the art.
  • the anti-cancer therapy comprises a chemotherapy, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • chemotherapeutic agents include alkylating agents, such as thiotepa and cyclo sphosphamide; alkyl sulfonates, such as busulfan, improsulfan, and piposulfan; aziridines, such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines, including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide, and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin
  • chemotherapeutic drugs which can be combined with anti-cancer therapies of the present disclosure are carboplatin (Paraplatin), cisplatin (Platinol, Platinol-AQ), cyclophosphamide (Cytoxan, Neosar), docetaxel (Taxotere), doxorubicin (Adriamycin), etoposide (VePesid), fluorouracil (5-FU), gemcitabine (Gemzar), irinotecan (Camptosar), methotrexate (Folex, Mexate, Amethop terin), paclitaxel (Taxol, Abraxane), topotecan (Hycamtin), vincristine (Oncovin, Vincasar PFS), and vinblastine (Velban).
  • the anti-cancer therapy comprises a kinase inhibitor, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • kinase inhibitors include those that target one or more receptor tyrosine kinases, e.g., EGFR, HER-2/ERBB2, IGF-IR, PDGFR-a, PDGFR- 0, cKIT, FLT4, FLT3, FGFR1, FGFR2, FGFR3, FGFR4, CSF1R, c-MET, ROS1, RON, c-RET, NTRK1, NTRK2, NTRK3, AXL or ALK; one or more cytoplasmic tyrosine kinases, e.g., c-SRC, c-YES, ABL, BCR- ABL, or JAK-2; one or more serine/threonine kinases, e.g., ATM, Aurora A & B, CDKs, mTOR, PKCi, PLKs, BRAF, CRAF, S6K, or STK11/LKB1; or one or more lipid kinases, e.g.
  • Small molecule kinase inhibitors include PHA-739358, nilotinib, dasatinib, PD166326, NSC 743411, lapatinib (GW-572016), canertinib (CI-1033), semaxinib (SU5416), vatalanib (PTK787/ZK222584), sunitinib (SU1 1248), sorafenib (BAY 43-9006), or leflunomide (SU101).
  • tyrosine kinase inhibitors include erlotinib (Tarceva), imatinib (Gleevec/Glivec), sorafenib (Nexavar), sunitinib (Sutent), deucravacitinib, avapritinib, capmatinib, pemigatinib, ripretinib, selpercatinib, selumetinib, tucatinib, entrectinib, erdafitinib, fedratinib, pexidartinib, upadacitinib, zanubrutinib, dasatinib, nilotinib, lapatinib, pazopanib, vandetanib, ruxolitinib, crizotinib, tofacitinib, regorafenib, ponatinib, caboz
  • the anti-cancer therapy comprises an anti-angiogenic agent, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • Angiogenesis inhibitors prevent the extensive growth of blood vessels (angiogenesis) that tumors require to survive.
  • Non-limiting examples of angiogenesismediating molecules or angiogenesis inhibitors which may be used in the methods of the present disclosure include soluble VEGF (for example: VEGF isoforms, e.g., VEGF121 and VEGF165; VEGF receptors, e.g., VEGFR1, VEGFR2; and co-receptors, e.g., Neuropilin-1 and Neuropilin-2), NRP-1, angiopoietin 2, TSP-1 and TSP-2, angiostatin and related molecules, endostatin, vasostatin, calreticulin, platelet factor-4, TIMP and CD Al, Meth-1 and Meth-2, IFNa, IFN-0 and IFN-y, CXCL10, IL-4, IL- 12 and IL- 18, prothrombin (kringle domain-2), antithrombin III fragment, prolactin, VEGI, SPARC, osteopontin, maspin, canstatin, proliferin-
  • known therapeutic candidates that may be used according to the methods of the disclosure include naturally occurring angiogenic inhibitors, including without limitation, angiostatin, endostatin, or platelet factor-4.
  • therapeutic candidates that may be used according to the methods of the disclosure include, without limitation, specific inhibitors of endothelial cell growth, such as TNP-470, thalidomide, and interleukin- 12.
  • Still other anti- angiogenic agents that may be used according to the methods of the disclosure include those that neutralize angiogenic molecules, including without limitation, antibodies to fibroblast growth factor, antibodies to vascular endothelial growth factor, antibodies to platelet derived growth factor, or antibodies or other types of inhibitors of the receptors of EGF, VEGF or PDGF.
  • anti-angiogenic agents that may be used according to the methods of the disclosure include, without limitation, suramin and its analogs, and tecogalan.
  • anti- angiogenic agents that may be used according to the methods of the disclosure include, without limitation, agents that neutralize receptors for angiogenic factors or agents that interfere with vascular basement membrane and extracellular matrix, including, without limitation, metalloprotease inhibitors and angiostatic steroids.
  • Another group of anti- angiogenic compounds that may be used according to the methods of the disclosure includes, without limitation, anti-adhesion molecules, such as antibodies to integrin alpha v beta 3.
  • anti-angiogenic compounds or compositions that may be used according to the methods of the disclosure include, without limitation, kinase inhibitors, thalidomide, itraconazole, carboxyamidotriazole, CM101, IFN-a, IL-12, SU5416, thrombospondin, cartilage-derived angiogenesis inhibitory factor, 2-methoxyestradiol, tetrathiomolybdate, thrombospondin, prolactin, and linomide.
  • the anti-angiogenic compound that may be used according to the methods of the disclosure is an antibody to VEGF, such as AvastinO/bevacizumab (Genentech).
  • the anti-cancer therapy comprises an anti-DNA repair therapy, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the anti-DNA repair therapy is a PARP inhibitor (e.g., talazoparib, rucaparib, olaparib), a RAD51 inhibitor (e.g., RI-1), or an inhibitor of a DNA damage response kinase, e.g., CHCK1 (e.g., AZD7762), ATM (e.g., KU-55933, KU-60019, NU7026, or VE-821), and ATR (e.g., NU7026).
  • PARP inhibitor e.g., talazoparib, rucaparib, olaparib
  • a RAD51 inhibitor e.g., RI-1
  • CHCK1 e.g., AZD7762
  • ATM e.g., KU-55933, KU-60019, NU7026
  • the anti-cancer therapy comprises a radiosensitizer, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • exemplary radiosensitizers include hypoxia radiosensitizers such as misonidazole, metronidazole, and trans-sodium crocetinate, a compound that helps to increase the diffusion of oxygen into hypoxic tumor tissue.
  • the radiosensitizer can also be a DNA damage response inhibitor interfering with base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), recombinational repair comprising homologous recombination (HR) and non-homologous end-joining (NHEJ), and direct repair mechanisms.
  • Single strand break (SSB) repair mechanisms include BER, NER, or MMR pathways, while double stranded break (DSB) repair mechanisms consist of HR and NHEJ pathways. Radiation causes DNA breaks that, if not repaired, are lethal. SSBs are repaired through a combination of BER, NER and MMR mechanisms using the intact DNA strand as a template.
  • the predominant pathway of SSB repair is BER, utilizing a family of related enzymes termed poly-(ADP-ribose) polymerases (PARP).
  • PARP poly-(ADP-ribose) polymerases
  • the radiosensitizer can include DNA damage response inhibitors such as PARP inhibitors.
  • the anti-cancer therapy comprises an anti-inflammatory agent, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • the anti-inflammatory agent is an agent that blocks, inhibits, or reduces inflammation or signaling from an inflammatory signaling pathway
  • the anti-inflammatory agent inhibits or reduces the activity of one or more of any of the following: IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12, IL-13, IL-15, IL-18, IL-23; interferons (ILNs), e.g., ILNa, IENP, ILNy, ILN-y inducing factor (IGIE); transforming growth factor-P (TGE-P); transforming growth factor-a (TGE-a); tumor necrosis factors, e.g., TNE-a, TNE-p, T
  • TNE-a tumor necrosis factors
  • the anti-inflammatory agent is an IL-1 or IL-1 receptor antagonist, such as anakinra (e.g., Kineret®), rilonacept, or canakinumab.
  • the anti-inflammatory agent is an IL-6 or IL-6 receptor antagonist, e.g., an anti-IL-6 antibody or an anti-IL-6 receptor antibody, such as tocilizumab (e.g., ACTEMRA®), olokizumab, clazakizumab, sarilumab, sirukumab, siltuximab, or ALX-0061.
  • the anti-inflammatory agent is a TNE-a antagonist, e.g., an anti-TNEa antibody, such as infliximab (Remicade®), golimumab (Simponi®), adalimumab (e.g., Humira®), certolizumab pegol (e.g., Cimzia®) or etanercept.
  • the anti-inflammatory agent is a corticosteroid.
  • corticosteroids include, but are not limited to, cortisone (hydrocortisone, hydrocortisone sodium phosphate, hydrocortisone sodium succinate, e.g., Ala-Cort®, Hydrocort Acetate®, hydrocortone phosphate Lanacort®, Solu-Cortef®), decadron (dexamethasone, dexamethasone acetate, dexamethasone sodium phosphate, e.g., Dexasone®, Diodex®, Hexadrol®, Maxidex®), methylprednisolone (6-methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, e.g., Duralone®, Medralone®, Medrol®, M- Prednisol®, Solu-Medrol®), prednisolone (e.g., Delta-Cortef®, ORAPRED®, Pedia
  • the anti-cancer therapy comprises an antimetabolite chemotherapeutic agent, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • Antimetabolite chemotherapeutic agents are agents that are structurally similar to a metabolite, but cannot be used by the body in a productive manner. Many antimetabolite chemotherapeutic agents interfere with the production of RNA or DNA.
  • antimetabolite chemotherapeutic agents include gemcitabine (e.g., GEMZAR®), 5 -fluorouracil (5-FU), capecitabine (e.g., XELODATM), 6-mercaptopurine, methotrexate, 6- thioguanine, pemetrexed, raltitrexed, arabinosylcytosine ARA-C cytarabine (e.g., CYTOSAR-U®), dacarbazine (DTIC-DOMED), azacytosine, deoxycytidine, pyrimidine, fludarabine (e.g., FLUDARA®), cladribine, and 2-deoxy-D-glucose.
  • an antimetabolite chemotherapeutic agent is gemcitabine.
  • Gemcitabine HC1 is sold by Eli Lilly under the trademark GEMZAR®.
  • the anti-cancer therapy comprises a platinum-based chemotherapeutic agent, e.g., alone or in combination with an immunotherapy, such as an immune checkpoint inhibitor.
  • Platinum-based chemotherapeutic agents are chemotherapeutic agents that comprise an organic compound containing platinum as an integral part of the molecule.
  • a chemotherapeutic agent is a platinum agent.
  • the platinum agent is selected from cisplatin, carboplatin, oxaliplatin, nedaplatin, triplatin tetranitrate, phenanthriplatin, picoplatin, or satraplatin.
  • the treatment or the one or more treatment options further comprise an additional anti-cancer therapy. In some embodiments of any of the methods provided herein, the treatment or the one or more treatment options further comprise administering an additional anti-cancer therapy to the individual. In some embodiments, the additional anti-cancer therapy is any anti-cancer therapy known in the art or described herein.
  • the additional anticancer therapy comprises one or more of a small molecule inhibitor, a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy, an anti-neoplastic agent, a growth inhibitory agent, a cytotoxic agent, a vaccine, a small molecule agonist, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), or any combination thereof.
  • a small molecule inhibitor e.g., a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy
  • the additional anti-cancer therapy is an immunotherapy.
  • the additional anti-cancer therapy is a heat shock protein 90 inhibitor (Golding et al., Molecular cancer vol. 17,1 52, 2018; Pall, Current opinion in oncology vol. 27,2 (2015): 118-24), an EGFR inhibitor (Golding et al., Molecular cancer vol. 17,1 52, 2018), a SHP2 inhibitor (Dardaei et al., Nature medicine vol. 24,4 (2018): 512-517), a MEK inhibitor (Shrestha et al., Scientific reports vol. 9,1 18842, 2019; Shrestha et al., The Journal of pharmacology and experimental therapeutics vol.
  • the methods further comprise acquiring knowledge of or detecting in a sample from the individual a base substitution, a short insertion/deletion (indel), a copy number alteration, or a genomic rearrangement in one or more genes or based on genetic information.
  • the one or more genes or genetic information comprise the ABL1, ACVR1B, AKT1, AKT2, AKT3, ALK, ALOX12B, AMER1, APC, AR, ARAF, ARFRP1, ARID1A, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, BAP1, BARD1, BCL2, BCL2L1, BCL2L2, BCL6, BCOR, BCORL1, BCR, BRAF, BRCA1, BRCA2, BRD4, BRIP1, BTG1, BTG2, BTK, CALR, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD22, CD274, CD70, CD74, CD79A, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHE
  • the one or more genes comprise the ABL, ALK, ALL, B4GALNT1, BAFF, BCL2, BRAF, BRCA, BTK, CD19, CD20, CD3, CD30, CD319, CD38, CD52, CDK4, CDK6, CML, CRACC, CS1, CTLA-4, dMMR, EGFR, ERBB1, ERBB2, FGFR1-3, FLT3, GD2, HDAC, HER1, HER2, HR, IDH2, IL-ip, IL-6, IL-6R, JAK1, JAK2, JAK3, KIT, KRAS, MEK, MET, MSI-H, mTOR, PARP, PD-1, PDGFR, PDGFRa, PDGFRP, PD-L1, PI3K5, PIGF, PTCH, RAF, RANKL, RET, ROS1, SLAMF7, VEGF, VEGFA, or VEGFB gene, or any combination thereof.
  • the treatment or the one or more treatment options further comprise an additional anti-cancer therapy.
  • the treatment or the one or more treatment options further comprise administering an additional anti-cancer therapy to the individual.
  • the additional anti-cancer therapy is any anti-cancer therapy known in the art or described herein.
  • the additional anti- cancer therapy comprises one or more of a small molecule inhibitor, a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy, an anti-neoplastic agent, a growth inhibitory agent, a cytotoxic agent, a vaccine, a small molecule agonist, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), or any combination thereof.
  • a small molecule inhibitor e.g., a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy
  • the individual has been previously treated, or is being treated, for cancer with a treatment for cancer, e.g., an anti-cancer therapy described herein or any other anti-cancer therapy or treatment known in the art, such as an endocrine therapy.
  • a treatment for cancer e.g., an anti-cancer therapy described herein or any other anti-cancer therapy or treatment known in the art, such as an endocrine therapy.
  • the cancer is breast cancer.
  • the breast cancer is hormone receptor positive (HR+) breast cancer.
  • the cancer is endometrial cancer.
  • the cancer is advanced or metastatic.
  • Certain aspects of the present disclosure relate to detection of an ESRI fusion nucleic acid molecule of the disclosure, e.g., in a patient sample.
  • the ESRI fusion nucleic acid molecule is detected in vitro.
  • an ESRI fusion polypeptide of the disclosure e.g., an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule of the disclosure, e.g., in a patient sample.
  • the ESRI fusion polypeptide is detected in vitro.
  • an ESRI fusion nucleic acid molecule of the disclosure is detected by sequencing part or all of a gene involved in the fusion nucleic acid molecule, e.g., an ESRI gene, and/or a corresponding fusion partner gene described herein (e.g., any of CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5), by next-generation or other sequencing of DNA, RNA, or cDNA.
  • an ESRI fusion nucleic acid molecule of the disclosure is detected by PCR amplification of DNA, RNA, or cDNA. In some embodiments, an ESRI fusion nucleic acid molecule of the disclosure is detected by in situ hybridization using one or more polynucleotides that hybridize to a locus involved in the fusion nucleic acid molecule, e.g., an ESRI locus, and/or a corresponding fusion partner gene locus described herein (e.g., any of CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfi5), e.g., using fluorescence in situ hybridization (FISH).
  • FISH fluorescence in situ hybridization
  • an ESRI fusion nucleic acid molecule of the disclosure is detected in a cancer or tumor cell, e.g., using tumor tissue, such as from a tumor biopsy or other tumor specimen; in a circulating cancer or tumor cell, e.g., using a liquid biopsy, such as from blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva; or in circulating tumor DNA (ctDNA), e.g., using a liquid biopsy, such as from blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • tumor tissue such as from a tumor biopsy or other tumor specimen
  • a liquid biopsy such as from blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva
  • ctDNA circulating tumor DNA
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using any suitable method known in the art, such as a nucleic acid hybridization assay, an amplification-based assay e.g., polymerase chain reaction, PCR), a PCR-RFLP assay, real-time PCR, sequencing (e.g., Sanger sequencing or next-generation sequencing), a screening analysis (e.g., using karyotype methods), fluorescence in situ hybridization (FISH), break away FISH, spectral karyotyping, multiplex-FISH, comparative genomic hybridization, in situ hybridization, single specific primer-polymerase chain reaction (SSP-PCR), high performance liquid chromatography (HPLC), or mass-spectrometric genotyping.
  • a nucleic acid hybridization assay e.g., an amplification-based assay e.g., polymerase chain reaction, PCR), a PCR-RFLP assay, real-time PCR, sequencing (e.g.,
  • an ESRI fusion nucleic acid molecule of the disclosure is detected by sequencing.
  • the sequencing comprises a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique.
  • the massively parallel sequencing (MPS) technique comprises nextgeneration sequencing (NGS).
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using an in situ hybridization method, such as a fluorescence in situ hybridization (FISH) method.
  • FISH fluorescence in situ hybridization
  • FISH analysis is used to identify the chromosomal rearrangement resulting in an ESRI fusion nucleic acid molecule as described herein.
  • FISH analysis is used to identify an RNA molecule comprising or encoding an ESRI fusion nucleic acid molecule of the disclosure.
  • Methods for performing FISH are known in the art and can be used in nearly any type of tissue.
  • nucleic acid probes which are detectably labeled e.g. fluorescently labeled, are allowed to bind to specific regions of DNA, e.g., a chromosome, or an RNA, e.g., an mRNA, and then examined, e.g., through a microscope.
  • DNA or RNA molecules are first fixed onto a slide, the labeled probe is then hybridized to the DNA or RNA molecules, and then visualization is achieved, e.g., using enzyme-linked label-based detection methods known in the art.
  • the resolution of FISH analysis is on the order of detection of 60 to 100000 nucleotides, e.g., 60 base pairs (bp) up to 100 kilobase pairs of DNA.
  • Nucleic acid probes used in FISH analysis comprise single stranded nucleic acids. Such probes are typically at least about 50 nucleotides in length. In some embodiments, probes comprise about 100 to about 500 nucleotides.
  • Probes that hybridize with centromeric DNA and locus- specific DNA or RNA are available commercially, for example, from Vysis, Inc. (Downers Grove, Ill.), Molecular Probes, Inc. (Eugene, Oreg.) or from Cytocell (Oxfordshire, UK).
  • probes can be made non-commercially from chromosomal or genomic DNA or other sources of nucleic acids through standard techniques. Examples of probes, labeling and hybridization methods are known in the art.
  • break-away FISH is used in the methods provided herein.
  • break-away FISH at least one probe targeting a fusion junction or breakpoint and at least one probe targeting an individual gene of the fusion, e.g., at one or more exons and or introns of the gene, are utilized.
  • both probes are observed (or a secondary color is observed due to the close proximity of the two genes of the gene fusion); and in cells having a fusion nucleic acid molecule described herein, only a single gene probe is observed due to the presence of a rearrangement resulting in the fusion nucleic acid molecule.
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using an array-based method, such as array-based comparative genomic hybridization (CGH) methods.
  • CGH comparative genomic hybridization
  • a first sample of nucleic acids e.g., from a sample, such as from a tumor, or a tissue or liquid biopsy
  • a second sample of nucleic acids e.g., a control, such as from a healthy cell/tissue
  • equal quantities of the two samples are mixed and co-hybridized to a DNA microarray of several thousand evenly spaced cloned DNA fragments or oligonucleotides, which have been spotted in triplicate on the array.
  • digital imaging systems are used to capture and quantify the relative fluorescence intensities of each of the hybridized fluorophores.
  • the resulting ratio of the fluorescence intensities is proportional to the ratio of the copy numbers of DNA sequences in the two samples.
  • differences in the ratio of the signals from the two labels are detected and the ratio provides a measure of the copy number.
  • Array-based CGH can also be performed with single-color labeling.
  • a control e.g., control nucleic acid sample, such as from a healthy cell/tissue
  • a test sample e.g., a nucleic acid sample obtained from an individual or from a tumor, or a tissue or liquid biopsy
  • Copy number differences are calculated based on absolute signals from the two arrays.
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using an amplification-based method.
  • a sample of nucleic acids such as a sample obtained from an individual, a tumor or a tissue or liquid biopsy, is used as a template in an amplification reaction (e.g., Polymerase Chain Reaction (PCR)) using one or more oligonucleotides or primers, e.g., such as one or more oligonucleotides or primers provided herein.
  • PCR Polymerase Chain Reaction
  • the presence of a fusion nucleic acid molecule of the disclosure in the sample can be determined based on the presence or absence of an amplification product.
  • Quantitative amplification methods are also known in the art and may be used according to the methods provided herein. Methods of measurement of DNA copy number at microsatellite loci using quantitative PCR analysis are known in the art. The known nucleotide sequence for genes is sufficient to enable one of skill in the art to routinely select primers to amplify any portion of the gene. Fluorogenic quantitative PCR can also be used. In fluorogenic quantitative PCR, quantitation is based on the amount of fluorescence signals, e.g., TaqMan and Sybr green.
  • LCR ligase chain reaction
  • transcription amplification e.g., transcription amplification
  • self-sustained sequence replication e.g., transcription amplification
  • dot PCR e.g., transcription amplification
  • linker adapter PCR e.g., linker adapter PCR
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using a sequencing method. Any method of sequencing known in the art can be used to detect an ESRI fusion nucleic acid molecule provided herein. Exemplary sequencing methods that may be used to detect a fusion nucleic acid molecule provided herein include those based on techniques developed by Maxam and Gilbert or Sanger. Automated sequencing procedures may also be used, e.g., including sequencing by mass spectrometry. [0204] In some embodiments, an ESRI fusion nucleic acid molecule of the disclosure is detected using hybrid capture-based sequencing (hybrid capture-based NGS), e.g., using adaptor ligation-based libraries.
  • hybrid capture-based sequencing hybrid capture-based NGS
  • an ESRI fusion nucleic acid molecule of the disclosure is detected using next-generation sequencing (NGS).
  • NGS next-generation sequencing
  • Next- generation sequencing includes any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules or clonally expanded proxies for individual nucleic acid molecules in a highly parallel fashion (e.g., greater than 10 5 molecules may be sequenced simultaneously).
  • Next generation sequencing methods suitable for use according to the methods provided herein include, without limitation, massively parallel short-read sequencing, template-based- sequencing, pyrosequencing, real-time sequencing comprising imaging the continuous incorporation of dye-labeling nucleotides during DNA synthesis, nanopore sequencing, sequencing by hybridization, nano-transistor array based sequencing, polony sequencing, scanning tunneling microscopy (STM)-based sequencing, or nanowire-molecule sensor based sequencing.
  • STM scanning tunneling microscopy
  • Exemplary NGS methods and platforms that may be used to detect an ESRI fusion nucleic acid molecule provided herein include, without limitation, the HeliScope Gene Sequencing system from Helicos BioSciences (Cambridge, MA., USA), the PacBio RS system from Pacific Biosciences (Menlo Park, CA, USA), massively parallel short-read sequencing such as the Solexa sequencer and other methods and platforms from Illumina Inc. (San Diego, CA, USA), 454 sequencing from 454 LifeSciences (Branford, CT, USA), Ion Torrent sequencing from ThermoFisher (Waltham, MA, USA), or the SOLiD sequencer from Applied Biosystems (Foster City, CA, USA).
  • the HeliScope Gene Sequencing system from Helicos BioSciences (Cambridge, MA., USA)
  • the PacBio RS system from Pacific Biosciences (Menlo Park, CA, USA)
  • massively parallel short-read sequencing such as the Solexa sequencer and other methods and
  • Additional exemplary methods and platforms that may be used to detect a fusion nucleic acid molecule include, without limitation, the Genome Sequencer (GS) FLX System from Roche (Basel, CHE), the G.007 polonator system, the Solexa Genome Analyzer, HiSeq 2500, HiSeq3000, HiSeq 4000, and NovaSeq 6000 platforms from Illumina Inc. (San Diego, CA, USA).
  • GS Genome Sequencer
  • CHE Genome Sequencer
  • G.007 polonator system the Solexa Genome Analyzer
  • HiSeq 2500 HiSeq3000
  • HiSeq 4000 HiSeq 4000
  • NovaSeq 6000 platforms from Illumina Inc. (San Diego, CA, USA).
  • the methods may comprise one or more of the steps of: (i) obtaining a sample from an individual (e.g., an individual suspected of having or determined to have cancer), (ii) extracting nucleic acid molecules (e.g., a mixture of tumor or cancer nucleic acid molecules and non-tumor or non- cancer nucleic acid molecules) from the sample, (iii) ligating one or more adapters to the nucleic acid molecules extracted from the sample (e.g., one or more amplification primers, flow cell adaptor sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences), (iv) amplifying the nucleic acid molecules (e.g., using a polymerase chain reaction (PCR) amplification technique, a non-PCR amplification technique, or an isothermal amplification technique), (v) capturing nucleic acid molecules from the amplified nucleic acid molecules (e.g., a polymerase chain reaction (PCR) a
  • the report comprises output from the methods described herein. In some instances, all or a portion of the report may be displayed in a graphical user interface of an online or web-based healthcare portal. In some instances, the report is transmitted via a computer network or peer-to-peer connection.
  • the methods may comprise one or more of the steps of: (a) providing a plurality of nucleic acid molecules obtained from a sample from an individual (e.g., an individual suspected of having or determined to have cancer), wherein the plurality of nucleic acid molecules comprises nucleic acid molecules corresponding to an ESRI fusion nucleic acid molecule of the disclosure; (b) ligating one or more adapters onto one or more nucleic acid molecules from the plurality of nucleic acid molecules; (c) amplifying the one or more ligated nucleic acid molecules from the plurality of nucleic acid molecules; (d) capturing amplified nucleic acid molecules from the amplified nucleic acid molecules; (e) sequencing, by a sequencer, the captured nucleic acid molecules to obtain a plurality of sequence reads that represent the captured nucleic acid molecules, wherein one or more of the plurality of sequence reads correspond to the ESRI fusion nucleic acid molecule; (a) providing a plurality of nucleic acid molecules obtained from
  • the methods further comprise receiving, at one or more processors, sequence read data for the plurality of sequence reads.
  • the analyzing the plurality of sequence reads comprises identifying, using the one or more processors, the presence or absence of sequence reads corresponding to the ESRI fusion nucleic acid molecule.
  • the amplified nucleic acid molecules are captured by hybridization with one or more bait molecules.
  • the methods may comprise one or more of the steps of: (a) providing a sample from an individual (e.g., an individual suspected of having or determined to have cancer), wherein the sample comprises a plurality of nucleic acid molecules; (b) preparing a nucleic acid sequencing library from the plurality of nucleic acid molecules in the sample; (c) amplifying said library; (d) selectively enriching for one or more nucleic acid molecules comprising nucleotide sequences corresponding to an ESRI fusion nucleic acid molecule of the disclosure in said library to produce an enriched sample; (e) sequencing the enriched sample, thereby producing a plurality of sequence reads; (f) analyzing the plurality of sequence reads for the presence of the ESRI fusion nucleic acid molecule; (g) detecting, based on the analyzing step, the presence or absence of the ESRI fusion nucleic acid molecule in the sample from the individual.
  • a sample from an individual e.g., an individual suspected of having or determined to
  • the plurality of nucleic acid molecules comprises a mixture of cancer nucleic acid molecules and non-cancer nucleic acid molecules.
  • the cancer nucleic acid molecules are derived from a tumor portion of a heterogeneous tissue biopsy sample, and the non-cancer nucleic acid molecules are derived from a normal portion of the heterogeneous tissue biopsy sample.
  • the sample comprises a liquid biopsy sample
  • the cancer nucleic acid molecules are derived from a circulating tumor DNA (ctDNA) fraction of the liquid biopsy sample
  • the non-cancer nucleic acid molecules are derived from a non-tumor fraction of the liquid biopsy sample or a cell-free DNA (cfDNA) fraction of the liquid biopsy sample.
  • the one or more adapters comprise amplification primers, flow cell adaptor sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences.
  • the one or more adapters comprise one or more sample index sequences.
  • sample indexes allow the sequencing of multiple samples on the same instrument flow cell or chip (i.e., multiplexing).
  • Sample indexes are typically between about 8 and about 10 bases in length, and comprise a nucleotide sequence specific to a sample that is used to assign sequence reads to the correct sample during data analysis.
  • the one or more adapters comprise one or more unique molecule identifiers (UMIs).
  • UMIs comprise short nucleotide sequences that include a unique barcode that is incorporated into each molecule in a given sample library.
  • UMIs are useful for identifying PCR duplicates created during library amplification steps, and/or for reducing the rate of false-positive variant calls and increasing variant detection, since variant alleles present in the original sample (true variants) can be distinguished from errors introduced during library preparation, target enrichment, or sequencing.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the library, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the captured nucleic acid molecules are captured from the amplified nucleic acid molecules by hybridization to one or more bait molecules.
  • the amplifying comprises performing a polymerase chain reaction (PCR) amplification technique, a non-PCR amplification technique, or an isothermal amplification technique.
  • PCR polymerase chain reaction
  • the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique.
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • GNS whole exome sequencing
  • targeted sequencing targeted sequencing
  • direct sequencing direct sequencing
  • Sanger sequencing a Sanger sequencing technique.
  • the sequencing comprises a massively parallel sequencing technique
  • the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • the sequencer comprises a next generation sequencer.
  • the methods further comprise selectively enriching for one or more nucleic acids in the sample comprising nucleotide sequences corresponding to an ESRI fusion nucleic acid molecule of the disclosure.
  • the selectively enriching produces an enriched sample.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the sample, thereby hybridizing the one or more bait molecules to one or more nucleic acids in the sample comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the selectively enriching comprises amplifying the one or more nucleic acids comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule using a polymerase chain reaction (PCR) to produce an enriched sample.
  • the methods further comprise sequencing the enriched sample.
  • the methods further comprise analyzing sequence data (e.g., obtained from sequencing as described above), for the presence or absence of one or more alterations (e.g., a base substitution, a short insertion/deletion (indel), a copy number alteration, or a genomic rearrangement) in one or more genes (e.g., one or more cancer-related genes, or a panel of known/suspected oncogenes and/or tumor suppressors, or any combination thereof).
  • sequence data e.g., obtained from sequencing as described above
  • one or more alterations e.g., a base substitution, a short insertion/deletion (indel), a copy number alteration, or a genomic rearrangement
  • genes e.g., one or more cancer-related genes, or a panel of known/suspected oncogenes and/or tumor suppressors, or any combination thereof.
  • the presence or absence of one or more gene alterations of the disclosure is detected using any suitable method known in the art, e.g., as described in Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • base substitution alterations are detected using Bayesian methodology, which allows detection of novel somatic mutations at low mutant allele frequency (MAF) and increased sensitivity for mutations at hotspot sites through the incorporation of tissue- specific prior expectations. See, e.g., Kim et al., Cancer Discov (2011) 1:44-53 and Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • insertion/deletion (indel) alterations are detected using any suitable method, such as de novo local assembly, e.g., using the de Bruijn approach, see, e.g., Compeau et al., Nat Biotechnol (2011) 29:987-991 and Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • gene fusion and genomic rearrangement alterations are detected using any suitable method, such as by analyzing chimeric read pairs (read pairs for which reads map to separate chromosomes, or at a distance of over 10 Mbp), see, e.g., Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • rearrangements are annotated for predicted function (e.g., creation of fusion gene or tumor suppressor inactivation).
  • the methods further comprise generating a molecular profile for the individual or the sample, based, at least in part, on detecting the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure.
  • the molecular profile for the individual or sample further comprises results from a comprehensive genomic profiling (CGP) test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP genomic profiling
  • the molecular profile further comprises results from a nucleic acid sequencing-based test.
  • a molecular profile may comprise information on the presence of genes (or variant sequences thereof), copy number variations, epigenetic traits, proteins (or modifications thereof), and/or other biomarkers in an individual’s genome and/or proteome, as well as information on the individual’s corresponding phenotypic traits and the interaction between genetic or genomic traits, phenotypic traits, and environmental factors.
  • the methods further comprise selecting a treatment, administering a treatment, or applying a treatment to the individual based on the generated molecular profile, wherein the treatment comprises an anticancer therapy, e.g., as described herein.
  • the methods further comprise generating a report indicating the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure in the sample.
  • the methods further comprise generating, by one or more processors, a report indicating the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure in the sample.
  • the report comprises the generated molecular profile.
  • the methods further comprise providing or transmitting the report, e.g., as described below.
  • the report is transmitted via a computer network or a peer-to-peer connection.
  • all or a portion of the report may be displayed in a graphical user interface of an online or web-based healthcare portal.
  • the methods for determining the presence or absence of an ESRI fusion nucleic acid molecule may be implemented as part of a genomic profiling process that comprises identification of the presence of variant sequences at one or more gene loci (e.g., one or more gene loci as listed above) in a sample derived from an individual as part of detecting, monitoring, predicting a risk factor, or selecting a treatment for a particular disease, e.g., cancer.
  • the variant panel selected for genomic profiling may comprise the detection of variant sequences at a selected set of gene loci (e.g., one or more gene loci as listed above).
  • the variant panel selected for genomic profiling may comprise detection of variant sequences at a number of gene loci (e.g., one or more gene loci as listed above) through comprehensive genomic profiling (CGP), a next-generation sequencing (NGS) approach used to assess hundreds of genes (including relevant cancer biomarkers) in a single assay.
  • CGP comprehensive genomic profiling
  • NGS next-generation sequencing
  • the disclosed methods can improve the validity of, e.g., disease detection calls by, for example, independently confirming the presence of the ESRI fusion nucleic acid molecule in a given patient sample.
  • the disclosed methods may be used with any of a variety of samples, e.g., as described in further detail below.
  • the sample may comprise a tissue biopsy sample, a liquid biopsy sample, or a normal control.
  • the sample may be a liquid biopsy sample and may comprise blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the sample may be a liquid biopsy sample and may comprise circulating tumor cells (CTCs).
  • CTCs circulating tumor cells
  • the sample may be a liquid biopsy sample and may comprise cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), or any combination thereof.
  • the nucleic acid molecules extracted from a sample may comprise a mixture of tumor or cancer nucleic acid molecules and non-tumor or non-cancer nucleic acid molecules.
  • the tumor nucleic acid molecules may be derived from a tumor portion of a heterogeneous tissue biopsy sample, and the non-tumor nucleic acid molecules may be derived from a normal portion of the heterogeneous tissue biopsy sample.
  • the sample may comprise a liquid biopsy sample
  • the tumor or cancer nucleic acid molecules may be derived from a circulating tumor DNA (ctDNA) fraction of the liquid biopsy sample while the non-tumor or non-cancer nucleic acid molecules may be derived from a non-tumor or non-cancer, cell-free DNA (cfDNA) fraction of the liquid biopsy sample.
  • ctDNA circulating tumor DNA
  • cfDNA cell-free DNA
  • the method further comprises determining the circulating tumor DNA (ctDNA) fraction of a liquid biopsy sample.
  • An ESRI fusion polypeptide provided herein, or a fragment thereof may be detected or measured, e.g., in a sample obtained from an individual, using any method known in the art, such as using antibodies (e.g., an antibody described herein), mass spectrometry (e.g., tandem mass spectrometry), a reporter assay (e.g., a fluorescence-based assay), immunoblots such as a Western blot, immunoassays such as enzyme-linked immunosorbent assays (ELISA), immunohistochemistry, other immunological assays (e.g., fluid or gel precipitin reactions, immunodiffusion, immunoelectrophoresis, radioimmunoassay (RIA), immunofluorescent assays), and analytic biochemical methods (e.g., electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography).
  • antibodies e.g.,
  • an ESRI fusion polypeptide provided herein, or a fragment thereof can be distinguished from a reference polypeptide, e.g., a non-mutant or wild type protein or polypeptide, with an antibody or antibody fragment that reacts differentially with a mutant protein or polypeptide (e.g., an ESRI fusion polypeptide provided herein or a fragment thereof) as compared to a reference protein or polypeptide.
  • an ESRI fusion polypeptide of the disclosure, or a fragment thereof can be distinguished from a reference polypeptide, e.g., a non-mutant or wild type protein or polypeptide, by binding to estradiol and/or DNA binding activity.
  • methods of detection of an ESRI fusion polypeptide of the disclosure comprising contacting a sample, e.g., a sample described herein, comprising an ESRI fusion polypeptide described herein, with a detection reagent provided herein (e.g., an antibody of the disclosure), and determining if the ESRI fusion polypeptide is present in the sample.
  • a detection reagent provided herein comprises a nucleic acid molecule, e.g., a DNA, RNA, or mixed DNA/RNA molecule, comprising a nucleotide sequence that is complementary to a nucleotide sequence on a target nucleic acid molecule, e.g., a nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule described herein or a fragment or portion thereof.
  • a detection reagent for detecting an ESRI fusion polypeptide of the disclosure, or a fragment thereof, e.g., an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof, e.g., according to the methods of detection provided herein.
  • a detection reagent provided herein comprises an antibody or antibody fragment that specifically binds to an ESRI fusion polypeptide of the disclosure, or to a fragment thereof.
  • a bait molecule comprises a capture nucleic acid molecule configured to hybridize to a target nucleic acid molecule comprising an ESRI fusion nucleic acid molecule of the disclosure, or a fragment or portion thereof.
  • the capture nucleic acid molecule is configured to hybridize to the ESRI fusion nucleic acid molecule of the target nucleic acid molecule.
  • the capture nucleic acid molecule is configured to hybridize to a fragment of an ESRI fusion nucleic acid molecule of the disclosure.
  • the fragment comprises (or is) between about 5 and about 25 nucleotides, between about 5 and about 300 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the fragment comprises (or is) about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 225 nucleotides, about 250 nucleotides, about 275 nucleotides, or about 300 nucleotides in length.
  • the fragment comprises a breakpoint or fusion junction of an ESRI fusion nucleic acid molecule of the disclosure.
  • the capture nucleic acid molecule comprises (or is) between about 5 and about 25 nucleotides, between about 5 and about 300 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides. In some embodiments, the capture nucleic acid molecule comprises (or is) about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 225 nucleotides, about 250 nucleotides, about 275 nucleotides, or about 300 nucleotides in length.
  • the capture nucleic acid molecule is configured to hybridize to a nucleotide sequence in an intron or an exon of an ESRI gene, or in a breakpoint joining the introns or exons of an ESRI gene (e.g., plus or minus any of between about 10 and about 20, about 20 and about 30, about 30 and about 40, about 40 and about 50, about 50 and about 60, about 60 and about 70, about 70 and about 80, about 80 and about 90, or about 90 and about 100, or more nucleotides) to an intron or exon of another gene, such as a corresponding gene fusion partner as described herein (e.g., any of CCDC170, SMAD4, LOCI 00422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5).
  • a corresponding gene fusion partner as described herein (e.g., any of CCDC170, SMAD4, LOCI 0042
  • the capture nucleic acid molecule is a DNA, RNA, or a DNA/RNA molecule. In some embodiments, the capture nucleic acid molecule comprises any of between about 50 and about 1000 nucleotides, between about 50 and about 500 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the capture nucleic acid molecule comprises any of between about 50 nucleotides and about 100 nucleotides, about 100 nucleotides and about 150 nucleotides, about 150 nucleotides and about 200 nucleotides, about 200 nucleotides and about 250 nucleotides, about 250 nucleotides and about 300 nucleotides, about 300 nucleotides and about 350 nucleotides, about 350 nucleotides and about 400 nucleotides, about 400 nucleotides and about 450 nucleotides, about 450 nucleotides and about 500 nucleotides, about 500 nucleotides and about 550 nucleotides, about 550 nucleotides and about 600 nucleotides, about 600 nucleotides and about 650 nucleotides, about 650 nucleotides and about 700 nucleotides, about 700 nucleotides and about 750 nucleotides, about 750 nucleot
  • the capture nucleic acid molecule comprises between about 10 and about 30 nucleotides, between about 50 and about 1000 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, or between about 100 and about 200 nucleotides. In some embodiments, the capture nucleic acid molecule comprises about 150 nucleotides. In some embodiments, the capture nucleic acid molecule is about 150 nucleotides. In some embodiments, the capture nucleic acid molecule comprises about 170 nucleotides. In some embodiments, the capture nucleic acid molecule is about 170 nucleotides.
  • a bait provided herein comprises a DNA, RNA, or a DNA/RNA molecule.
  • a bait provided herein includes a label, a tag or detection reagent.
  • the label, tag or detection reagent is a radiolabel, a fluorescent label, an enzymatic label, a sequence tag, biotin, or another ligand.
  • a bait provided herein includes a detection reagent such as a fluorescent marker.
  • a bait provided herein includes (e.g., is conjugated to) an affinity tag or reagent, e.g., that allows capture and isolation of a hybrid formed by a bait and a nucleic acid molecule hybridized to the bait.
  • the affinity tag or reagent is an antibody, an antibody fragment, biotin, or any other suitable affinity tag or reagent known in the art.
  • a bait is suitable for solution phase hybridization.
  • Baits can be produced and used according to methods known in the art, e.g., as described in WO2012092426 Al and/or or in Frampton et al (2013) Nat Biotechnol, 31:1023- 1031, incorporated herein by reference.
  • biotinylated baits e.g., RNA baits
  • RNA baits can be produced by obtaining a pool of synthetic long oligonucleotides, originally synthesized on a microarray, and amplifying the oligonucleotides to produce the bait sequences.
  • the baits are produced by adding an RNA polymerase promoter sequence at one end of the bait sequences, and synthesizing RNA sequences using RNA polymerase.
  • libraries of synthetic oligodeoxynucleotides can be obtained from commercial suppliers, such as Agilent Technologies, Inc., and amplified using known nucleic acid amplification methods.
  • a bait provided herein is between about 100 nucleotides and about 300 nucleotides. In some embodiments, a bait provided herein is between about 130 nucleotides and about 230 nucleotides. In some embodiments, a bait provided herein is between about 150 nucleotides and about 200 nucleotides. In some embodiments, a bait provided herein comprises a target- specific bait sequence (e.g., a capture nucleic acid molecule described herein) and universal tails on each end. In some embodiments, the targetspecific sequence, e.g., a capture nucleic acid molecule described herein, is between about 40 nucleotides and about 300 nucleotides.
  • a target-specific bait sequence e.g., a capture nucleic acid molecule described herein
  • the target-specific sequence e.g., a capture nucleic acid molecule described herein
  • the target-specific sequence is between about 100 nucleotides and about 200 nucleotides. In some embodiments, the target- specific sequence, e.g., a capture nucleic acid molecule described herein, is between about 120 nucleotides and about 170 nucleotides. In some embodiments, the target- specific sequence, e.g., a capture nucleic acid molecule described herein, is about 150 nucleotides or about 170 nucleotides.
  • a bait provided herein comprises an oligonucleotide comprising about 200 nucleotides, of which about 150 nucleotides or about 170 nucleotides are target- specific (e.g., a capture nucleic acid molecule described herein), and the other 50 nucleotides or 30 nucleotides (e.g., 25 or 15 nucleotides on each end of the bait) are universal arbitrary tails, e.g., suitable for PCR amplification.
  • target-specific e.g., a capture nucleic acid molecule described herein
  • the other 50 nucleotides or 30 nucleotides e.g., 25 or 15 nucleotides on each end of the bait
  • a bait provided herein hybridizes to a nucleotide sequence corresponding to an intron or an exon of one gene of an ESRI fusion molecule described herein (e.g., an ESRI gene), in an intron or an exon of the other gene of a fusion molecule described herein (e.g., a corresponding gene fusion partner as described herein, e.g., any of CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5 and/or a breakpoint joining the introns and/or exons.
  • the baits described herein can be used for selection of exons and short target sequences.
  • a bait of the disclosure distinguishes a nucleic acid molecule, e.g., a genomic or transcribed nucleic acid molecule, e.g., a cDNA or RNA, having a breakpoint of an ESRI fusion nucleic acid molecule described herein, from a reference nucleotide sequence, e.g., a nucleotide sequence not having the breakpoint.
  • the bait hybridizes to a breakpoint of an ESRI fusion nucleic acid molecule described herein, and to a sequence on either side of the breakpoint (e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any of between 1 and about 5, about 5 and about 10, about 10 and about 15, about 15 and about 20, about 20 and about 25, about 25 and about 30, about 30 and about 35, about 35 and about 40, about 40 and about 45, about 45 and about 50, about 50 and about 55, about 55 and about 60, about 60 and about 65, about 70 and about 75, about 75 and about 80, about 80 and about 85, about 85 and about 90, about 90 and about 95, or about 95 and about 100, or more nucleotides on either side of the breakpoint).
  • a breakpoint of an ESRI fusion nucleic acid molecule described herein e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any
  • a probe provided herein comprises a nucleic acid sequence configured to hybridize to a target nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule of the disclosure, or a fragment or portion thereof.
  • the probe comprises a nucleic acid sequence configured to hybridize to the ESRI fusion nucleic acid molecule of the disclosure, or the fragment or portion thereof, of the target nucleic acid molecule.
  • the probe comprises a nucleic acid sequence configured to hybridize to a fragment or portion of the ESRI fusion nucleic acid molecule of the target nucleic acid molecule.
  • the fragment or portion comprises between about 5 and about 25 nucleotides, between about 5 and about 300 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the probe comprises a nucleotide sequence configured to hybridize to a breakpoint of an ESRI fusion nucleic acid molecule of the disclosure, and may be further configured to hybridize to between about 10 and about 100 nucleotides or more, e.g., any of between about 10 and about 20, about 20 and about 30, about 30 and about 40, about 40 and about 50, about 50 and about 60, about 60 and about 70, about 70 and about 80, about 80 and about 90, or about 90 and about 100, or more nucleotides flanking either side of the breakpoint.
  • the probe comprises a nucleotide sequence configured to hybridize to a nucleotide sequence in an intron or an exon of a gene involved in an ESRI fusion nucleic acid molecule described herein, e.g., an ESRI gene, or in a breakpoint joining the introns or exons of the gene (e.g., plus or minus any of between about 10 and about 20, about 20 and about 30, about 30 and about 40, about 40 and about 50, about 50 and about 60, about 60 and about 70, about 70 and about 80, about 80 and about 90, or about 90 and about 100, or more nucleotides) to an intron or exon of another gene e.g., a corresponding gene fusion partner as described herein, e.g., any of CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2. IYD, IMPG1, STAG2, TNRC6B, or C6orfl5).
  • the probe comprises a nucleic acid molecule which is a DNA, RNA, or a DNA/RNA molecule.
  • the probe comprises a nucleic acid molecule comprising any of between about 10 and about 20 nucleotides, between about 12 and about 20 nucleotides, between about 10 and about 1000 nucleotides, between about 50 and about 500 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the probe comprises a nucleic acid molecule comprising any of 10 nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14 nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, 20 nucleotides, 21 nucleotides, 22 nucleotides, 23 nucleotides, 24 nucleotides, 25 nucleotides, 26 nucleotides, 27 nucleotides, 28 nucleotides, 29 nucleotides, or 30 nucleotides.
  • the probe comprises a nucleic acid molecule comprising any of between about 40 nucleotides and about 50 nucleotides, about 50 nucleotides and about 100 nucleotides, about 100 nucleotides and about 150 nucleotides, about 150 nucleotides and about 200 nucleotides, about 200 nucleotides and about 250 nucleotides, about 250 nucleotides and about 300 nucleotides, about 300 nucleotides and about 350 nucleotides, about 350 nucleotides and about 400 nucleotides, about 400 nucleotides and about 450 nucleotides, about 450 nucleotides and about 500 nucleotides, about 500 nucleotides and about 550 nucleotides, about 550 nucleotides and about 600 nucleotides, about 600 nucleotides and about 650 nucleotides, about 650 nucleotides and about 700 nucleotides, about 700 nucle
  • a probe provided herein comprises a DNA, RNA, or a DNA/RNA molecule.
  • a probe provided herein includes a label or a tag.
  • the label or tag is a radiolabel (e.g., a radioisotope), a fluorescent label (e.g., a fluorescent compound), an enzymatic label, an enzyme co-factor, a sequence tag, biotin, or another ligand.
  • a probe provided herein includes a detection reagent such as a fluorescent marker.
  • a probe provided herein includes (e.g., is conjugated to) an affinity tag, e.g., that allows capture and isolation of a hybrid formed by a probe and a nucleic acid molecule hybridized to the probe.
  • the affinity tag is an antibody, an antibody fragment, biotin, or any other suitable affinity tag or reagent known in the art.
  • a probe is suitable for solution phase hybridization.
  • probes provided herein may be used according to the methods of detection of ESRI fusion nucleic acid molecules provided herein.
  • a probe provided herein may be used for detecting an ESRI fusion nucleic acid molecule of the disclosure in a sample, e.g., a sample obtained from an individual.
  • the probe may be used for identifying cells or tissues that express an ESRI fusion nucleic acid molecule of the disclosure, e.g., by measuring levels of the ESRI fusion nucleic acid molecule.
  • the probe may be used for detecting levels of an ESRI fusion nucleic acid molecule of the disclosure, e.g., mRNA levels, in a sample of cells from an individual.
  • a probe provided herein specifically hybridizes to a nucleic acid molecule comprising a rearrangement (e.g., a deletion, inversion, insertion, duplication, or other rearrangement) resulting in an ESRI fusion nucleic acid molecule of the disclosure.
  • a probe of the disclosure distinguishes a nucleic acid, e.g., a genomic or transcribed nucleic acid, e.g., a cDNA or RNA, having a breakpoint of an ESRI fusion nucleic acid molecule of the disclosure from a reference nucleotide sequence, e.g., a nucleotide sequence not having the breakpoint.
  • isolated pairs of allele-specific probes wherein, for example, the first probe of the pair specifically hybridizes to an ESRI fusion nucleic acid molecule of the disclosure, and the second probe of the pair specifically hybridizes to a corresponding wild type sequence (e.g., a wild type ESRI nucleic acid molecule; and/or a wild type nucleic acid molecule corresponding to a gene fusion partner as described herein, e.g., any of CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfi5).
  • a corresponding wild type sequence e.g., a wild type ESRI nucleic acid molecule; and/or a wild type nucleic acid molecule corresponding to a gene fusion partner as described herein, e.g., any of CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB
  • Probe pairs can be designed and produced for any of the ESRI fusion nucleic acid molecules described herein and are useful in detecting a somatic mutation in a sample.
  • a first probe of a pair specifically hybridizes to a mutation (e.g., the breakpoint of an alteration, rearrangement, inversion, duplication, deletion, insertion or translocation resulting in an ESRI fusion nucleic acid molecule described herein), and a second probe of a pair specifically hybridizes to a sequence upstream or downstream of the mutation.
  • one or more probes provided herein are suitable for use in in situ hybridization methods, e.g., as described above, such as FISH.
  • Chromosomal probes are typically about 50 to about 10 5 nucleotides in length. Longer probes typically comprise smaller fragments of about 100 to about 500 nucleotides. Probes that hybridize with centromeric DNA and locus-specific DNA are available commercially, for example, from Vysis, Inc. (Downers Grove, Ill.), Molecular Probes, Inc. (Eugene, Oreg.) or from Cytocell (Oxfordshire, UK). Alternatively, probes can be made non-commercially from chromosomal or genomic DNA through standard techniques.
  • sources of DNA that can be used include genomic DNA, cloned DNA sequences, somatic cell hybrids that contain one, or a part of one, chromosome (e.g., human chromosome) along with the normal chromosome complement of the host, and chromosomes purified by flow cytometry or microdissection.
  • the region of interest can be isolated through cloning, or by site-specific amplification via the polymerase chain reaction (PCR).
  • Probes of the disclosure may also hybridize to RNA molecules, e.g., mRNA, such as an RNA that is or comprises an ESRI fusion nucleic acid molecule of the disclosure.
  • probes such as probes for use in the FISH methods described herein, are used for determining whether a cytogenetic abnormality is present in one or more cells, e.g., in a region of a chromosome or an RNA bound by one or more probes provided herein.
  • the cytogenetic abnormality may be a cytogenetic abnormality that results in an ESRI fusion nucleic acid molecule of the disclosure.
  • cytogenetic abnormalities include, without limitation, deletions (e.g., deletions of entire chromosomes or deletions of fragments of one or more chromosomes), duplications (e.g., of entire chromosomes, or of regions smaller than an entire chromosome), translocations (e.g., non-reciprocal translocations, balanced translocations, reciprocal translocations), intra-chromosomal inversions, point mutations, deletions, gene copy number changes, germ-line mutations, and gene expression level changes.
  • deletions e.g., deletions of entire chromosomes or deletions of fragments of one or more chromosomes
  • duplications e.g., of entire chromosomes, or of regions smaller than an entire chromosome
  • translocations e.g., non-reciprocal translocations, balanced translocations, reciprocal translocations
  • intra-chromosomal inversions point mutations, deletions, gene copy number changes, germ
  • probes such as probes for use in the FISH methods described herein, are labeled such that a chromosomal region or a region on an RNA to which the probes hybridize can be detected.
  • Probes typically are directly labeled with a fluorophore, allowing the probe to be visualized without a secondary detection molecule.
  • Probes can also be labeled by nick translation, random primer labeling or PCR labeling. Labeling may be accomplished using fluorescent (direct)-or haptene (indirect)-labeled nucleotides.
  • labels include: AMCA-6-dUTP, CascadeBlue-4- dUTP, Fluorescein- 12-dUTP, Rhodamine-6-dUTP, TexasRed-6-dUTP, Cy3-6-dUTP, Cy5- dUTP, Biotin(BIO)-l l-dUTP, Digoxygenin(DIG)-l l-dUTP and Dinitrophenyl (DNP)-l l- dUTP.
  • Probes can also be indirectly labeled with biotin or digoxygenin, or labeled with radioactive isotopes such as 32 P and 3 H, and secondary detection molecules may be used, or further processing may be performed, to visualize the probes.
  • a probe labeled with biotin can be detected by avidin conjugated to a detectable marker, e.g., avidin can be conjugated to an enzymatic marker such as alkaline phosphatase or horseradish peroxidase.
  • Enzymatic markers can be detected in standard colorimetric reactions using a substrate and/or a catalyst for the enzyme.
  • Catalysts for alkaline phosphatase include 5-bromo-4-chloro-3- indolylphosphate and nitro blue tetrazolium.
  • Diaminobenzoate can be used as a catalyst for horseradish peroxidase.
  • Probes can also be prepared such that a fluorescent or other label is added after hybridization of the probe to its target to detect that the probe hybridized to the target.
  • probes can be used that have antigenic molecules incorporated into the nucleotide sequence. After hybridization, these antigenic molecules are detected, for example, using specific antibodies reactive with the antigenic molecules. Such antibodies can, for example, themselves incorporate a fluorochrome, or can be detected using a second antibody with a bound fluorochrome.
  • fluorescent probes e.g., used in FISH techniques, fluorescence can be viewed with a fluorescence microscope equipped with an appropriate filter for each fluorophore, or by using dual or triple band-pass filter sets to observe multiple fluorophores.
  • techniques such as flow cytometry can be used to examine the hybridization pattern of the chromosomal probes.
  • the probe hybridizes to a breakpoint of an ESRI fusion nucleic acid molecule of the disclosure and a sequence on either side of the breakpoint (e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any of between 1 and about 5, about 5 and about 10, about 10 and about 15, about 15 and about 20, about 20 and about 25, about 25 and about 30, about 30 and about 35, about 35 and about 40, about 40 and about 45, about 45 and about 50, about 50 and about 55, about 55 and about 60, about 60 and about 65, about 70 and about 75, about 75 and about 80, about 80 and about 85, about 85 and about 90, about 90 and about 95, or about 95 and about 100, or more nucleotides on either side of the breakpoint).
  • a breakpoint of an ESRI fusion nucleic acid molecule of the disclosure e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any of between
  • an oligonucleotide e.g., useful as primers.
  • an oligonucleotide e.g., a primer, provided herein comprises a nucleotide sequence configured to hybridize to a target nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule of the disclosure, or a fragment or portion thereof.
  • the oligonucleotide comprises a nucleotide sequence configured to hybridize to the ESRI fusion nucleic acid molecule of the target nucleic acid molecule.
  • the oligonucleotide comprises a nucleotide sequence configured to hybridize to a fragment or portion of the ESRI fusion nucleic acid molecule of the target nucleic acid molecule.
  • the oligonucleotide e.g., the primer, comprises a nucleotide sequence configured to hybridize to a breakpoint of an ESRI fusion nucleic acid molecule of the disclosure, and may be further configured to hybridize to between about 10 and about 12, about 12 and about 15, about 15 and about 17, about 17 and about 20, about 20 and about 25, or about 25 and about 30, or more nucleotides flanking either side of the breakpoint.
  • the oligonucleotide e.g., the primer, comprises a nucleotide sequence configured to hybridize to a nucleotide sequence in an intron or an exon of a gene involved in an ESRI fusion nucleic acid mole of the disclosure (e.g., an ESRI gene), to a breakpoint of an ESRI fusion nucleic acid molecule described herein, and/or to an intron or exon of another gene e.g., a corresponding gene fusion partner as described herein, e.g., any of CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5 ⁇ ).
  • a gene involved in an ESRI fusion nucleic acid mole of the disclosure e.g., an ESRI gene
  • a breakpoint of an ESRI fusion nucleic acid molecule described herein e.g.
  • the oligonucleotide comprises a nucleotide sequence corresponding to an ESRI fusion nucleic acid molecule of the disclosure. In some embodiments, the oligonucleotide comprises a nucleotide sequence corresponding to a fragment or a portion of the ESRI fusion nucleic acid molecule. In some embodiments, the fragment or portion comprises between about 10 and about 30 nucleotides, between about 12 and about 20 nucleotides, or between about 12 and about 17 nucleotides. In some embodiments, the oligonucleotide comprises a nucleotide sequence complementary to an ESRI fusion nucleic acid molecule provided herein.
  • the oligonucleotide comprises a nucleotide sequence complementary to a fragment or a portion of the ESRI fusion nucleic acid molecule provided herein.
  • the fragment or portion comprises between about 10 and about 30 nucleotides, between about 12 and about 20 nucleotides, or between about 12 and about 17 nucleotides.
  • an oligonucleotide e.g., a primer
  • an oligonucleotide e.g., a primer
  • a polymerization reaction e.g., PCR
  • an oligonucleotide e.g., a primer, provided herein may be useful for initiating DNA synthesis via PCR (polymerase chain reaction) or a sequencing method.
  • the oligonucleotide may be used to amplify a nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof, e.g., using PCR.
  • the oligonucleotide may be used to sequence a nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule provided herein, or a fragment thereof.
  • the oligonucleotide may be used to amplify a nucleic acid molecule comprising a breakpoint of an ESRI fusion nucleic acid molecule described herein, e.g., using PCR. In some embodiments, the oligonucleotide may be used to sequence a nucleic acid molecule comprising a breakpoint of an ESRI fusion nucleic acid molecule described herein.
  • pairs of oligonucleotides e.g., pairs of primers, are provided herein, which are configured to hybridize to a nucleic acid molecule that is or comprises an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof.
  • a pair of oligonucleotides of the disclosure may be used for directing amplification of the ESRI fusion nucleic acid molecule or fragment thereof, e.g., using a PCR reaction.
  • pairs of oligonucleotides e.g., pairs of primers, are provided herein, which are configured to hybridize to a nucleic acid molecule comprising a breakpoint of an ESRI fusion nucleic acid molecule described herein, e.g., for use in directing amplification of the corresponding ESRI fusion nucleic acid molecule or fragment thereof, e.g., using a PCR reaction.
  • an oligonucleotide e.g., a primer
  • a single stranded nucleic acid molecule e.g., for use in sequencing or amplification methods.
  • an oligonucleotide provided herein is a double stranded nucleic acid molecule.
  • a double stranded oligonucleotide is treated, e.g., denatured, to separate its two strands prior to use, e.g., in sequencing or amplification methods.
  • Oligonucleotides provided herein comprise a nucleotide sequence of sufficient length to hybridize to their target, e.g., an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof, and to prime the synthesis of extension products, e.g., during PCR or sequencing.
  • an oligonucleotide e.g., a primer
  • a primer comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
  • an oligonucleotide provided herein comprises at least about 8 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises at least about 10 deoxyribonucleotides or ribonucleotides.
  • an oligonucleotide provided herein comprises at least about 12 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises at least about 15 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises at least about 20 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises at least about 30 deoxyribonucleotides or ribonucleotides.
  • an oligonucleotide provided herein comprises between about 10 and about 30 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 10 and about 25 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 10 and about 20 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 10 and about 15 deoxyribonucleotides or ribonucleotides.
  • an oligonucleotide provided herein comprises between about 12 and about 20 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 17 and about 20 deoxyribonucleotides or ribonucleotides.
  • the length and nucleotide sequence of an oligonucleotide provided herein is determined according to methods known in the art, e.g., based on factors such as the specific application (e.g., PCR, sequencing library preparation, sequencing), reaction conditions (e.g., buffers, temperature), and the nucleotide composition of the nucleotide sequence of the oligonucleotide or of its target complementary sequence.
  • an oligonucleotide e.g., a primer
  • a nucleic acid e.g., a genomic or transcribed nucleic acid, e.g., a cDNA or RNA
  • a reference nucleotide sequence e.g., a nucleotide sequence not having the breakpoint.
  • a primer or primer set for amplifying a nucleic acid molecule comprising a cytogenetic abnormality such as an alteration, rearrangement, chromosomal inversion, deletion, translocation, duplication, or other rearrangement resulting in an ESRI fusion nucleic acid molecule of the disclosure.
  • a primer or primer set for amplifying a nucleic acid molecule comprising an alteration, rearrangement, chromosomal inversion, insertion, deletion, translocation, duplication or other rearrangement resulting in an ESRI fusion nucleic acid molecule of the disclosure.
  • allele-specific oligonucleotides e.g., primers, wherein a first oligonucleotide of a pair specifically hybridizes to a mutation (e.g., a breakpoint of an ESRI fusion nucleic acid molecule described herein), and a second oligonucleotide of a pair specifically hybridizes to a sequence upstream or downstream of the mutation.
  • a mutation e.g., a breakpoint of an ESRI fusion nucleic acid molecule described herein
  • pairs of oligonucleotides e.g., primers, wherein a first oligonucleotide of a pair specifically hybridizes to a sequence upstream of a mutation (e.g., a breakpoint of an ESRI fusion nucleic acid molecule described herein), and a second oligonucleotide of the pair specifically hybridizes to a sequence downstream of the mutation.
  • a mutation e.g., a breakpoint of an ESRI fusion nucleic acid molecule described herein
  • the oligonucleotide hybridizes to a breakpoint of an ESRI fusion nucleic acid molecule described herein and a sequence on either side of the breakpoint (e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any of between 1 and about 5, about 5 and about 10, about 10 and about 15, about 15 and about 20, about 20 and about 25, about 25 and about 30, about 30 and about 35, about 35 and about 40, about 40 and about 45, about 45 and about 50, about 50 and about 55, about 55 and about 60, about 60 and about 65, about 70 and about 75, about 75 and about 80, about 80 and about 85, about 85 and about 90, about 90 and about 95, or about 95 and about 100, or more nucleotides on either side of the breakpoint).
  • a sequence on either side of the breakpoint e.g., any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides on either side of the breakpoint, or any of between 1 and about
  • antibodies or antibody fragments that specifically bind to an ESRI fusion polypeptide of the disclosure, or a fragment thereof, e.g., an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof.
  • the antibody or antibody fragment may be of any suitable type of antibody or antibody fragment, including, but not limited to, a monoclonal, polyclonal, or multispecific (e.g., a bispecific) antibody or antibody fragment, so long as the antibody or antibody fragment exhibits a specific antigen binding activity, e.g., binding to an ESRI fusion polypeptide of the disclosure, or a fragment thereof.
  • a monoclonal, polyclonal, or multispecific (e.g., a bispecific) antibody or antibody fragment so long as the antibody or antibody fragment exhibits a specific antigen binding activity, e.g., binding to an ESRI fusion polypeptide of the disclosure, or a fragment thereof.
  • an ESRI fusion polypeptide of the disclosure is used as an immunogen to generate one or more antibodies or antibody fragments of the disclosure, e.g., using standard techniques for polyclonal and monoclonal antibody preparation.
  • an ESRI fusion polypeptide provided herein is used to provide antigenic peptide fragments (e.g., comprising any of at least about 8, at least about 10, at least about 15, at least about 20, at least about 30 or more amino acids) for use as immunogens to generate one or more antibodies or antibody fragments of the disclosure, e.g., using standard techniques for polyclonal and monoclonal antibody preparation.
  • an antibody or antibody fragment of the disclosure may be prepared by immunizing a suitable (i.e., immunocompetent) subject such as a rabbit, goat, mouse, or other mammal or vertebrate.
  • a suitable (i.e., immunocompetent) subject such as a rabbit, goat, mouse, or other mammal or vertebrate.
  • An appropriate immunogenic preparation can contain, for example, recombinantly-expressed or chemically-synthesized polypeptides, e.g., an ESRI fusion polypeptide of the disclosure, or a fragment thereof.
  • the preparation can further include an adjuvant, such as Freund’s complete or incomplete adjuvant, or a similar immunostimulatory agent.
  • an antibody or antibody fragment provided herein is a polyclonal antibody. Methods of producing polyclonal antibodies and fragments thereof are known in the art. In some embodiments, an antibody or antibody fragment provided herein is a monoclonal antibody, wherein a population of the antibody or fragment molecules contain only one species of an antigen binding site capable of immunoreacting or binding with a particular epitope, e.g., an epitope on an ESRI fusion polypeptide provided herein.
  • a monoclonal antibody or antibody fragment of the disclosure may also be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the polypeptide of interest, e.g., an ESRI fusion polypeptide provided herein or a fragment thereof.
  • Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAP Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display libraries can be found in, for example, U.S. Patent No.
  • monoclonal antibodies or antibody fragments of the disclosure are recombinant, such as chimeric or humanized monoclonal antibodies or antibody fragments, comprising both human and nonhuman portions.
  • Such chimeric and/or humanized monoclonal antibodies or antibody fragments can be produced by recombinant DNA techniques known in the art, for example, using methods described in PCT Publication No. WO 87/02671; European Patent Application 184,187; European Patent Application 171,496; European Patent Application 173,494; PCT Publication No. WO 86/01533; U.S. Patent No. 4,816,567; European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521- 3526; Sun et al. (1987) Proc.
  • a monoclonal antibody or antibody fragment of the disclosure is a human monoclonal antibody or antibody fragment.
  • human monoclonal antibodies or antibody fragments are prepared using methods known in the art, e.g., using transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can
  • the antibody or antibody fragment of the disclosure is an isolated antibody or antibody fragment, which has been separated from a component of its natural environment or a cell culture used to produce the antibody or antibody fragment.
  • an antibody or antibody fragment of the disclosure is purified to greater than 95% or 99% purity as determined by, for example, electrophoretic (e.g., SDS-PAGE, isoelectric focusing (IEF), capillary electrophoresis) or chromatographic (e.g., ion exchange or reverse phase HPLC) methods.
  • electrophoretic e.g., SDS-PAGE, isoelectric focusing (IEF), capillary electrophoresis
  • chromatographic e.g., ion exchange or reverse phase HPLC
  • an antibody or antibody fragment of the disclosure can be used to isolate an ESRI fusion polypeptide provided herein, or a fragment thereof, by standard techniques, such as affinity chromatography or immunoprecipitation.
  • an antibody or antibody fragment of the disclosure can be used to detect an ESRI fusion polypeptide provided herein, or a fragment thereof, e.g., in a tissue sample, cellular lysate, or cell supernatant, in order to evaluate the level and/or pattern of expression of the ESRI fusion polypeptide. Detection can be facilitated by coupling the antibody or antibody fragment to a detectable substance.
  • an antibody or antibody fragment of the disclosure is coupled to a detectable substance, such as enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include, e.g., horseradish peroxidase, alkaline phosphatase,
  • suitable prosthetic group complexes include, e.g., streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include, e.g., umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes, but is not limited to, luminol;
  • bioluminescent materials include, e.g., luciferase
  • radioactive materials include, e.g., I, I, S or H.
  • An antibody or antibody fragment of the disclosure may also be used diagnostically, e.g., to detect and/or monitor protein levels (e.g., protein levels of an ESRI fusion polypeptide provided herein) in tissues or body fluids (e.g., in a tumor cell-containing tissue or body fluid), e.g., according to the methods provided herein.
  • protein levels e.g., protein levels of an ESRI fusion polypeptide provided herein
  • tissues or body fluids e.g., in a tumor cell-containing tissue or body fluid
  • an antibody or antibody fragment provided herein has a dissociation constant (Kd) of ⁇ IpM, ⁇ 100 nM, ⁇ 10 nM, ⁇ 1 nM, ⁇ 0.1 nM, ⁇ 0.01 nM, or ⁇ 0.001 nM (e.g., 10' 8 M or less, e.g., from 10' 8 M to 10' 13 M, e.g., from 10' 9 M to 10' 13 M) for its target, e.g., an ESRI fusion polypeptide of the disclosure.
  • Kd dissociation constant
  • antibody or antibody fragment affinity e.g., Kd
  • RIA radiolabeled antigen binding assay
  • SPR surface plasmon resonance
  • antibody affinity is determined using the Fab version of an antibody of the disclosure and its antigen (e.g., an ESRI fusion-polypeptide provided herein), e.g., using RIA or SPR.
  • an antibody fragment provided herein is a Fab, Fab’, Fab’- SH, F(ab’)2, Fv, single-chain antibody molecule (e.g., scFv), scFv-Fc fragment, and other fragments described herein or known in the art.
  • an antibody fragment provided herein is a diabody. Diabodies are antibody fragments with two antigenbinding sites that may be bivalent or bispecific.
  • an antibody fragment provided herein is a triabody or a tetrabody.
  • an antibody fragment provided herein is a single-domain antibody fragment. Single-domain antibody fragments comprise all or a portion of the heavy chain variable domain or all or a portion of the light chain variable domain of an antibody.
  • a single-domain antibody fragment is a human single-domain antibody fragment.
  • Antibody fragments can be made by various techniques, including but not limited to proteolytic digestion of an intact antibody, as well as production by recombinant host cells (e.g., E. coli or phage), as known in the art and as described herein.
  • recombinant host cells e.g., E. coli or phage
  • an antibody or antibody fragment provided herein is a chimeric antibody.
  • a chimeric antibody or antibody fragment comprises a non-human variable region (e.g., a variable region derived from a mouse, rat, hamster, rabbit, or non-human primate, such as a monkey), and a human constant region or portions thereof.
  • a chimeric antibody or antibody fragment is a “class switched” antibody or antibody fragment, in which the class or subclass of the antibody or antibody fragment has been changed from that of the parent antibody or antibody fragment.
  • Chimeric antibodies include antigen-binding fragments thereof.
  • a chimeric antibody or antibody fragment is a humanized antibody or antibody fragment.
  • a non-human antibody or antibody fragment is humanized to reduce immunogenicity to humans, while retaining the specificity and affinity of the parental non-human antibody or antibody fragment.
  • a humanized antibody or antibody fragment comprises one or more variable domains in which HVRs, e.g., CDRs, (or portions thereof), are derived from a non-human antibody, and framework regions (FRs) (or portions thereof) are derived from human antibody sequences.
  • HVRs e.g., CDRs, (or portions thereof)
  • FRs framework regions
  • a humanized antibody or antibody fragment optionally will also comprise at least a portion of a human constant region.
  • FR residues in a humanized antibody or antibody fragment are substituted with corresponding residues from a non-human antibody or antibody fragment (e.g., the antibody or antibody fragment from which the HVR residues are derived), e.g., to restore or improve specificity or affinity.
  • Humanized antibodies or antibody fragments, and methods of making them are known in the art.
  • Human framework regions that may be used for humanization include but are not limited to: framework regions selected using the "best- fit" method; framework regions derived from the consensus sequence of human antibodies of a particular subgroup of light or heavy chain variable regions; human mature (somatically mutated) framework regions or human germline framework regions; and framework regions derived from screening FR libraries.
  • an antibody or antibody fragment provided herein is a human antibody.
  • Human antibodies or antibody fragments can be produced using various techniques known in the art. For example, human antibodies or antibody fragments may be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human antibodies or intact antibodies with human variable regions in response to antigenic challenge. Such animals typically contain all or a portion of the human immunoglobulin loci, which replace the endogenous immunoglobulin loci, or are present extrachromosomally or integrated randomly into the animal’s chromosomes. In such transgenic animals, e.g., mice, the endogenous immunoglobulin loci have generally been inactivated.
  • Human variable regions from intact antibodies generated by such animals may be further modified, e.g., by combining with a different human constant region.
  • Human antibodies or antibody fragments can also be made by hybridoma-based methods known in the art, e.g., using known human myeloma and mouse-human heteromyeloma cell lines for the production of human monoclonal antibodies.
  • Human antibodies or antibody fragments may also be generated by isolating Fv clone variable domain sequences selected from human-derived phage display libraries. Such variable domain sequences may then be combined with a desired human constant domain or portions thereof. Techniques for selecting human antibodies or fragments thereof from libraries are known in the art and described herein.
  • Antibodies or antibody fragments of the disclosure may be isolated by screening combinatorial libraries for antibodies or fragments thereof with the desired activity or activities. For example, a variety of methods are known in the art for generating phage display libraries and screening such libraries for antibodies or antibody fragments possessing the desired binding characteristics. In certain phage display methods, repertoires of VH and VL genes are separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be screened for antigen-binding phage. Phage typically display antibody fragments, either as single-chain Fv (scFv) fragments or as Fab fragments.
  • scFv single-chain Fv
  • naive antibody repertoire can be cloned (e.g., from human) to provide a single source of antibodies or fragments thereof to a wide range of non-self and also self antigens without any immunization.
  • Naive libraries can also be made synthetically by cloning un-rearranged V- gene segments from stem cells, and using PCR primers containing random sequences to amplify the highly variable CDR3 regions and to accomplish rearrangement in vitro.
  • Antibodies or antibody fragments isolated from human antibody libraries are considered human antibodies or human antibody fragments herein.
  • an antibody or antibody fragment provided herein is multispecific, e.g., bispecific.
  • Multispecific antibodies or antibody fragments are monoclonal antibodies or antibody fragments that have binding specificities for at least two different sites or at least two different antigens.
  • one of the binding specificities can be to an ESRI fusion polypeptide of the disclosure, and the other can be to any other antigen.
  • Techniques for making multispecific antibodies or antibody fragments are known in the art and include, but are not limited to, recombinant co-expression of two immunoglobulin heavy chain-light chain pairs having different specificities, and “knob-in-hole” engineering.
  • Multispecific antibodies or antibody fragments may also be made by engineering electrostatic steering effects (e.g., by introducing mutations in the constant region) for making heterodimeric Fes; cross-linking two or more antibodies or fragments; using leucine zippers to produce bispecific antibodies or antibody fragments; using “diabody” technology for making bispecific antibody fragments; using single-chain Fv (scFv) dimers; and preparing trispecific antibodies or antibody fragments.
  • Engineered antibodies or antibody fragments with three or more functional antigen binding sites, including “Octopus antibodies,” are also included in the disclosure.
  • Antibodies or antibody fragments of the disclosure also include “Dual Acting FAbs” or “DAF,” e.g., comprising an antigen binding site that binds to an ESRI fusion polypeptide of the disclosure as well as another, different antigen.
  • DAF Double Acting FAbs
  • amino acid sequence variants of the antibodies or antibody fragments provided herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of the antibody or antibody fragment.
  • Amino acid sequence variants of an antibody or antibody fragment of the disclosure may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the antibody or antibody fragment, or by peptide synthesis. Such modifications include, for example, deletions, and/or insertions, and/or substitutions of residues within the amino acid sequences of the antibody or antibody fragment. Any combination of deletions, insertions, and substitutions can be made to arrive at the final antibody or antibody fragment, provided that the final antibody or antibody fragment possesses the desired characteristics, e.g., antigen-binding.
  • antibody or antibody fragment variants having one or more amino acid substitutions are provided.
  • Sites of interest for substitutional mutagenesis include the HVRs and FRs.
  • Amino acid substitutions may be introduced into an antibody or antibody fragment of interest, and the products may be screened for a desired activity, e.g., retained/improved antigen binding, decreased immunogenicity, or improved or reduced antibody-dependent cell-mediated cytotoxicity (ADCC) and/or complement-dependent cytotoxicity (CDC).
  • a desired activity e.g., retained/improved antigen binding, decreased immunogenicity, or improved or reduced antibody-dependent cell-mediated cytotoxicity (ADCC) and/or complement-dependent cytotoxicity (CDC).
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • CDC complement-dependent cytotoxicity
  • an antibody or antibody fragment of the present disclosure is altered to increase or to decrease the extent to which the antibody is glycosylated. Addition or deletion of glycosylation sites to an antibody or antibody fragment may be conveniently accomplished by altering the amino acid sequence of the antibody or antibody fragment, such that one or more glycosylation sites is created or removed.
  • Antibody or antibody fragment variants having bisected oligosaccharides are further provided, e.g., in which a biantennary oligosaccharide attached to the Fc region of the antibody or antibody fragment is bisected by GlcNAc. In some embodiments, antibody or antibody fragment variants of the disclosure may have increased fucosylation.
  • antibody or antibody fragment variants of the disclosure may have reduced fucosylation. In some embodiments, antibody or antibody fragment variants of the disclosure may have improved ADCC function. In some embodiments, antibody or antibody fragment variants of the disclosure may have decreased ADCC function. Antibody or antibody fragment variants with at least one galactose residue in the oligosaccharide attached to the Fc region are also provided. Such variants may have improved CDC function. In some embodiments, antibody or antibody fragment variants of the disclosure may have increased or decreased CDC function.
  • one or more amino acid modifications may be introduced into the Fc region of an antibody or antibody fragment of the present disclosure, thereby generating an Fc region variant.
  • the Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g. a substitution) at one or more amino acid positions.
  • the present disclosure contemplates an antibody or antibody fragment variant that possesses some but not all effector functions, which make it a desirable candidate for applications in which the half-life of the antibody or antibody fragment in vivo is important, yet certain effector functions (such as CDC and ADCC) are unnecessary or deleterious.
  • In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities.
  • Fc receptor (FcR) binding assays can be conducted to ensure that the antibody or antibody fragment lacks Fc-gamma-R binding (hence likely lacking ADCC activity), but retains FcRn binding ability.
  • the primary cells that mediate ADCC e.g., NK cells, express Fc-gamma-RIII only, whereas monocytes express Fc-gamma-RI, Fc-gamma-RII and Fc-gamma-RIII.
  • Antibodies or antibody fragments with reduced effector function include those with substitution of one or more of Fc region residues 238, 265, 269, 270, 297, 327 and 329.
  • Such Fc mutants include Fc mutants with substitutions at two or more of amino acid positions 265, 269, 270, 297 and 327, including the so-called “DANA” Fc mutant with substitutions of residues 265 and 297 to alanine.
  • an antibody or antibody fragment variant with improved or diminished binding to FcRs are also included in the disclosure.
  • an antibody or antibody fragment variant comprises an Fc region with one or more amino acid substitutions that improve ADCC, e.g., substitutions at positions 298, 333, and/or 334 of the Fc region.
  • numbering of Fc region residues is according to EU numbering of residues.
  • alterations are made in the Fc region that result in altered (z.e., either improved or diminished) Clq binding and/or CDC.
  • antibodies or antibody fragments of the disclosure have increased half-lives and improved binding to the neonatal Fc receptor (FcRn), e.g., comprising one or more substitutions that improve binding of the Fc region to FcRn.
  • FcRn neonatal Fc receptor
  • Such Fc variants include those with substitutions at one or more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307, 311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434, e.g., substitution of Fc region residue 434. See, also, Duncan & Winter, Nature 322:738-40 (1988); U.S. Patent No. 5,648,260; U.S. Patent No. 5,624,821; and WO 94/29351 for other examples of Fc region variants.
  • an antibody or antibody fragment provided herein is cysteine-engineered, e.g., “thioMAb,” in which one or more residues of the antibody or antibody fragment are substituted with cysteine residues.
  • the substituted residues occur at accessible sites of the antibody or antibody fragment.
  • reactive thiol groups are thereby positioned at accessible sites of the antibody or antibody fragment, and may be used to conjugate the antibody or antibody fragment to other moieties, such as drug moieties or linker-drug moieties, e.g., to create an immunoconjugate, as described further herein.
  • any one or more of the following residues may be substituted with cysteine: V205 (Kabat numbering) of the light chain; Al 18 (EU numbering) of the heavy chain; and S400 (EU numbering) of the heavy chain Fc region.
  • Cysteine-engineered antibodies or antibody fragments may be generated using any suitable method known in the art.
  • an antibody or antibody fragment provided herein comprises a label or a tag.
  • the label or tag is a radiolabel, a fluorescent label, an enzymatic label, a sequence tag, biotin, or other ligands.
  • labels or tags include, but are not limited to, 6xHis-tag, biotin-tag, Glutathione-S-transferase (GST)-tag, green fluorescent protein (GFP)-tag, c-myc-tag, FLAG-tag, Thioredoxin-tag, Glu-tag, Nus-tag, V5- tag, calmodulin-binding protein (CBP)-tag, Maltose binding protein (MBP)-tag, Chitin-tag, alkaline phosphatase (AP)-tag, HRP-tag, Biotin Caboxyl Carrier Protein (BCCP)-tag, Calmodulin-tag, S-tag, Strep-tag, haemoglutinin (HA)-tag, digoxigenin (DIG)-tag, DsRed, RFP, Luciferase, Short Tetracysteine Tags, Halo-tag, and Nus-tag.
  • the label or tag comprises a detection agent, such as a fluorescent molecule
  • an antibody or antibody fragment provided herein is conjugated to a drug molecule, e.g., an anti-cancer agent described herein, or a cytotoxic agent such as mertansine or monomethyl auristatin E (MMAE)r
  • a drug molecule e.g., an anti-cancer agent described herein, or a cytotoxic agent such as mertansine or monomethyl auristatin E (MMAE)r
  • an antibody or antibody fragment provided herein may be further modified to contain additional nonproteinaceous moieties.
  • Such moieties may be suitable for derivatization of the antibody or antibody fragment, e.g., including but not limited to water soluble polymers.
  • Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1, 3- dioxolane, poly-l,3,6-trioxane, ethylene/maleic anhydride copolymer, polyamino acids (either homopolymers or random copolymers), and dextran or poly (n- vinyl pyrrolidone)poly ethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, polyethylene glycol propionaldehyde, and mixtures thereof.
  • PEG polyethylene glycol
  • copolymers of ethylene glycol/propylene glycol carboxymethylcellulose
  • dextran polyvin
  • the polymers may be of any molecular weight, and may be branched or unbranched.
  • the number of polymers attached to the antibody or antibody fragment may vary, and if more than one polymer is attached, the polymers can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody or antibody fragment to be improved, or whether the antibody or antibody fragment derivative will be used in a therapy under defined conditions.
  • provided herein are antibodies or antibody fragments conjugated to carbon nanotubes, e.g., for use in methods to selectively heat the antibody or antibody fragment using radiation to a temperature at which cells proximal to the antibody or antibody fragment are killed.
  • a variety of materials can be the source of, or serve as, samples for use in any of the methods of the disclosure, such as the methods for detection of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure, or fragments thereof.
  • the sample can be, or be derived from: solid tissue such as from a fresh, frozen and/or preserved organ, tissue sample, biopsy (e.g., tumor, tissue or liquid biopsy), resection, smear, or aspirate; scrapings; bone marrow or bone marrow specimens; a bone marrow aspirate; blood or any blood constituents; blood cells; bodily fluids such as cerebrospinal fluid, amniotic fluid, urine, saliva, sputum, peritoneal fluid or interstitial fluid; pleural fluid; ascites; tissue or fine needle biopsy samples; surgical specimens; cellcontaining body fluids; free-floating nucleic acids; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washings or lavages such as ductal lavages or bronchoalveolar lavages; cells from any time in gestation or development of an individual
  • a sample is or comprises cells obtained from an individual.
  • the sample is or is derived from blood or blood constituents, e.g., obtained from a liquid biopsy.
  • the sample is or is derived from a tumor sample.
  • the sample is or comprises biological tissue or fluid.
  • the sample can contain compounds that are not naturally intermixed with the source of the sample in nature, such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics, and the like.
  • the sample is preserved as a frozen sample or as a formaldehyde- or paraformaldehyde-fixed paraffin-embedded (FFPE) tissue preparation.
  • FFPE formaldehyde- or paraformaldehyde-fixed paraffin-embedded
  • the sample comprises circulating tumor cells (CTCs).
  • CTCs circulating tumor cells
  • the sample comprises one or more cells associated with a tumor, e.g., tumor cells or tumor-infiltrating lymphocytes (TIL).
  • TIL tumor-infiltrating lymphocytes
  • the sample includes one or more premalignant or malignant cells.
  • the sample is acquired from a hematologic malignancy (or pre-malignancy), e.g., a hematologic malignancy (or pre-malignancy) described herein.
  • the sample is acquired from a cancer, such as a cancer described herein.
  • the sample is acquired from a solid tumor, a soft tissue tumor or a metastatic lesion.
  • the sample includes tissue or cells from a surgical margin.
  • the sample is or is acquired from a liquid biopsy of blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the sample includes cell-free DNA (cfDNA) and/or circulating tumor DNA (ctDNA), e.g., from a biopsy of blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the sample includes one or more circulating tumor cells (CTCs) e.g., a CTC acquired from a blood sample).
  • the sample is a cell not associated with a tumor or cancer, e.g., a non-tumor or non-cancer cell or a peripheral blood lymphocyte.
  • a sample is a primary sample obtained directly from a source of interest by any appropriate means.
  • a primary biological sample is obtained by a method chosen from biopsy (e.g., fine needle aspiration or tissue biopsy), surgery, or collection of body fluid (e.g., blood, lymph, or feces).
  • body fluid e.g., blood, lymph, or feces.
  • a sample refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample.
  • Such a processed sample may comprise, for example, nucleic acids (e.g., for use in any of the methods for detection of ESRI fusion nucleic acid molecules provided herein) or proteins (e.g., for use in any of the methods for detection of ESRI fusion polypeptides provided herein) extracted from a sample or obtained by subjecting a primary sample to techniques such as amplification methods, reverse transcription of mRNA, or isolation and/or purification of certain components such as nucleic acids and/or proteins.
  • the sample comprises nucleic acids, e.g., genomic DNA, cDNA, or mRNA.
  • the sample comprises cell-free DNA (cfDNA).
  • the sample comprises cell-free RNA (cfRNA). In some embodiments, the sample comprises circulating tumor DNA (ctDNA). In certain embodiments, the nucleic acids are purified or isolated (e.g., removed from their natural state). In some embodiments, the sample comprises tumor or cancer nucleic acids, such as nucleic acids from a tumor or cancer sample, e.g., genomic DNA, RNA, or cDNA derived from RNA, or from a liquid biopsy, e.g., ctDNA from blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva. In certain embodiments, a tumor or cancer nucleic acid sample, or a ctDNA sample, is purified or isolated (e.g., it is removed from its natural state).
  • a tumor or cancer nucleic acid sample, or a ctDNA sample is purified or isolated (e.g., it is removed from its natural state).
  • the sample comprises tumor or cancer proteins or polypeptides, such as proteins or polypeptides from a tumor or a cancer sample, or from a liquid biopsy, e.g., from blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the proteins or polypeptides are purified or isolated (e.g., removed from their natural state).
  • the sample is obtained from an individual having a cancer, such as a cancer described herein.
  • the sample comprises an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure, or fragments or portions thereof.
  • the methods provided herein comprise obtaining one or more samples from the individual (e.g., the individual having a cancer).
  • the one or more samples are obtained or derived from a cancer (e.g., a cancer in an individual).
  • the one or more samples comprise at least 20% tumor cell nuclear area.
  • the sample is a control sample or a reference sample, e.g., not containing an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide described herein.
  • the reference sample is purified or isolated (e.g., it is removed from its natural state).
  • the reference or control sample comprises a wild type or a non-mutated nucleic acid molecule or polypeptide counterpart to any of the ESRI fusion nucleic acid molecules or ESRI fusion polypeptides described herein.
  • the reference sample is from a non-tumor or cancer sample, e.g., a blood control, a normal adjacent tumor (NAT), or any other non-cancerous sample from the same or a different individual.
  • NAT normal adjacent tumor
  • an ESRI fusion nucleic acid molecule of the disclosure is detected in a sample comprising genomic or subgenomic DNA fragments, or RNA (e.g., mRNA), isolated from a sample, e.g., a tumor or cancer sample, a normal adjacent tissue (NAT) sample, a tissue sample, or a blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva sample obtained from an individual.
  • the sample comprises cDNA derived from an mRNA sample or from a sample comprising mRNA.
  • an ESRI fusion nucleic acid molecule of the disclosure is detected in a sample comprising cell-free DNA (cfDNA), cell-free RNA, and/or circulating tumor DNA (ctDNA). In some embodiments, an ESRI fusion nucleic acid molecule of the disclosure is detected in a sample comprising cell-free DNA (cfDNA) and/or circulating tumor DNA (ctDNA). In some embodiments, an ESRI fusion nucleic acid molecule of the disclosure is detected in a sample comprising circulating tumor DNA (ctDNA).
  • any of the methods of the present disclosure comprise acquiring knowledge of or detecting any of the biomarkers described herein (e.g., an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide, and/or one or more alterations in one or more genes) in one or more samples (e.g., as described above) obtained from an individual (e.g., an individual having a cancer).
  • biomarkers described herein e.g., an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide, and/or one or more alterations in one or more genes
  • the samples used to acquire knowledge of or detect any of the biomarkers described herein are the same sample (i.e., one or more, or all, of an ESRI fusion nucleic acid molecule, an ESRI fusion polypeptide, and one or more alterations in one or more genes are detected or determined in one sample).
  • the samples used to acquire knowledge of or detect any of the biomarkers described herein comprise more than one sample (e.g., some of the biomarkers may be detected or determined in one sample, and some of the biomarkers may be detected or determined in another sample).
  • an ESRI fusion nucleic acid molecule or fusion polypeptide may be detected in one sample, and one or more alterations in one or more genes may be detected or determined in an another sample from the same individual.
  • an ESRI fusion nucleic acid molecule may be detected in one sample, and an ESRI fusion polypeptide may be detected or determined in an another sample from the same individual.
  • the methods provided herein comprise generating a report, and/or providing a report to a party.
  • a report according to the present disclosure comprises information about one or more of: an ESRI fusion nucleic acid molecule or ESRI fusion polypeptide of the disclosure; a cancer of the disclosure, e.g., comprising an ESRI fusion nucleic acid molecule or ESRI fusion polypeptide of the disclosure; or a treatment, a therapy, or one or more treatment options for an individual having a cancer, such as a cancer of the disclosure (e.g., comprising an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide described herein).
  • a report according to the present disclosure comprises information about the presence or absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample obtained from an individual, such as an individual having a cancer, e.g., a cancer provided herein.
  • a report according to the present disclosure indicates that an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure is present in a sample obtained from the individual.
  • a report according to the present disclosure indicates that an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure is not present in a sample obtained from the individual.
  • a report according to the present disclosure indicates that an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure has been detected in a sample obtained from the individual. In one embodiment, a report according to the present disclosure indicates that an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure has not been detected in a sample obtained from the individual. In some embodiments, the report comprises an identifier for the individual from which the sample was obtained.
  • the report includes information on the role of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure, or its wild type counterparts, in disease, such as in cancer.
  • Such information can include one or more of: information on prognosis of a cancer, such as a cancer provided herein, e.g., comprising an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide described herein; information on resistance of a cancer, such as a cancer provided herein, e.g., comprising an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide described herein, to one or more treatments e.g., an endocrine therapy); information on potential or suggested therapeutic options (e.g., such as an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods provided herein); or information on therapeutic options that should be avoided.
  • a cancer provided herein e.g., comprising an ESRI
  • the report includes information on the likely effectiveness, acceptability, and/or advisability of applying a therapeutic option (e.g., such as an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods provided herein) to an individual having a cancer, such as a cancer provided herein, e.g., comprising an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide described herein and identified in the report.
  • the report includes information or a recommendation on the administration of a treatment (e.g., an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods provided herein).
  • the information or recommendation includes the dosage of the treatment and/or a treatment regimen (e.g., in combination with other treatments, such as a second therapeutic agent).
  • the report comprises information or a recommendation for at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more treatments.
  • a report according to the present disclosure is generated by a method comprising one or more of the following steps: obtaining a sample, such as a sample described herein, from an individual, e.g., an individual having a cancer, such as a cancer provided herein; detecting an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in the sample, or acquiring knowledge of the presence of the ESRI fusion nucleic acid molecule or ESRI fusion polypeptide of the disclosure in the sample; and generating a report.
  • a report generated according to the methods provided herein comprises one or more of: information about the presence or absence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in the sample; an identifier for the individual from which the sample was obtained; information on the role of the ESRI fusion nucleic acid molecule or ESRI fusion polypeptide of the disclosure, or its wild type counterparts, in disease (e.g., such as in cancer); information on prognosis, resistance, or potential or suggested therapeutic options (such as an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods provided herein); information on the likely effectiveness, acceptability, or the advisability of applying a therapeutic option (such as an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods provided herein) to the individual; a recommendation or information on the administration of a treatment (such as an anti-cancer therapy provided herein, or a treatment selected or identified according to the methods
  • a report according to the present disclosure may be in an electronic, web-based, or paper form.
  • the report may be provided to an individual or a patient (e.g., an individual or a patient with a cancer, such as a cancer provided herein, e.g., comprising an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure), or to an individual or entity other than the individual or patient (e.g., other than the individual or patient with the cancer), such as one or more of a caregiver, a physician, an oncologist, a hospital, a clinic, a third party payor, an insurance company, or a government entity.
  • the report is provided or delivered to the individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from obtaining a sample from an individual (e.g., an individual having a cancer).
  • the report is provided or delivered to an individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from detecting an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample obtained from an individual (e.g., an individual having cancer).
  • the report is provided or delivered to an individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from acquiring knowledge of the presence of an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide of the disclosure in a sample obtained from an individual (e.g., an individual having cancer).
  • all or a portion of the report may be displayed in a graphical user interface of an online or web-based healthcare portal.
  • methods for detecting ESRI fusion nucleic acid molecules comprise providing a sample from an individual (e.g., an individual having cancer), wherein the sample comprises one or more nucleic acids.
  • an ESRI fusion nucleic acid molecule is detected directly from one or more nucleic acids from the sample.
  • an ESRI fusion nucleic acid molecule is detected from an amplicon, sequence read, or other nucleic acid otherwise derived from one or more nucleic acids from the sample.
  • the methods further comprise preparing a nucleic acid sequencing library from the one or more nucleic acids in the sample.
  • Methods for the preparation of nucleic acid sequencing libraries e.g., suitable for any of the sequencing methods described herein (e.g., NGS and/or hybrid-capture NGS), are known in the art.
  • the sequencing library is prepared as described in Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • nucleic acids e.g., double stranded DNA (dsDNA)
  • dsDNA double stranded DNA
  • nucleic acids are fragmented to a length of about 200 base pairs.
  • the fragmented nucleic acids are purified, e.g., using any suitable method, such as using AMPure XP Beads (Agencourt) and/or solid phase reversible immobilization (SPRI) methods.
  • sequencing library construction using the purified nucleic acids is carried out using any suitable method, e.g., using commercially available library preparation kits, such as an NEBNext kit (e.g., available from New England Biolabs).
  • library preparation is performed using a “with-bead” protocol. See, e.g., Fisher et al., Genome Biol (2011) 12:R1.
  • the library preparation method is selected based on the sequencing method used, e.g., an NEBNext kit is suitable for use with NGS sequencing platforms from Illumina Inc.
  • a sequencing library indexed e.g., with barcodes such as six base pair barcodes, is amplified, e.g., using any suitable method, such as PCR.
  • amplified nucleic acids are purified using any suitable method, such as SPRI purification.
  • the methods further comprise quantifying the amplified and/or purified nucleic acids, e.g., by qPCR.
  • the methods further comprise sizing the amplified and/or purified nucleic acids using any suitable method, such as using a LabChip GX system, e.g., available from Caliper Life Sciences. In some embodiments, size selection is not performed.
  • Next-generation sequencing includes any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules or clonally expanded proxies for individual nucleic acid molecules in a highly parallel fashion (e.g., greater than 10 5 molecules may be sequenced simultaneously).
  • Next generation sequencing methods suitable for use according to the methods provided herein are known in the art and include, without limitation, massively parallel short-read sequencing, template-based sequencing, pyrosequencing, real-time sequencing comprising imaging the continuous incorporation of dye-labeling nucleotides during DNA synthesis, nanopore sequencing, sequencing by hybridization, nano-transistor array based sequencing, polony sequencing, scanning tunneling microscopy (STM)-based sequencing, or nanowire-molecule sensor based sequencing.
  • STM scanning tunneling microscopy
  • Exemplary NGS methods and platforms that may be used to detect ESRI fusion nucleic acid molecules include, without limitation, the HeliScope Gene Sequencing system from Helicos BioSciences (Cambridge, MA., USA), the PacBio RS system from Pacific Biosciences (Menlo Park, CA, USA), massively parallel short-read sequencing such as the Solexa sequencer and other methods and platforms from Illumina Inc.
  • ESRI fusion nucleic acid molecules include, without limitation, the Genome Sequencer (GS) FLX System from Roche (Basel, CHE), the G.007 polonator system, the Solexa Genome Analyzer, HiSeq 2500, HiSeq3000, HiSeq 4000, and NovaSeq 6000 platforms from Illumina Inc. (San Diego, CA, USA).
  • the methods further comprise selectively enriching for one or more nucleic acids (e.g., one or more nucleic acids corresponding to an ESRI gene/coding sequence or a portion thereof) to produce an enriched sample.
  • the selectively enriching is performed on a sequencing library, e.g., a sequencing library prepared according to the methods described herein.
  • the selectively enriching is performed as described in Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • the methods comprise performing solution hybridization using 5’- biotinylated DNA oligonucleotide baits, which may be prepared or synthesized using any suitable method known in the art, e.g., as described in Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • the methods comprise denaturing the sequencing library.
  • denaturing is performed at a temperature of about 95 °C, e.g., for about 5 minutes.
  • the methods further comprise incubating the denatured sequencing library at a temperature of about 68 °C, e.g., for about 5 minutes.
  • the methods further comprise mixing the sequencing library with baits, and optionally Cot, salmon sperm, and/or adaptor- specific blocker DNA in hybridization buffer. In some embodiments, the mixture is incubated for about 24 hours. In some embodiments, the methods further comprise capturing sequencing library-bait duplexes using any suitable method, such as using paramagnetic MyOne streptavidin beads (available from Invitrogen). In some embodiments, the methods further comprise washing to remove off- target library. In some embodiments, the methods further comprise amplifying the captured sequencing library, e.g., using PCR. In some embodiments, the methods further comprise purifying the amplification products using any suitable method, such as SPRI purification.
  • the methods further comprise quantifying the amplified and/or purified nucleic acids, e.g., by qPCR or any other suitable method.
  • the methods further comprise sizing the amplified and/or purified nucleic acids using any suitable method, such as using a LabChip GX system, e.g., available from Caliper Life Sciences.
  • the methods further comprise sequencing using any suitable method or system known in the art, e.g., as described herein.
  • sequencing is performed using a next-generation sequencer, such as an Illumina HiSeq 2000 system.
  • sequencing is performed using paired-end sequencing.
  • the sequencing is performed as described in Frampton et al., (2013) Nat Biotechnol, 31:1023-1031.
  • the methods may comprise one or more of the steps of: (i) obtaining a sample from an individual (e.g., an individual having, suspected of having, or determined to have cancer), (ii) extracting nucleic acid molecules (e.g., a mixture of tumor or cancer nucleic acid molecules and non-tumor or non-cancer nucleic acid molecules) from the sample, (iii) ligating one or more adapters to the nucleic acid molecules extracted from the sample (e.g., one or more amplification primers, flow cell adapter sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences), (iv) amplifying the nucleic acid molecules (e.g., using a polymerase chain reaction (PCR) amplification technique, a non-PCR amplification technique, or an isothermal amplification technique), (v) capturing nucleic acid molecules from the amplified nucleic
  • the report comprises output from the methods described herein. In some instances, all or a portion of the report may be displayed in a graphical user interface of an online or web-based healthcare portal. In some instances, the report is transmitted via a computer network or peer-to-peer connection.
  • the one or more adapters comprise amplification primers, flow cell adaptor sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences.
  • the one or more adapters comprise one or more sample index sequences.
  • sample indexes allow the sequencing of multiple samples on the same instrument flow cell or chip (i.e., multiplexing). Sample indexes are typically between about 8 and about 10 bases in length, and comprise a nucleotide sequence specific to a sample that is used to assign sequence reads to the correct sample during data analysis.
  • the one or more adapters comprise one or more unique molecule identifiers (UMIs).
  • UMIs comprise short nucleotide sequences that include a unique barcode that is incorporated into each molecule in a given sample library. UMIs are useful for identifying PCR duplicates created during library amplification steps, and/or for reducing the rate of false-positive variant calls and increasing variant detection, since variant alleles present in the original sample (true variants) can be distinguished from errors introduced during library preparation, target enrichment, or sequencing.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the library, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the captured nucleic acid molecules are captured from the amplified nucleic acid molecules by hybridization to one or more bait molecules.
  • the amplifying comprises performing a polymerase chain reaction (PCR) amplification technique, a non-PCR amplification technique, or an isothermal amplification technique.
  • PCR polymerase chain reaction
  • the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique.
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • GNS whole exome sequencing
  • targeted sequencing targeted sequencing
  • direct sequencing direct sequencing
  • Sanger sequencing a Sanger sequencing technique.
  • the sequencing comprises a massively parallel sequencing technique
  • the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • the sequencer comprises a next generation sequencer.
  • the methods further comprise selectively enriching for one or more nucleic acids in the sample comprising nucleotide sequences corresponding to ESRI.
  • the selectively enriching produces an enriched sample.
  • the selectively enriching comprises: (a) combining one or more bait molecules with the sample, thereby hybridizing the one or more bait molecules to one or more nucleic acids in the sample comprising nucleotide sequences corresponding to ESRI and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the selectively enriching comprises amplifying the one or more nucleic acids comprising nucleotide sequences corresponding to ESRI using a polymerase chain reaction (PCR) to produce an enriched sample.
  • the methods further comprise sequencing the enriched sample.
  • non-transitory computer-readable storage media comprise one or more programs for execution by one or more processors of a device, the one or more programs including instructions which, when executed by the one or more processors, cause the device to perform a method according to any of the embodiments described herein.
  • FIG. 6 illustrates an example of a computing device or system in accordance with one embodiment.
  • Device 600 can be a host computer connected to a network.
  • Device 600 can be a client computer or a server.
  • device 600 can be any suitable type of microprocessor-based device, such as a personal computer, workstation, server or handheld computing device (portable electronic device) such as a phone or tablet.
  • the device can include, for example, one or more processor(s) 610, input devices 620, output devices 630, memory or storage devices 640, communication devices 660, and nucleic acid sequencers 670.
  • Software 650 residing in memory or storage device 640 may comprise, e.g., an operating system as well as software for executing the methods described herein, e.g., for detecting an ESRI fusion nucleic acid molecule of the present disclosure.
  • Input device 620 and output device 630 can generally correspond to those described herein, and can either be connectable or integrated with the computer.
  • Input device 620 can be any suitable device that provides input, such as a touch screen, keyboard or keypad, mouse, or voice-recognition device.
  • Output device 630 can be any suitable device that provides output, such as a touch screen, haptics device, or speaker.
  • Storage 640 can be any suitable device that provides storage (e.g., an electrical, magnetic or optical memory including a RAM (volatile and non-volatile), cache, hard drive, or removable storage disk).
  • Communication device 660 can include any suitable device capable of transmitting and receiving signals over a network, such as a network interface chip or device.
  • Software module 650 which can be stored as executable instructions in storage 640 and executed by processor(s) 610, can include, for example, an operating system and/or the processes that embody the functionality of the methods of the present disclosure, e.g., for detecting an ESRI fusion nucleic acid molecule of the present disclosure (e.g., as embodied in the devices as described herein).
  • Software module 650 can also be stored and/or transported within any non-transitory computer-readable storage medium for use by or in connection with an instruction execution system, apparatus, or device, such as those described herein, that can fetch instructions associated with the software from the instruction execution system, apparatus, or device and execute the instructions.
  • a computer-readable storage medium can be any medium, such as storage 640, that can contain or store processes for use by or in connection with an instruction execution system, apparatus, or device. Examples of computer-readable storage media may include memory units like hard drives, flash drives and distribute modules that operate as a single functional unit.
  • various processes described herein may be embodied as modules configured to operate in accordance with the embodiments and techniques described above. Further, while processes may be shown and/or described separately, those skilled in the art will appreciate that the above processes may be routines or modules within other processes.
  • Software module 650 can also be propagated within any transport medium for use by or in connection with an instruction execution system, apparatus, or device, such as those described above, that can fetch instructions associated with the software from the instruction execution system, apparatus, or device and execute the instructions.
  • a transport medium can be any medium that can communicate, propagate or transport programming for use by or in connection with an instruction execution system, apparatus, or device.
  • the transport readable medium can include, but is not limited to, an electronic, magnetic, optical, electromagnetic or infrared wired or wireless propagation medium.
  • Device 600 may be connected to a network (e.g., network 704, as shown in FIG. 7 and described below), which can be any suitable type of interconnected communication system.
  • the network can implement any suitable communications protocol and can be secured by any suitable security protocol.
  • the network can comprise network links of any suitable arrangement that can implement the transmission and reception of network signals, such as wireless network connections, T1 or T3 lines, cable networks, DSL, or telephone lines.
  • Device 600 can be implemented using any operating system, e.g., an operating system suitable for operating on the network.
  • Software module 650 can be written in any suitable programming language, such as C, C++, Java or Python.
  • application software embodying the functionality of the present disclosure can be deployed in different configurations, such as in a client/server arrangement or through a Web browser as a Webbased application or Web service, for example.
  • the operating system is executed by one or more processors, e.g., processor(s) 610.
  • Device 600 can further include a sequencer 670, which can be any suitable nucleic acid sequencing instrument.
  • sequencers can include, without limitation, Roche/454’s Genome Sequencer (GS) FLX System, Illumina/Solexa’s Genome Analyzer (GA), Illumina’s HiSeq 2500, HiSeq 3000, HiSeq 4000 and NovaSeq 6000 Sequencing Systems, Life/APG’s Support Oligonucleotide Ligation Detection (SOLiD) system, Polonator’s G.007 system, Helicos BioSciences’ HeliScope Gene Sequencing system, or Pacific Biosciences’ PacBio RS system.
  • FIG. 7 illustrates an example of a computing system in accordance with one embodiment.
  • device 600 e.g., as described above and illustrated in FIG. 6
  • network 704 which is also connected to device 706.
  • device 706 is a sequencer.
  • Exemplary sequencers can include, without limitation, Roche/454’s Genome Sequencer (GS) FLX System, Illumina/Solexa’s Genome Analyzer (GA), Illumina’s HiSeq 2500, HiSeq 3000, HiSeq 4000 and NovaSeq 6000 Sequencing Systems, Life/APG’s Support Oligonucleotide Ligation Detection (SOLiD) system, Polonator’s G.007 system, Helicos BioSciences’ HeliScope Gene Sequencing system, or Pacific Biosciences’ PacBio RS system.
  • Devices 600 and 706 may communicate, e.g., using suitable communication interfaces via network 704, such as a Local Area Network (LAN), Virtual Private Network (VPN), or the Internet.
  • network 704 can be, for example, the Internet, an intranet, a virtual private network, a cloud network, a wired network, or a wireless network.
  • Devices 600 and 706 may communicate, in part or in whole, via wireless or hardwired communications, such as Ethernet, IEEE 802.1 lb wireless, or the like. Additionally, devices 600 and 706 may communicate, e.g., using suitable communication interfaces, via a second network, such as a mobile/cellular network.
  • Communication between devices 600 and 706 may further include or communicate with various servers such as a mail server, mobile server, media server, telephone server, and the like.
  • devices 600 and 706 can communicate directly (instead of, or in addition to, communicating via network 704), e.g., via wireless or hardwired communications, such as Ethernet, IEEE 802.11b wireless, or the like.
  • devices 600 and 706 communicate via communications 708, which can be a direct connection or can occur via a network (e.g., network 704).
  • One or all of devices 600 and 706 generally include logic (e.g., http web server logic) or are programmed to format data, accessed from local or remote databases or other sources of data and content, for providing and/or receiving information via network 704 according to various examples described herein.
  • logic e.g., http web server logic
  • devices 600 and 706 are programmed to format data, accessed from local or remote databases or other sources of data and content, for providing and/or receiving information via network 704 according to various examples described herein.
  • FIG. 8 illustrates an exemplary process 800 for detecting an ESRI fusion nucleic acid molecule of the present disclosure (e.g., in a sample from an individual having breast cancer), in accordance with some embodiments of the present disclosure.
  • Process 800 is performed, for example, using one or more electronic devices implementing a software program.
  • process 800 is performed using a client-server system, and the blocks of process 800 are divided up in any manner between the server and a client device.
  • the blocks of process 800 are divided up between the server and multiple client devices.
  • portions of process 800 are described herein as being performed by particular devices of a client-server system, it will be appreciated that process 800 is not so limited.
  • the executed steps can be executed across many systems, e.g., in a cloud environment.
  • process 800 is performed using only a client device or only multiple client devices.
  • some blocks are, optionally, combined, the order of some blocks is, optionally, changed, and some blocks are, optionally, omitted.
  • additional steps may be performed in combination with the process 800. Accordingly, the operations as illustrated (and described in greater detail below) are exemplary by nature and, as such, should not be viewed as limiting.
  • a plurality of sequence reads of one or more nucleic acid molecules is obtained, wherein the one or more nucleic acid molecules are derived from a sample obtained from an individual, e.g., as described herein.
  • the sample is obtained from an individual having breast cancer.
  • the sequence reads are obtained using a sequencer, e.g., as described herein or otherwise known in the art.
  • the nucleic acid molecules comprise one or more nucleic acid molecules corresponding to: an ESRI fusion nucleic acid molecule of the disclosure; or a gene involved in an ESRI fusion nucleic acid molecule of the disclosure; or fragments thereof.
  • the sample is purified, enriched (e.g., for nucleic acid(s) corresponding to: an ESRI fusion nucleic acid molecule of the disclosure; or a gene involved in an ESRI fusion nucleic acid molecule of the disclosure; or fragments thereof), and/or subjected to PCR amplification.
  • an exemplary system e.g., one or more electronic devices
  • the system detects (e.g., based on the analysis) an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof, in the sample.
  • the ESRI fusion nucleic acid molecule is any of the ESRI fusion nucleic acid molecules described herein.
  • the plurality of sequence reads is obtained by sequencing nucleic acids obtained from any of the samples described herein, e.g., tissue and/or liquid biopsies, etc.
  • the sample is obtained from the cancer.
  • the sample comprises a tissue biopsy sample, a liquid biopsy sample, or a normal control.
  • the sample is from a tumor biopsy, tumor specimen, or circulating tumor cell.
  • the sample is a liquid biopsy sample and comprises blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • the sample comprises cells and/or nucleic acids from the cancer.
  • the sample comprises mRNA, DNA, circulating tumor DNA (ctDNA), cell-free DNA, or cell-free RNA from the cancer.
  • the sample is a liquid biopsy sample and comprises circulating tumor cells (CTCs).
  • the sample is a liquid biopsy sample and comprises cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), or any combination thereof.
  • the plurality of sequence reads is obtained by sequencing.
  • the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique.
  • the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • the disclosed methods for determining the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure may be implemented as part of a genomic profiling process that comprises identification of the presence of variant sequences at one or more gene loci in a sample derived from an individual as part of detecting, monitoring, predicting a risk factor, or selecting a treatment for a particular disease, e.g., cancer.
  • the variant panel selected for genomic profiling may comprise the detection of variant sequences at a selected set of gene loci.
  • the variant panel selected for genomic profiling may comprise detection of variant sequences at a number of gene loci through comprehensive genomic profiling (CGP), a next-generation sequencing (NGS) approach used to assess hundreds of genes (including relevant cancer biomarkers) in a single assay.
  • CGP comprehensive genomic profiling
  • NGS next-generation sequencing
  • Inclusion of the disclosed methods for determining the presence or absence of an ESRI fusion nucleic acid molecule of the disclosure as part of a genomic profiling process can improve the validity of, e.g., disease detection calls, made on the basis of the genomic profiling by, for example, independently confirming the presence of the ESRI fusion nucleic acid molecule of the disclosure in a given patient sample.
  • the one or more gene loci comprise the ABL1, ACVR1B, AKT1, AKT2, AKT3, ALK, AL0X12B, AMER1, APC, AR, ARAF, ARFRP1, ARID1A, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, BAP1, BARD1, BCL2, BCL2L1, BCL2L2, BCL6, BCOR, BCORL1, BCR, BRAF, BRCA1, BRCA2, BRD4, BRIP1, BTG1, BTG2, BTK, CALR, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD22, CD274, CD70, CD74, CD79A, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHEK
  • the one or more gene loci comprise the ABL, ALK, ALL, B4GALNT1, BAFF, BCL2, BRAF, BRCA, BTK, CD19, CD20, CD3, CD30, CD319, CD38, CD52, CDK4, CDK6, CML, CRACC, CS1, CTLA-4, dMMR, EGFR, ERBB1, ERBB2, FGFR1-3, FLT3, GD2, HD AC, HER1, HER2, HR, IDH2, IL-ip, IL-6, IL-6R, JAK1, JAK2, JAK3, KIT, KRAS, MEK, MET, MSLH, mTOR, PARP, PD-1, PDGFR, PDGFRa, PDGFRp, PD-L1, PI3K5, PIGF, PTCH, RAF, RANKL, RET, ROS1, SLAMF7, VEGF, VEGFA, or VEGFB gene locus, or any combination thereof.
  • the comprehensive genomic profiling may comprise information on the presence of genes (or variant sequences thereof), copy number variations, epigenetic traits, proteins (or modifications thereof), and/or other biomarkers in an individual’s genome and/or proteome, as well as information on the individual’s corresponding phenotypic traits and the interaction between genetic or genomic traits, phenotypic traits, and environmental factors.
  • the comprehensive genomic profiling may comprise results from a comprehensive genomic profiling (CGP) test, a nucleic acid sequencing-based test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP comprehensive genomic profiling
  • a molecular profile for a sample or for an individual is generated based at least in part on detecting an ESRI fusion nucleic acid molecule of the disclosure, or a fragment thereof, in a sample.
  • the molecular profile may comprise information on the presence of genes (or variant sequences thereof), copy number variations, epigenetic traits, proteins (or modifications thereof), and/or other biomarkers in an individual’ s genome and/or proteome, as well as information on the individual’s corresponding phenotypic traits and the interaction between genetic or genomic traits, phenotypic traits, and environmental factors.
  • the molecular profile may comprise results from a comprehensive genomic profiling (CGP) test (e.g., as describe above), a nucleic acid sequencing-based test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP genomic profiling
  • the molecular profile further comprises/indicates/comprises information on presence or absence of mutations in one or more additional genes, e.g., a panel of known/suspected oncogenes and/or tumor suppressors.
  • the molecular profile is obtained from a genomic profiling assay (such as a cancer- or tumor-related genomic profiling assay), e.g., as obtained using any of the sequencing methodologies described herein.
  • the molecular profile includes information from whole-genome or whole-exome sequencing.
  • the molecular profile includes information from targeted sequencing.
  • the molecular profile includes information from NGS.
  • the molecular profile comprises/indicates/comprises information on presence or absence of mutations such as short variant alterations (e.g., a base substitution, insertion, or deletion), copy-number alterations (e.g., an amplification or a homozygous deletion), and/or rearrangements (e.g., a gene fusion or other genomic or chromosomal rearrangement) of one or more genes, e.g., a panel of known/suspected oncogenes and/or tumor suppressors, one or more cancer-related genes, or any combination thereof.
  • the individual is administered a treatment based at least in part on the molecular profile.
  • the treatment is an anti-cancer therapy known in the art or described herein.
  • the one or more genes comprise the ABL1, ACVR1B, AKT1, AKT2, AKT3, ALK, ALOX12B, AMER1, APC, AR, ARAF, ARFRP1, ARID1A, ASXL1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXL, BAP1, BARD1, BCL2, BCL2L1, BCL2L2, BCL6, BCOR, BCORL1, BCR, BRAF, BRCA1, BRCA2, BRD4, BRIP1, BTG1, BTG2, BTK, CALR, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD22, CD274, CD70, CD74, CD79A, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2
  • the one or more genes comprise the ABL, ALK, ALL, B4GALNT1, BAFF, BCL2, BRAF, BRCA, BTK, CD19, CD20, CD3, CD30, CD319, CD38, CD52, CDK4, CDK6, CML, CRACC, CS1, CTLA-4, dMMR, EGFR, ERBB1, ERBB2, FGFR1-3, FLT3, GD2, HDAC, HER1, HER2, HR, IDH2, IL-ip, IL-6, IL-6R, JAK1, JAK2, JAK3, KIT, KRAS, MEK, MET, MSI-H, mTOR, PARP, PD-1, PDGFR, PDGFRa, PDGFRP, PD-L1, PI3K5, PIGF, PTCH, RAF, RANKL, RET, ROS1, SLAMF7, VEGF, VEGFA, or VEGFB gene, or any combination thereof.
  • a report is generated, e.g., as described in further detail above.
  • the report comprises/indicates/comprises information on the presence or absence of an ESRI fusion nucleic acid molecule or polypeptide of the disclosure in the cancer in an individual (e.g., in one or more samples from the individual).
  • the report comprises/indicates/comprises information on results of a genomic profiling process of a cancer in an individual (e.g., in one or more samples from the individual), e.g., as described above.
  • the report comprises/indicates/comprises information on results of comprehensive genomic profiling of a cancer in an individual (e.g., in one or more samples from the individual), e.g., as described above.
  • the report comprises/indicates/comprises information on a molecular profile generated for the individual or the sample, e.g., as described above.
  • the report comprises/indicates/comprises information on a treatment or one or more treatment options selected or identified for the individual, based, at least in part, on the presence of an ESRI fusion nucleic acid molecule or polypeptide of the disclosure in the cancer in an individual (e.g., in one or more samples from the individual), and optionally based on results of a genomic profiling process, comprehensive genomic profiling, and/or a molecular profile generated for the individual or a sample, e.g., as described above.
  • the report is provided or transmitted to the individual, a caregiver, a healthcare provider, a physician, an oncologist, an electronic medical record system, a hospital, a clinic, a third- party payer, an insurance company, or a government office, e.g., as described in further detail above.
  • the report is transmitted via a computer network or a peer-to- peer connection.
  • an individual is administered a treatment based, at least in part, on the report.
  • all or a portion of the report may be displayed in a graphical user interface of an online or web-based healthcare portal.
  • the cancer is breast cancer (e.g., HR+ breast cancer) or endometrial cancer.
  • kits or articles of manufacture comprising one or more reagents for detecting an ESRI fusion nucleic acid molecule of the disclosure in a sample; or an ESRI fusion polypeptide encoded by an ESRI fusion nucleic acid molecule of the disclosure.
  • the kits or articles of manufacture comprise one or more probes of the disclosure for detecting an ESRI fusion nucleic acid molecule of the disclosure in a sample, e.g., according to any detection method known in the art or described herein.
  • kits or articles of manufacture comprise one or more baits (e.g., one or more bait molecules) of the disclosure for detecting an ESRI fusion nucleic acid molecule of the disclosure in a sample, e.g., according to any detection method known in the art or described herein.
  • the kits or articles of manufacture comprise one or more oligonucleotides (e.g., one or more primers) of the disclosure for detecting an ESRI fusion nucleic acid molecule of the disclosure in a sample, e.g., according to any detection method known in the art or described herein.
  • the kit or article of manufacture comprises a reagent (e.g., one or more oligonucleotides, primers, probes or baits of the present disclosure) for detecting a wild-type counterpart of an ESRI fusion nucleic acid molecule of the disclosure (e.g., a wild type ESRI gene, and/or a wild type fusion partner gene as described herein).
  • a reagent e.g., one or more oligonucleotides, primers, probes or baits of the present disclosure
  • a wild-type counterpart of an ESRI fusion nucleic acid molecule of the disclosure e.g., a wild type ESRI gene, and/or a wild type fusion partner gene as described herein.
  • one or more oligonucleotides, primers, probes or baits are capable of hybridizing to an ESRI fusion nucleic acid molecule of the disclosure, or to a wild-type counterpart of the ESRI fusion nucleic acid molecule (e.g., a wild type ESRI gene, and/or a wild type fusion partner gene as described herein).
  • the one or more oligonucleotides, primers, probes or baits of the present disclosure are capable of distinguishing an ESRI fusion nucleic acid molecule of the disclosure, from a wild-type counterpart of the ESRI fusion nucleic acid molecule (e.g., a wild type ESRI gene, and/or a wild type fusion partner gene as described herein).
  • a wild-type counterpart of the ESRI fusion nucleic acid molecule e.g., a wild type ESRI gene, and/or a wild type fusion partner gene as described herein.
  • the kit is for use according to any method of detecting fusion nucleic acid molecules known in the art or described herein, such as sequencing, PCR, in situ hybridization methods, a nucleic acid hybridization assay, an amplification-based assay, a PCR-RFLP assay, real-time PCR, sequencing, next-generation sequencing, a screening analysis, FISH, spectral karyotyping, MFISH, comparative genomic hybridization, in situ hybridization, sequence-specific priming (SSP) PCR, HPLC, and mass-spectrometric genotyping.
  • any method of detecting fusion nucleic acid molecules known in the art or described herein, such as sequencing, PCR, in situ hybridization methods, a nucleic acid hybridization assay, an amplification-based assay, a PCR-RFLP assay, real-time PCR, sequencing, next-generation sequencing, a screening analysis, FISH, spectral karyotyping, MFISH, comparative genomic hybridization, in situ hybridization, sequence
  • kits provided herein further comprises instructions for detecting an ESRI fusion nucleic acid molecule of the disclosure, e.g., using one or more oligonucleotides, primers, probes or baits of the present disclosure.
  • kits or articles of manufacture comprise one or more antibodies or antibody fragments of the disclosure for detecting an ESRI fusion polypeptide of the disclosure in a sample, e.g., according to any detection method known in the art or described herein.
  • the kit or article of manufacture comprises a reagent (e.g., one or more antibodies or antibody fragments of the present disclosure) for detecting the wild-type counterparts of an ESRI fusion polypeptide provided herein (e.g., a wild type ESRI polypeptide, and/or a wild type polypeptide encoded by a fusion partner gene as described herein).
  • kits or articles of manufacture comprise one or more antibodies or antibody fragments of the present disclosure capable of binding to an ESRI fusion polypeptide provided herein, or to wild-type counterparts of the ESRI fusion polypeptide provided herein (e.g., a wild type ESRI polypeptide, and/or a wild type polypeptide encoded by a fusion partner gene as described herein).
  • the kit is for use according to any protein or polypeptide detection assay known in the art or described herein, such as mass spectrometry (e.g., tandem mass spectrometry), a reporter assay (e.g., a fluorescence-based assay), immunoblots such as a Western blot, immunoassays such as enzyme-linked immunosorbent assays (ELISA), immunohistochemistry, other immunological assays (e.g., fluid or gel precipitin reactions, immunodiffusion, immunoelectrophoresis, radioimmunoassay (RIA), immunofluorescent assays), and analytic biochemical methods (e.g., electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography).
  • the kit further comprises instructions for detecting an ESRI fusion polypeptide of the disclosure, e.g., using one or more antibodies or antibody fragments
  • kits or articles of manufacture comprising an anti-cancer therapy, such as an anti-cancer therapy described herein, e.g., an anti-cancer agent other than a SERM or an aromatase inhibitor, and a package insert comprising instructions for using the anti-cancer therapy in a method of treating or delaying progression of cancer, e.g., by administration to an individual from whom a sample comprising an ESRI fusion nucleic acid molecule or polypeptide of the disclosure has been obtained.
  • the anti- cancer therapy is any of the anti-cancer therapies described herein for use in any of the methods for treating or delaying progression of cancer of the disclosure.
  • kits or articles of manufacture comprising an anti-cancer therapy, such as an anti-cancer therapy described herein, e.g., an endocrine therapy, and a package insert comprising instructions for using the anti-cancer therapy in a method of treating or delaying progression of cancer, e.g., by administration to an individual from whom a sample in which the absence of an ESRI fusion nucleic acid molecule or polypeptide of the disclosure has been detected.
  • an anti-cancer therapy such as an anti-cancer therapy described herein, e.g., an endocrine therapy
  • a package insert comprising instructions for using the anti-cancer therapy in a method of treating or delaying progression of cancer, e.g., by administration to an individual from whom a sample in which the absence of an ESRI fusion nucleic acid molecule or polypeptide of the disclosure has been detected.
  • the kit or article of manufacture may include, for example, a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, and the like.
  • the container may be formed from a variety of materials such as glass or plastic.
  • the container holds or contains a composition comprising one or more reagents for detecting an ESRI fusion nucleic acid molecule or polypeptide of the disclosure (e.g., one or more oligonucleotides, primers, probes, baits, antibodies or antibody fragments of the present disclosure) or one or more anti-cancer therapies of the disclosure.
  • the container holds or contains a composition comprising one or more anti-cancer therapies of the disclosure and may have a sterile access port (e.g., the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • a sterile access port e.g., the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the kit or article of manufacture may further include a second container comprising a diluent or buffer, e.g., a pharmaceutically-acceptable diluent buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution, and/or dextrose solution.
  • a diluent or buffer e.g., a pharmaceutically-acceptable diluent buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution, and/or dextrose solution.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution, and/or dextrose solution.
  • BWFI bacteriostatic water for injection
  • phosphate-buffered saline such as bacterio
  • the kit or article of manufacture of the present disclosure also includes information or instructions, for example in the form of a package insert, indicating that the one or more reagents and/or anti-cancer therapies are used for detecting an ESRI fusion nucleic acid molecule or polypeptide of the disclosure, or for treating cancer, as described herein.
  • the insert or label may take any form, such as paper or on electronic media such as a magnetically recorded medium (e.g., floppy disk), a CD-ROM, a Universal Serial Bus (USB) flash drive, and the like.
  • the label or insert may also include other information concerning the pharmaceutical compositions and dosage forms in the kit or article of manufacture.
  • vectors comprising or encoding an ESRI fusion nucleic acid molecule of the disclosure, or a bait, a probe, or an oligonucleotide described herein, or fragments thereof.
  • a vector provided herein comprises or encodes an ESRI fusion nucleic acid molecule of the disclosure, or a nucleic acid molecule encoding an ESRI fusion polypeptide described herein.
  • a vector provided herein is a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked (e.g., ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof).
  • a vector is a plasmid, a cosmid or a viral vector. The vector may be capable of autonomous replication, or it can integrate into a host DNA.
  • Viral vectors e.g., comprising fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof are also contemplated herein, including, e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses.
  • a vector provided herein comprises an ESRI fusion nucleic acid molecule, a bait, a probe, or an oligonucleotide of the disclosure in a form suitable for expression thereof in a host cell.
  • the vector includes one or more regulatory sequences operatively linked to the nucleotide sequence to be expressed.
  • the one or more regulatory sequences include promoters (e.g., promoters derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40), enhancers, and other expression control elements e.g., polyadenylation signals).
  • a regulatory sequence directs constitutive expression of a nucleotide sequence (e.g., ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof). In some embodiments, a regulatory sequence directs tissue- specific expression of a nucleotide sequence (e.g., ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof).
  • a regulatory sequence directs inducible expression of a nucleotide sequence (e.g., ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof).
  • a nucleotide sequence e.g., ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof.
  • inducible regulatory sequences include, without limitation, promoters regulated by a steroid hormone, by a polypeptide hormone, or by a heterologous polypeptide, such as a tetracycline-inducible promoter.
  • tissue- or cell-type-specific regulatory sequences include, without limitation, the albumin promoter, lymphoid- specific promoters, promoters of T cell receptors or immunoglobulins, neuron- specific promoters, pancreasspecific promoters, mammary gland- specific promoters, and developmentally-regulated promoters.
  • a vector provided herein comprises or encodes an ESRI fusion nucleic acid molecule, a bait, a probe, or an oligonucleotide of the disclosure in the sense or the anti-sense orientation.
  • a vector e.g., an expression vector
  • a polypeptide e.g., an ESRI fusion polypeptide described herein, or a fragment or mutant form thereof.
  • the design of a vector provided herein depends on such factors as the choice of the host cell to be transformed, the level of expression desired, and the like.
  • expression vectors are designed for the expression of the ESRI fusion nucleic acid molecules, baits, probes, or oligonucleotides described herein, or fragments thereof, in prokaryotic or eukaryotic cells, such as E. coli cells, insect cells (e.g., using baculovirus expression vectors), yeast cells, or mammalian cells.
  • a vector described herein is transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • a vector e.g., an expression vector
  • host cells e.g., comprising ESRI fusion nucleic acid molecules, ESRI fusion polypeptides, baits, probes, vectors, or oligonucleotides of the disclosure.
  • a host cell e.g., a recombinant host cell or recombinant cell
  • comprises a vector described herein e.g., an expression vector described herein.
  • an ESRI fusion nucleic acid molecule, bait, probe, vector, or oligonucleotide provided herein further includes sequences which allow it to integrate into the host cell’s genome (e.g., through homologous recombination at a specific site).
  • a host cell provided herein is a prokaryotic or eukaryotic cell.
  • host cells include, without limitation, bacterial cells (e.g., E. coll), insect cells, yeast cells, or mammalian cells (e.g., human cells, rodent cells, mouse cells, rabbit cells, pig cells, Chinese hamster ovary cells (CHO), or COS cells, e.g., COS-7 cells, CV-1 origin SV40 cells).
  • a host cell described herein includes the particular host cell, as well as the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent host cell.
  • ESRI fusion nucleic acid molecules, baits, probes, vectors, or oligonucleotides of the disclosure may be introduced into host cells using any suitable method known in the art, such as conventional transformation or transfection techniques (e.g., using calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation).
  • suitable method known in the art such as conventional transformation or transfection techniques (e.g., using calcium phosphate or calcium chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation).
  • the method further includes isolating an ESRI fusion polypeptide from the medium or the host cell.
  • Embodiment 1 A method for selecting a therapy for an individual having breast cancer or for identifying an individual having breast cancer who may benefit from a treatment comprising an anti-cancer agent other than a selective estrogen receptor modulator (SERM) or an aromatase inhibitor, the method comprising detecting in a sample from the individual an estrogen receptor 1 (ESRI) fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid
  • Embodiment 2 A method of identifying one or more treatment options for an individual having breast cancer, the method comprising detecting or acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1,
  • Embodiment 3 A method of selecting a treatment for an individual having breast cancer, comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein responsive to the acquisition of said knowledge: (i) the individual is classified as a candidate to receive a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment that comprises an anti-cancer agent other than a SERM or an aromatas
  • Embodiment 4 A method of predicting survival of an individual having breast cancer, or an individual having breast cancer treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, the method comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein responsive to the acquisition of said knowledge, the individual is predicted to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as compared to survival
  • Embodiment 5 A method of treating or delaying progression of breast cancer, comprising:
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI00422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and
  • Embodiment 6 A method of treating or delaying progression of breast cancer, comprising administering to an individual having breast cancer an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor, wherein the anti-cancer agent is administered responsive to acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Embodiment 7 A method of treating or delaying progression of breast cancer, comprising:
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual having breast cancer, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; and
  • Embodiment 8 A method of monitoring, evaluating or screening an individual having breast cancer, comprising acquiring knowledge of an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof; wherein responsive to the acquisition of said knowledge, the individual is predicted to benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor and/or to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as compared to an individual whose breast
  • Embodiment 9 A method of assessing an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide, in breast cancer in an individual, the method comprising:
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2. IYD, IMPG1, STAG2. TNRC6B. or C6orfl5, or a portion thereof; and
  • Embodiment 10 A method of detecting an ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide in breast cancer, the method comprising detecting an ESRI fusion nucleic acid molecule, or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from an individual having breast cancer, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI 00422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Embodiment 11 A method of detecting the presence or absence of breast cancer in an individual, the method comprising:
  • ESRI fusion nucleic acid molecule or an ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof.
  • Embodiment 12 The method of embodiment 11, comprising detecting the presence of breast cancer in a sample from the individual; and/or detecting the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in a sample from the individual.
  • Embodiment 13 A method for monitoring progression or recurrence of breast cancer in an individual, the method comprising:
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2. TNRC6B. or C6oifl5, or a portion thereof.
  • Embodiment 14 The method of embodiment 13, wherein the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample identifies the individual as having decreased risk of breast cancer progression or breast cancer recurrence when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • Embodiment 15 The method of embodiment 13 or embodiment 14, further comprising selecting a treatment, administering a treatment, adjusting a treatment, adjusting a dose of a treatment, or applying a treatment to the individual based, at least in part, on detecting the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the first sample and/or in the second sample, wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • a method for monitoring resistance to endocrine therapy in an individual with breast cancer the method comprising:
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B. or C6orfl5, or a portion thereof.
  • Embodiment 17 The method of embodiment 16, further comprising, after providing the assessment of resistance to endocrine therapy, administering to the individual an effective amount of a treatment that comprises an anti-cancer agent other than a SERM or an aromatase inhibitor; wherein optionally the method further comprises halting administration of an endocrine therapy to the individual based, at least in part, on the detection of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • Embodiment 18 A method for monitoring sensitivity to endocrine therapy in an individual with breast cancer, the method comprising:
  • the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC100422737, SNAP91, ZBTB2. IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Embodiment 19 The method of embodiment 18, further comprising, after providing the assessment of sensitivity to endocrine therapy, administering to the individual an effective amount of an endocrine therapy.
  • Embodiment 20 The method of any one of embodiments 16-19, further comprising, prior to the detection, administering to the individual an effective amount of an endocrine therapy.
  • Embodiment 21 The method of any one of embodiments 16-20, wherein the endocrine therapy comprises treatment with a SERM or an aromatase inhibitor.
  • Embodiment 22 A method of detecting an ESRI fusion nucleic acid molecule, the method comprising:
  • nucleic acid molecules obtained from a sample from an individual having breast cancer comprising nucleic acid molecules corresponding to an ESRI fusion nucleic acid molecule, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof;
  • sequencing by a sequencer, the captured nucleic acid molecules to obtain a plurality of sequence reads that represent the captured nucleic acid molecules, wherein one or more of the plurality of sequence reads correspond to the ESRI fusion nucleic acid molecule;
  • Embodiment 23 The method of embodiment 22, wherein the sequencer comprises a next-generation sequencer.
  • Embodiment 24 A method of detecting an ESRI fusion nucleic acid molecule, the method comprising: (a) providing a sample from an individual having breast cancer, wherein the sample comprises a plurality of nucleic acid molecules;
  • nucleic acid molecules comprising nucleotide sequences corresponding to an ESRI fusion nucleic acid molecule in said library to produce an enriched sample, wherein the an ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOCI 00422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof;
  • Embodiment 25 The method of embodiment 22 or embodiment 24, wherein the one or more adapters comprise amplification primers, flow cell adapter sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences.
  • the one or more adapters comprise amplification primers, flow cell adapter sequences, substrate adapter sequences, sample index sequences, or unique molecular identifier (UMI) sequences.
  • UMI unique molecular identifier
  • Embodiment 26 The method of embodiment 24, wherein the selectively enriching comprises: (a) combining one or more bait molecules with the library, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule, and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • Embodiment 27 The method of any one of embodiments 22-26, wherein the amplified nucleic acid molecules are captured by hybridization with one or more bait molecules.
  • Embodiment 28 The method of any one of embodiments 22-27, wherein the amplifying comprises performing a polymerase chain reaction (PCR) amplification technique, a non- PCR amplification technique, or an isothermal amplification technique.
  • PCR polymerase chain reaction
  • Embodiment 29 The method of any one of embodiments 1, 2, 7, and 9-21, further comprising selectively enriching for one or more nucleic acid molecules in the sample comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule; wherein the selectively enriching produces an enriched sample.
  • Embodiment 30 The method of embodiment 29, wherein the selectively enriching comprises: (a) combining one or more bait molecules with the sample, thereby hybridizing the one or more bait molecules to one or more nucleic acid molecules in the sample comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • Embodiment 31 The method of any one of embodiments 26-28 and 30, wherein the one or more bait molecules comprise a capture nucleic acid molecule configured to hybridize to a nucleotide sequence corresponding to the ESRI fusion nucleic acid molecule.
  • Embodiment 32 The method of embodiment 31, wherein the capture nucleic acid molecule comprises between about 10 and about 30 nucleotides, between about 50 and about 1000 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, or between about 100 and about 200 nucleotides.
  • Embodiment 33 The method of any one of embodiments 26-28 and 30-32, wherein the one or more bait molecules are conjugated to an affinity reagent or to a detection reagent.
  • Embodiment 34 The method of embodiment 33, wherein the affinity reagent is an antibody, an antibody fragment, or biotin, or wherein the detection reagent is a fluorescent marker.
  • Embodiment 35 The method of any one of embodiments 31-34, wherein the capture nucleic acid molecule comprises a DNA, RNA, or mixed DNA/RNA molecule.
  • Embodiment 36 The method of any one of embodiments 24-25 and 29, wherein the selectively enriching comprises amplifying the one or more nucleic acid molecules comprising nucleotide sequences corresponding to the ESRI fusion nucleic acid molecule using a polymerase chain reaction (PCR) to produce an enriched sample.
  • PCR polymerase chain reaction
  • Embodiment 37 The method of any one of embodiments 29-36, further comprising sequencing the enriched sample.
  • Embodiment 39 The method of embodiment 38, wherein the cancer nucleic acid molecules are derived from a tumor portion of a heterogeneous tissue biopsy sample, and the non-cancer nucleic acid molecules are derived from a normal portion of the heterogeneous tissue biopsy sample.
  • Embodiment 40 The method of embodiment 38, wherein the sample comprises a liquid biopsy sample, and wherein the cancer nucleic acid molecules are derived from a circulating tumor DNA (ctDNA) fraction of the liquid biopsy sample, and the non-cancer nucleic acid molecules are derived from a non-tumor fraction of the liquid biopsy sample.
  • ctDNA circulating tumor DNA
  • Embodiment 41 The method of embodiment 40, wherein the ctDNA fraction of the liquid biopsy sample comprises at least 1% of nucleic acid molecules in the liquid biopsy sample.
  • Embodiment 42 The method of any one of embodiments 16-41, wherein the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the sequencing comprises a massively parallel sequencing technique, and the massively parallel sequencing technique comprises next-generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next-generation sequencing
  • Embodiment 43 A method of identifying a candidate treatment for breast cancer in an individual in need thereof, comprising: performing DNA sequencing on a sample obtained from the individual to determine a sequencing mutation profile, wherein the sequencing mutation profile identifies presence of an ESRI fusion nucleic acid molecule in the sample, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6oifl5, or a portion thereof; wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • Embodiment 44 The method of embodiment 43, wherein the presence of the ESRI fusion nucleic acid molecule in the sample identifies the individual as one who may benefit from a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor; and/or predicts the individual to have longer survival when treated with a treatment comprising an anti-cancer agent other than a SERM or an aromatase inhibitor, as compared to survival of an individual whose breast cancer comprises an ESRI fusion nucleic acid molecule when treated with a treatment comprising a SERM or an aromatase inhibitor.
  • Embodiment 45 The method of embodiment 43 or embodiment 44, wherein the sequencing comprises use of a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the sequencing comprises a massively parallel sequencing technique, and the massively parallel sequencing technique comprises next generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next generation sequencing
  • Embodiment 46 The method of any one of embodiments 43-45, wherein the sequencing mutation profile identifies a fragment of the ESRI fusion nucleic acid molecule comprising a breakpoint or fusion junction.
  • Embodiment 47 The method of any one of embodiments 1-46, further comprising generating a report, wherein the report: (a) indicates the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample from the individual; and/or (b) indicates a treatment or one or more treatment options identified or selected for the individual based, at least in part, on the presence of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample from the individual, wherein the treatment or the one or more treatment options comprise an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • Embodiment 48 The method of any one of embodiments 1-47, further comprising generating a molecular profile for the individual, based, at least in part, on detecting or acquiring knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample from the individual.
  • Embodiment 49 The method of embodiment 48, wherein the molecular profile for the individual further comprises results from a comprehensive genomic profiling (CGP) test, a gene expression profiling test, a cancer hotspot panel test, a DNA methylation test, a DNA fragmentation test, an RNA fragmentation test, or any combination thereof.
  • CGP genomic profiling
  • Embodiment 50 The method of embodiment 48 or embodiment 49, wherein the molecular profile for the individual further comprises results from a nucleic acid sequencingbased test.
  • Embodiment 51 The method of any one of embodiments 48-50, further comprising selecting a treatment, administering a treatment, or applying a treatment to the individual based on the generated molecular profile, wherein the treatment comprises an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • Embodiment 52 The method of any one of embodiments 48-51, further comprising generating a report, wherein the report comprises the molecular profile for the individual.
  • Embodiment 53 The method of embodiment 52, wherein the report further comprises information on a treatment or one or more treatment options identified or selected for the individual based, at least in part, on the molecular profile for the individual, wherein the treatment or one or more treatment options comprise an anti-cancer agent other than a SERM or an aromatase inhibitor.
  • Embodiment 54 The method of any one of embodiments 2 and 47-53, further comprising providing the report to the individual, a caregiver, a healthcare provider, a physician, an oncologist, an electronic medical record system, a hospital, a clinic, a third- party payer, an insurance company, or a government office.
  • Embodiment 55 The method of any one of embodiments 1-54, wherein the individual is a human.
  • Embodiment 56 The method of any one of embodiments 1-55, further comprising obtaining the sample from the individual.
  • Embodiment 57 The method of any one of embodiments 1-56, wherein the sample is obtained or derived from the breast cancer.
  • Embodiment 58 The method of any one of embodiments 1-57, wherein the sample comprises a tissue biopsy sample, a liquid biopsy sample, or a normal control.
  • Embodiment 59 The method of any one of embodiments 1-57, wherein the sample is from a tumor biopsy, tumor specimen, or circulating tumor cell.
  • Embodiment 60 The method of any one of embodiments 1-57, wherein the sample is a liquid biopsy sample comprising blood, plasma, cerebrospinal fluid, sputum, stool, urine, or saliva.
  • Embodiment 61 The method of any one of embodiments 1-60, wherein the sample comprises cells and/or nucleic acids from the breast cancer.
  • Embodiment 62 The method of embodiment 61, wherein the sample comprises mRNA, DNA, circulating tumor DNA (ctDNA), cell-free DNA, or cell-free RNA from the breast cancer.
  • Embodiment 63 The method of any one of embodiments 1-57, wherein the sample is a liquid biopsy sample comprising circulating tumor cells (CTCs).
  • CTCs circulating tumor cells
  • Embodiment 64 The method of any one of embodiments 1-57, wherein the sample is a liquid biopsy sample comprising cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), or any combination thereof.
  • cfDNA cell-free DNA
  • ctDNA circulating tumor DNA
  • Embodiment 65 The method of any one of embodiments 2-6, 8, and 47-64, wherein the acquiring knowledge of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, comprises detecting the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample.
  • Embodiment 66 The method of any one of embodiments 1, 2, 7, and 9-65, wherein detecting the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, in the sample comprises detecting a fragment of the ESRI fusion nucleic acid molecule, or of the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule, comprising a breakpoint or fusion junction.
  • Embodiment 67 The method of any one of embodiments 1, 2, 7, and 9-66, wherein the ESRI fusion nucleic acid molecule is detected in the sample by one or more of: a nucleic acid hybridization assay, an amplification-based assay, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, real-time PCR, a screening analysis, fluorescence in situ hybridization (FISH), spectral karyotyping, multicolor FISH (mFISH), comparative genomic hybridization, in situ hybridization, sequence-specific priming (SSP) PCR, high-performance liquid chromatography (HPLC), mass-spectrometric genotyping, or sequencing.
  • a nucleic acid hybridization assay an amplification-based assay, a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay, real-time PCR, a screening analysis, fluorescence in situ hybridization (FISH), spectral
  • Embodiment 68 The method of embodiment 67, wherein the sequencing comprises a massively parallel sequencing (MPS) technique, whole genome sequencing (WGS), whole exome sequencing, targeted sequencing, direct sequencing, or a Sanger sequencing technique; optionally wherein the massively parallel sequencing (MPS) technique comprises next-generation sequencing (NGS).
  • MPS massively parallel sequencing
  • WGS whole genome sequencing
  • NGS next-generation sequencing
  • Embodiment 69 The method of any one of embodiments 1, 2, 7, 9-21, and 47-66, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule is detected in the sample by one or more of: immunoblotting, enzyme linked immunosorbent assay (ELISA), immunohistochemistry, or mass spectrometry.
  • immunoblotting enzyme linked immunosorbent assay (ELISA)
  • ELISA enzyme linked immunosorbent assay
  • immunohistochemistry or mass spectrometry.
  • Embodiment 70 The method of any one of embodiments 1-69, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule is oncogenic; optionally wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule promotes cancer cell survival, angiogenesis, cancer cell proliferation, and any combination thereof.
  • Embodiment 71 The method of any one of embodiments 1-70, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule confers resistance to an endocrine therapy.
  • Embodiment 72 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises one or more of a small molecule inhibitor, an antibody, a cellular therapy, a nucleic acid, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), a treatment for cancer comprising an ESRI gene fusion or rearrangement, an anti-cancer agent being tested in a clinical trial, a treatment for cancer comprising an ESRI gene fusion or rearrangement being tested in a clinical trial, or any combination thereof.
  • a small molecule inhibitor an antibody, a cellular therapy, a nucleic acid, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting
  • Embodiment 73 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a selective estrogen receptor covalent antagonist (SERCA).
  • Embodiment 74 The method of embodiment 73, wherein the anti-cancer agent is H3B- 5942 or H3B-6545.
  • SERCA selective estrogen receptor covalent antagonist
  • Embodiment 75 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a selective estrogen receptor degrader (SERD).
  • SESD selective estrogen receptor degrader
  • Embodiment 76 The method of embodiment 75, wherein the anti-cancer agent is fulvestrant, elacestrant, amcenestrant, camizestrant, giredestrant, rintodestrant, imlunestrant, ZB-716, Zn-c5, LSZ102, LY3484356, or D-0502, or a pharmaceutically acceptable salt thereof.
  • the anti-cancer agent is fulvestrant, elacestrant, amcenestrant, camizestrant, giredestrant, rintodestrant, imlunestrant, ZB-716, Zn-c5, LSZ102, LY3484356, or D-0502, or a pharmaceutically acceptable salt thereof.
  • Embodiment 77 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a PROTAC.
  • Embodiment 78 The method of embodiment 77, wherein the PROTAC is ARV-471.
  • Embodiment 79 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a CDK4/6 inhibitor.
  • Embodiment 80 The method of embodiment 79, wherein the CDK4/6 inhibitor is palbociclib, abemaciclib, ribociclib, or a pharmaceutically acceptable salt thereof.
  • Embodiment 81 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a SERD and a CDK4/6 inhibitor.
  • Embodiment 82 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises a PI3K inhibitor.
  • Embodiment 83 The method of embodiment 82, wherein the PI3K inhibitor is GSK2636771, buparlisib, AZD8186, copanlisib, LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib, pictilisib, GDC0032, IPI145, INK1117, SAR260301, KIN-193, duvelisib, GS-9820, GSK2636771, GDC-0980, AMG319, paxalisib, or alpelisib, or a pharmaceutically acceptable salt thereof.
  • the PI3K inhibitor is GSK2636771, buparlisib, AZD8186, copanlisib, LY294002, PX-866, TGX115, TGX126, BEZ235, SF1126, idelalisib, pictilisib, GDC0032, IPI145
  • Embodiment 84 The method of any one of embodiments 1-71, wherein the anti-cancer agent comprises an mTOR inhibitor.
  • Embodiment 85 The method of embodiment 84, wherein the mTORCl inhibitor is temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, or OSI027, or a pharmaceutically acceptable salt thereof.
  • the mTORCl inhibitor is temsirolimus, everolimus, ridaforolimus, dactolisib, GSK2126458, XL765, AZD8055, AZD2014, MLN128, PP242, NVP-BEZ235, LY3023414, PQR309, PKI587, or OSI027, or a pharmaceutically acceptable salt thereof.
  • Embodiment 86 The method of embodiment 72, wherein the nucleic acid inhibits the expression of the ESRI fusion nucleic acid molecule, or the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule.
  • Embodiment 87 The method of embodiment 86, wherein the nucleic acid is a doublestranded RNA (dsRNA), a small interfering RNA (siRNA), or a small hairpin RNA (shRNA).
  • dsRNA doublestranded RNA
  • siRNA small interfering RNA
  • shRNA small hairpin RNA
  • Embodiment 88 The method of embodiment 72, wherein the cellular therapy is an adoptive therapy, a T cell-based therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR)-T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, a macrophage-based therapy, an induced pluripotent stem cell-based therapy, a B cell-based therapy, or a dendritic cell (DC)-based therapy.
  • a T cell-based therapy a natural killer (NK) cell-based therapy
  • CAR chimeric antigen receptor
  • TCR recombinant T cell receptor
  • a macrophage-based therapy an induced pluripotent stem cell-based therapy
  • B cell-based therapy or a dendritic cell (DC)-based therapy.
  • DC dendritic cell
  • Embodiment 89 The method of any one of embodiments 1-8, 14, 15, 17, and 43-88, wherein the treatment or the one or more treatment options further comprise an additional anti-cancer therapy.
  • Embodiment 90 The method of embodiment 89, wherein the additional anti-cancer therapy comprises one or more of a small molecule inhibitor, a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angiogenic therapy, an anti-DNA repair therapy, an anti-inflammatory therapy, an anti-neoplastic agent, a growth inhibitory agent, a cytotoxic agent, a vaccine, a small molecule agonist, a virus-based therapy, an antibody-drug conjugate, a recombinant protein, a fusion protein, a natural compound, a peptide, a PROteolysis-TArgeting Chimera (PROTAC), or any combination thereof.
  • a small molecule inhibitor e.g., a chemotherapeutic agent, a cancer immunotherapy, an antibody, a cellular therapy, a nucleic acid, a surgery, a radiotherapy, an anti-angi
  • Embodiment 91 The method of embodiment 89, wherein the anti-cancer agent comprises a SERD, and wherein the additional anti-cancer therapy comprises a CDK4/6 inhibitor.
  • Embodiment 92 The method of embodiment 90, wherein the cellular therapy is an adoptive therapy, a T cell-based therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR)-T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, a macrophage-based therapy, an induced pluripotent stem cell-based therapy, a B cell-based therapy, or a dendritic cell (DC)-based therapy.
  • NK natural killer
  • CAR chimeric antigen receptor
  • TCR recombinant T cell receptor
  • Embodiment 93 The method of embodiment 90, wherein the nucleic acid comprises a double-stranded RNA (dsRNA), a small interfering RNA (siRNA), or a small hairpin RNA (shRNA).
  • dsRNA double-stranded RNA
  • siRNA small interfering RNA
  • shRNA small hairpin RNA
  • Embodiment 94 The method of any one of embodiments 1-8, 14, 15, 17, 21, and 43-93, wherein the SERM is tamoxifen, raloxifene, EM652, GW7604, keoxifene, toremifene, apeledoxifene, broparestrol, clomifene, cyclofenil, lasofoxifene, ormeloxifene, or ospemifene.
  • Embodiment 95 The method of any one of embodiments 1-8, 14, 15, 17, 21, and 43-94, wherein the aromatase inhibitor is aminoglutethimide, testolactone, anastrozole, letrozole, exemestane, vorozole, formestane, fadrozole, 4-hydroxyandrostenedione, 1,4,6-androstatrien- 3, 17-dione (ATD), or 4- Androstene-3, 6, 17-trione (“6-OXO”).
  • the aromatase inhibitor is aminoglutethimide, testolactone, anastrozole, letrozole, exemestane, vorozole, formestane, fadrozole, 4-hydroxyandrostenedione, 1,4,6-androstatrien- 3, 17-dione (ATD), or 4- Androstene-3, 6, 17-trione (“6-OXO”).
  • Embodiment 96 The method of any one of embodiments 1-95, wherein the breast cancer is advanced or metastatic.
  • Embodiment 97 The method of any one of embodiments 1-96, wherein the breast cancer is hormone receptor positive (HR+) breast cancer.
  • HR+ hormone receptor positive
  • Embodiment 98 The method of any one of embodiments 1-97, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, encoding an ESRI DNA binding domain, or a portion thereof, to any one of genes CCDC170, SMAD4, LOC 100422737, SNAP91, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Embodiment 99 The method of any one of embodiments 1-98, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI DNA binding domain, or a portion thereof, fused to a polypeptide encoded by any one of genes CCDC170, SMAD4, LOC100422737, SNAP9I, ZBTB2, IYD, IMPG1, STAG2, TNRC6B, or C6orfl5, or a portion thereof.
  • Embodiment 100 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a CCDC170 gene, or a portion thereof.
  • Embodiment 101 The method of embodiment 100, wherein the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exon 2 of the ESRI gene.
  • Embodiment 102 The method of embodiment 100 or embodiment 101, wherein the ESRI fusion nucleic acid molecule comprises the CCDC170 gene, or a portion thereof, fused to exons 1-2 of the ESRI gene.
  • Embodiment 103 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a CCDC170 polypeptide, or a portion thereof.
  • Embodiment 104 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a SMAD4 gene, or a portion thereof.
  • Embodiment 105 The method of embodiment 104, wherein the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • Embodiment 106 The method of embodiment 104 or embodiment 105, wherein the ESRI fusion nucleic acid molecule comprises the SMAD4 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • Embodiment 107 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SMAD4 polypeptide, or a portion thereof.
  • Embodiment 108 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a EOC 100422737 gene, or a portion thereof.
  • Embodiment 109 The method of embodiment 108, wherein the ESRI fusion nucleic acid molecule comprises the EOC 100422737 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • Embodiment 110 The method of embodiment 108 or embodiment 109, wherein the ESRI fusion nucleic acid molecule comprises the EOC 100422737 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • Embodiment 111 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a EOC 100422737 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a EOC100422737 polypeptide, or a portion thereof.
  • Embodiment 112 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a SNAP91 gene, or a portion thereof.
  • Embodiment 113 The method of embodiment 112, wherein the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • Embodiment 114 The method of embodiment 112 or embodiment 113, wherein the ESRI fusion nucleic acid molecule comprises the SNAP91 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • Embodiment 115 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a SNAP91 polypeptide, or a portion thereof.
  • Embodiment 116 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a ZBTB2 gene, or a portion thereof.
  • Embodiment 117 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a ZBTB2 polypeptide, or a portion thereof.
  • Embodiment 118 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to an IYD gene, or a portion thereof.
  • Embodiment 119 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an IYD polypeptide, or a portion thereof.
  • Embodiment 120 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to an IMPG1 gene, or a portion thereof.
  • Embodiment 121 The method of embodiment 120, wherein the ESRI fusion nucleic acid molecule comprises the 1MPG1 gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • Embodiment 122 The method of embodiment 120 or embodiment 121, wherein the ESRI fusion nucleic acid molecule comprises the 1MPG1 gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • Embodiment 123 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to an 1MPG1 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to an 1MPG1 polypeptide, or a portion thereof.
  • Embodiment 124 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction an ESRI gene, or a portion thereof, fused to a STAG2 gene, or a portion thereof.
  • Embodiment 125 The method of embodiment 124, wherein the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • Embodiment 126 The method of embodiment 124 or embodiment 125, wherein the ESRI fusion nucleic acid molecule comprises the STAG2 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • Embodiment 127 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a STAG2 polypeptide, or a portion thereof.
  • Embodiment 128 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a TNRC6B gene, or a portion thereof.
  • Embodiment 129 The method of embodiment 128, wherein the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exon 4 of the ESRI gene.
  • Embodiment 130 The method of embodiment 128 or embodiment 129, wherein the ESRI fusion nucleic acid molecule comprises the TNRC6B gene, or a portion thereof, fused to exons 1-4 of the ESRI gene.
  • Embodiment 131 The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a TNRC6B polypeptide, or a portion thereof.
  • Embodiment 132 The method of any one of embodiments 1-99, wherein the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof, and wherein the ESRI fusion nucleic acid molecule comprises, in the 5’ to 3’ direction, an ESRI gene, or a portion thereof, fused to a C6orfl5 gene, or a portion thereof.
  • Embodiment 133 The method of embodiment 132, wherein the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exon 5 of the ESRI gene.
  • Embodiment 134 The method of embodiment 132 or embodiment 133, wherein the ESRI fusion nucleic acid molecule comprises the C6orfl5 gene, or a portion thereof, fused to exons 1-5 of the ESRI gene.
  • Embodiment 135. The method of any one of embodiments 1-99, wherein the ESRI fusion polypeptide encoded by the ESRI fusion nucleic acid molecule comprises a fusion between an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof, and wherein the ESRI fusion polypeptide comprises, in the N- to C-terminus direction, an ESRI polypeptide, or a portion thereof, fused to a C6orfl5 polypeptide, or a portion thereof.

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  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

L'invention concerne des molécules d'acide nucléique de fusion ESR1 et des polypeptides, des procédés associés à la détection de molécules d'acide nucléique de fusion ESR1 et des polypeptides dans le cadre du cancer, ainsi que des méthodes de traitement et des utilisations associées à celles-ci. La détection d'une molécule ou d'un polypeptide d'acide nucléique de fusion ESR1 peut être utilisée pour identifier des individus chez qui un traitement avec une thérapie anticancéreuse autre qu'un SERM ou un inhibiteur d'aromatase peut être bénéfique.
PCT/US2024/058267 2023-12-04 2024-12-03 Fusions de gènes esr1 et leurs utilisations Pending WO2025122500A1 (fr)

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US63/606,010 2023-12-04

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WO2025122500A1 true WO2025122500A1 (fr) 2025-06-12

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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023086951A1 (fr) * 2021-11-12 2023-05-19 Foundation Medicine, Inc. Fraction d'adn tumoral circulant et ses utilisations
US11771682B2 (en) * 2016-06-22 2023-10-03 Ellipses Pharma Ltd. AR+ breast cancer treatment methods

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11771682B2 (en) * 2016-06-22 2023-10-03 Ellipses Pharma Ltd. AR+ breast cancer treatment methods
WO2023086951A1 (fr) * 2021-11-12 2023-05-19 Foundation Medicine, Inc. Fraction d'adn tumoral circulant et ses utilisations

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