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WO2025188905A1 - Anticorps anti-s100a et compositions et procédés associés - Google Patents

Anticorps anti-s100a et compositions et procédés associés

Info

Publication number
WO2025188905A1
WO2025188905A1 PCT/US2025/018586 US2025018586W WO2025188905A1 WO 2025188905 A1 WO2025188905 A1 WO 2025188905A1 US 2025018586 W US2025018586 W US 2025018586W WO 2025188905 A1 WO2025188905 A1 WO 2025188905A1
Authority
WO
WIPO (PCT)
Prior art keywords
antibody
seq
antigen binding
binding fragment
nos
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/US2025/018586
Other languages
English (en)
Other versions
WO2025188905A8 (fr
Inventor
Zhiqiang An
Ningyan Zhang
Hui Deng
Kyuson Yun
Thomas Wong
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
University of Texas System
University of Texas at Austin
Methodist Hospital
Original Assignee
University of Texas System
University of Texas at Austin
Methodist Hospital
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by University of Texas System, University of Texas at Austin, Methodist Hospital filed Critical University of Texas System
Publication of WO2025188905A1 publication Critical patent/WO2025188905A1/fr
Publication of WO2025188905A8 publication Critical patent/WO2025188905A8/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2818—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD28 or CD152
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2881—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against CD71
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A61K2039/507—Comprising a combination of two or more separate antibodies
    • 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
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/31—Immunoglobulins specific features characterized by aspects of specificity or valency multispecific
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value

Definitions

  • the present disclosure generally relates antibodies and antigen-binding fragments thereof that bind S100A4 or S100A9, and compositions, methods, and uses thereof, including in the treatment of and prevention of cancers.
  • Cancer is a leading cause of death in the United States and worldwide. Certain forms of cancer can exhibit resistance to therapy and/or tumor recurrence, including gliomas and breast cancer, particularly following epithelial-mesenchymal transition (EMT) and/or metastasis. Such cancers can exhibit poor prognosis. For example, glioblastoma is the most aggressive form of brain tumor, with median overall survival of less than 2 years with standard of care. Metastatic cancers are responsible for -90% of cancer associated deaths. There is a need to develop improved treatments for such cancers. Provided herein are solutions to these and other needs.
  • EMT epithelial-mesenchymal transition
  • antibody and antigen-binding fragments thereof that bind to human S100A4 protein and/or human S100A9 protein.
  • the current disclosure fulfills a need in the art by providing compositions and methods for treating individuals for cancer using the anti-S100A4 antibodies or antigen-binding fragments thereof.
  • administration of the antibodies or antigen-binding fragments thereof may be or be part of a therapeutic strategy for treating or preventing cancer, such as glioblastoma or breast cancer, and/or metastasis thereof.
  • Administration of the compositions may also provide therapeutic utility in the treatment of various immune disorders such as autoimmune disease and chronic inflammatory disease.
  • the method can comprise administering any of the compositions provided herein, such as any of the polypeptides, antibodies, and/or antigen binding fragments thereof, to a subject.
  • the method can comprise any number of steps, which may include any of the following steps: administering the composition, administering an additional therapy (such as an additional cancer therapy or checkpoint inhibitor), and monitoring the subject.
  • the preceding steps can occur in any order and each step may be performed one or more times, in any order relative to the other steps. It is also specifically contemplated, in certain aspects, that any of the preceding steps may be excluded from the methods.
  • the subject is a mammal. In some aspects, the subject is a human.
  • an antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3; wherein the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45- 48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63), or sequence
  • the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45- 48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • S100A4-1 SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7
  • S100A4-5 SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21
  • S100A4-9 SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35
  • S100A4-11
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7). In some aspects, the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively are set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35). In some aspects, the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • the antibody or antigen binding fragment thereof comprises a heavy chain variable region and a light chain variable region, respectively, comprising the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4- 11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58), or sequences having at least 70%, 80%, 85%, 90%, 95%, 99% or 100% sequence identity thereto.
  • the heavy chain variable region and light chain variable region respectively, comprise the amino acid sequences set forth in:S100A4-l (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58).
  • amino acid sequences of the heavy chain variable region and light chain variable region are set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58).
  • amino acid sequences of the heavy chain variable region and light chain variable region, respectively are set forth in S100A4-1 (SEQ ID NOS: 1 and 2).
  • the amino acid sequences of the heavy chain variable region and light chain variable region, respectively are set forth in S100A4-5 (SEQ ID NOS: 15 and 16). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-9 (SEQ ID NOS: 29 and 30). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-11 (SEQ ID NOS: 43 and 44). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-19 (SEQ ID NOS: 57 and 58).
  • the antibody or antigen binding fragment thereof specifically binds to S100A4 protein. In some aspects, the antibody or antigen binding fragment thereof specifically binds to human S100A4 protein. In some aspects, the antibody or antigen binding fragment thereof binds to human S100A4 protein with a higher binding affinity than to S100A4 protein from another species. In some aspects, the antibody or antigen binding fragment thereof binds to human S100A4 protein with a higher binding affinity than to mouse S100A4 protein.
  • the antibody or antigen binding fragment thereof binds human S100A4 protein with a dissociation constant (KD) of less than 100 nanomolar (nM), less than 10 nM, less than 5 nM, or less than 1 nM (or any range derivable therein). In some aspects, the antibody or antigen binding fragment thereof binds human S100A4 protein with a KD of between about 100 nM and about 1 picomolar (pM), for example, 100 nM, lOnM, 5 nM, 1 nM, 100 pM, 10 pM or 1 pM (or any range derivable therein).
  • KD dissociation constant
  • the antibody or antigen binding fragment thereof binds human SI 00 A4 protein with a KD of at or about 1 nanomolar (nM). In some aspects, the antibody or antigen binding fragment thereof binds S100A4 protein and an additional SI 00 protein. In some aspects, the additional SI 00 protein is S100A9. In some aspects, the S100A9 is human S100A9. In some aspects, the antibody or antigen binding fragment thereof specifically binds to S100A9 protein. In some aspects, the antibody or antigen binding fragment thereof specifically binds to human S100A9 protein. In some aspects, the antibody or antigen binding fragment thereof binds to human S100A9 protein. In some aspects, the antibody or antigen binding fragment thereof binds to human S100A9 protein with a higher binding affinity than to S100A9 protein from another species.
  • the antibody or antigen binding fragment thereof binds to human S100A9 protein with a higher binding affinity than to mouse S100A9 protein. In some aspects, the antibody or antigen binding fragment thereof binds human S100A9 protein with a dissociation constant (KD) of less than 100 nanomolar (nM), less than 10 nM, less than 5 nM, or less than 1 nM (or any range derivable therein).
  • KD dissociation constant
  • the antibody or antigen binding fragment thereof binds human S100A9 protein with a KD of between about 100 nM and about 1 picomolar (pM), for example, 100 nM, lOnM, 5 nM, 1 nM, 100 pM, 10 pM or 1 pM (or any range derivable therein). In some aspects, the antibody or antigen binding fragment thereof binds human S100A9 protein with a KD of at or about 1 nanomolar (nM). In some aspects, the antibody or antigen binding fragment thereof binds S100A9 protein and an additional S100 protein. In some aspects, the additional S100 protein is S100A4. In some aspects, the S100A9 is human S100A4.
  • the antibody is a blocking antibody. In some aspects, the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A4 protein. In some aspects, the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A9 protein. In some aspects, the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A4 protein and S100A9 protein. In some aspects, the antibody or antigen fragment competes for binding of S100A4 or S100A9 protein with an antibody selected from a group consisting of S100A4-1, S100A4-5, S100A4-9, S100A4-11, and S100A4-19.
  • the antibody is or is not a human antibody, humanized antibody, recombinant antibody, chimeric antibody, an antibody derivative, a veneered antibody, a diabody, a monoclonal antibody, a single domain antibody, or a single chain antibody.
  • the antibody or antigen binding fragment thereof is or is not humanized.
  • the humanized antibody is derived from a non-human species.
  • the non-human species is rabbit or mouse.
  • the antigen binding fragment is a single chain variable fragment (scFv), F(ab’)2, Fab’, Fab, Fv, or IgG.
  • the antibody is or is not a bispecific antibody comprising a first portion comprising any anti-S100A4 or anti-S100A9 antibody or antigen binding fragment provided herein, and a second antigen binding domain.
  • the second antigen binding domain comprises a second antigen binding fragment.
  • the second antigen binding domain comprises a single chain variable fragment (scFv).
  • the second antigen binding domain is or is not fused to the heavy chain C-terminus of the anti- S100A4 antibody portion or the anti-S100A9 antibody portion.
  • the second antigen binding domain binds transferrin receptor (TfR).
  • the second antigen binding domain comprises HCDRs from the heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and LCDRs from the light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • the second antigen binding domain comprises HCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NOS: 73-75) and LCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • the second antigen binding domain comprises a heavy chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and a light chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • the bispecific antibody crosses the blood-brain barrier when administered to a subject. In some aspects, the administration is or is not systemic. In some aspects, the bispecific antibody is internalized intracellularly. In some aspects, the bispecific antibody is internalized intracellularly by cells expressing transferrin receptor. In some aspects, the bispecific antibody is internalized intracellularly by tumor cells. In some aspects, the bispecific antibody is internalized intracellularly by glioblastoma tumor cells. In some aspects, the bispecific antibody is intemalized intracellularly by glioma stem cells. In some aspects, the bispecific antibody binds intracellular S100A4 and/or S100A9.
  • a polypeptide comprising any antibody or antigen binding fragment provided herein, or a component thereof.
  • a polypeptide comprising at least two antigen binding fragments, wherein at least one antigen binding fragment is any antigen binding fragment provided herein.
  • the polypeptide is multivalent.
  • the polypeptide is bispecific.
  • the bispecific polypeptide comprises a first antigen binding fragment and a second antigen binding fragment, wherein the first antigen binding fragment is any anti-S100A4 or anti- S100A9 antigen binding fragment provided herein.
  • the second antigen binding fragment binds transferrin receptor (TfR).
  • the second antigen binding fragment comprises HCDRs from the heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and LCDRs from the light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • the second antigen binding fragment comprises HCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NOS: 73-75) and LCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • the second antigen binding fragment comprises a heavy chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and a light chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • the bispecific polypeptide crosses the blood-brain barrier when administered to a subject. In some aspects, the administration is systemic. In some aspects, the bispecific polypeptide is internalized intracellularly. In some aspects, the bispecific polypeptide is internalized intracellularly by cells expressing transferrin receptor. In some aspects, the bispecific polypeptide is internalized intracellularly by tumor cells. In some aspects, the bispecific polypeptide is internalized intracellularly by glioblastoma tumor cells. In some aspects, the bispecific polypeptide is internalized intracellularly by glioma stem cells. In some aspects, the bispecific polypeptide binds intracellular S100A4 and/or S100A9.
  • composition comprising any antibody or antigen binding fragment thereof provided herein, or any polypeptide provided herein.
  • the composition comprises a pharmaceutical excipient.
  • the composition is formulated for administration to a subject.
  • the composition is formulated for administration to a subject.
  • the composition is formulated for administration via parenteral, intravenous, subcutaneous, intramuscular, or intranasal administration.
  • provided herein is one or more nucleic acids encoding any antibody or antigen binding fragment thereof, or any polypeptide, provided herein.
  • nucleic acid encoding an antibody heavy chain wherein the nucleic acid has, has at least, or has at most 70%, 80%, 85%, 90%, 95%, 99%, or 100% (or any range derivable therein) sequence identity to one of SEQ ID NOS: 8, 22, 36, 50, and 64.
  • nucleic acid encoding an antibody light chain wherein the nucleic acid has at least, or has at most, 70%, 80%, 85%, 90%, 95%, 99%, or 100% (or any range derivable therein) sequence identity to one of SEQ ID NOS: 9, 23, 37, 51, and 65.
  • provided herein is a vector comprising any of the nucleic acid(s) provided herein.
  • a host cell comprising any nucleic acid(s) or vector provided herein.
  • a method of making an antibody, antigen binding fragment thereof, or polypeptide comprising culturing the host cell under conditions that allow the host cell to express the antibody, antigen binding fragment thereof, or polypeptide.
  • the method further comprising isolating the expressed antibody, antigen binding fragment thereof, or polypeptide.
  • a pharmaceutical composition comprising any antibody or antigen binding fragment thereof, or any polypeptide, provided herein, and a pharmaceutically acceptable carrier or excipient.
  • provided herein is a method of treating or preventing a disease, disorder, or condition in a subject comprising administering to the subject a therapeutically effective amount of any antibody or antigen binding fragment thereof provided herein, any polypeptide provided herein, any composition provided herein, any nucleic acid(s) provided herein, any vector provided herein, any host cell provided herein, or any pharmaceutical composition provided herein.
  • the disease, disorder, or condition is an autoimmune disease or a chronic inflammatory disease.
  • the disease, disorder, or condition is rheumatoid arthritis.
  • the disease, disorder, or condition is fibrosis.
  • the disease, disorder, or condition is psoriasis.
  • the disease, disorder, or condition is atherosclerosis. In some aspects, the disease, disorder, or condition is chronic cellular stress. In some aspects, the disease, disorder, or condition is cancer and/or metastasis thereof. In some aspects, the cancer expresses S100A4 and/or S100A9. In some aspects, the cancer does not express S100A4 and/or S100A9. In some aspects, the subject has been determined to have a cancer that expresses S100A4 and/or S100A9. In some aspects, the subject has been diagnosed with cancer. In some aspects, the subject has been determined to be at risk for cancer or cancer metastasis. In some aspects, the subject has previously been treated for cancer. In some aspects, the cancer has been determined to be resistant to the previous treatment.
  • the cancer is breast cancer. In some aspects, the cancer is glioblastoma. In some aspects, the method comprises administering to the subject any bispecific polypeptide provided herein. In some aspects, the administration is systemic. In some aspects, the administration is intratumoral. In some aspects, the subject is human. In some aspects, the subject is administered an additional therapeutic. In some aspects, the additional therapeutic comprises a therapeutic for treating cancer. In some aspects, the additional therapeutic is a checkpoint inhibitor.
  • provided herein is a use of any antibody or antigen binding fragment thereof provided herein, any polypeptide provided herein, any composition provided herein, any nucleic acid(s) provided herein, any vector provided herein, any host cell provided herein, or any pharmaceutical composition provided herein, in the manufacture of a medicament for treating or preventing a disease, disorder, or condition in a subject, wherein the disease, disorder, or condition is an autoimmune disease, chronic inflammatory disease, or cancer and/or metastasis thereof.
  • a method for evaluating a biological sample comprising contacting the biological sample with any antibody or antigen binding fragment thereof provided herein, or any polypeptide provided herein.
  • the antibody or antigen binding fragment thereof, or the polypeptide is operatively linked to a detectable label.
  • the method further comprises incubating the sample under conditions that allow for the binding of the antibody or antigen binding fragment thereof, or the polypeptide, to an antigen in the sample.
  • the method comprises detecting the binding of the antigen in the sample to the antibody or antigen binding fragment thereof, or the polypeptide.
  • the antigen is an S100A4 protein and/or an S100A9 protein.
  • the method comprises determining the presence, abundance, and/or location of S100A4 protein and/or S100A9 protein in the sample.
  • the sample is from a human subject.
  • provided herein is a method of treating or preventing a disease, disorder, or condition in a subject, the method comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of any of the antibodies listed in Table 1.
  • a method of treating or preventing a disease, disorder, or condition in a subject the method comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of the antibody S 100A4- 11.
  • provided herein is a method of treating or preventing a disease, disorder, or condition in a subject, the method comprising administering to a subject a therapeutic agent comprising any antibody or antigen binding fragment thereof provided herein, any polypeptide provided herein, any composition provided herein, any nucleic acid(s) provided herein, any vector provided herein, any host cell provided herein, or any pharmaceutical composition provided herein.
  • the disease, disorder, or condition is an autoimmune disease, chronic inflammatory disease, or cancer and/or metastasis thereof.
  • the cancer is breast cancer or glioblastoma.
  • the cancer expresses S100A4 and/or S100A9. In some aspects, the cancer does not express S100A4 and/or S100A9.
  • an anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7).
  • an anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21).
  • an anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35).
  • an anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49).
  • an anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • an anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7).
  • an anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21).
  • an anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35).
  • an anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49).
  • an anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • the bispecific antibody comprises (i) a first antigen binding fragment capable of binding S100A4 and/or S100A9; and (ii) a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73- 76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • the bispecific antibody comprises (i) a first antigen binding fragment capable of binding SI 00 A4 and/or SI 00A9; and (ii) a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • the bispecific antibody comprises (i) a first antigen binding fragment capable of binding S100A4 and/or SI 00A9; and (ii) a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • the bispecific antibody comprises (i) a first antigen binding fragment capable of binding S100A4 and/or S100A9; and (ii) a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • the bispecific antibody comprises (i) a first antigen binding fragment capable of binding S100A4 and/or S100A9; and (ii) a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR- 4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti-S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-1
  • TfR anti-transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti-S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-5
  • TfR anti-transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti-S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-9
  • TfR anti-transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti-S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-11
  • TfR anti-transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti- S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR- 4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-19
  • TfR anti-transferrin receptor
  • An antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3; wherein the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63), or sequences having at least 80%, 85%,
  • S100A4-1 SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7
  • S100A4-5 SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21
  • S100A4-9 SEQ ID NOS: 31-34, AAS,
  • A3 The antibody or antigen binding fragment thereof of aspect 1 or 2, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • S100A4-1 SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7
  • S100A4-5 SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21
  • S100A4-9 SEQ ID NOS: 31-
  • A4 The antibody or antigen binding fragment thereof of any of aspects 1-3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49).
  • A5. The antibody or antigen binding fragment thereof of any of aspects 1-4, wherein the antibody or antigen binding fragment thereof comprises a heavy chain variable region and a light chain variable region, respectively, comprising the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58), or sequences having at least 70%, 80%, 85%, 90%, 95%, 99% or 100% sequence identity thereto.
  • S100A4-1 SEQ ID NOS: 1 and 2
  • S100A4-5 SEQ ID NOS: 15 and 16
  • S100A4-9 SEQ ID NOS: 29 and 30
  • S100A4-11 SEQ ID NOS: 43 and 44
  • S100A4-19 SEQ ID NOS: 57 and 58
  • A7 The antibody or antigen binding fragment thereof of aspect 5 or 6, wherein the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58).
  • A8 The antibody or antigen binding fragment thereof of any of aspects 5-7, wherein the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-11 (SEQ ID NOS: 43 and 44).
  • A9 The antibody or antigen binding fragment thereof of any of aspects 1-8, wherein the antibody or antigen binding fragment thereof specifically binds to S100A4 protein.
  • A10 The antibody or antigen binding fragment thereof of any of aspects 1-9, wherein the antibody or antigen binding fragment thereof binds to human S100A4 protein with a higher binding affinity than to S100A4 protein from another species.
  • A12 The antibody or antigen binding fragment thereof of any of aspects 9-10, wherein the antibody or antigen binding fragment thereof binds S100A4 protein and an additional SI 00 protein.
  • A13 The antibody or antigen binding fragment thereof of any of aspects 11, wherein the additional SI 00 protein is S100A9.
  • A14. The antibody or antigen binding fragment thereof of any of aspects 1-8, wherein the antibody or antigen binding fragment thereof specifically binds to S100A9 protein.
  • A15 The antibody or antigen binding fragment thereof of any of aspects 1-8, wherein the antibody or antigen binding fragment thereof binds to human S100A9 protein with a higher binding affinity than to S100A9 protein from another species.
  • a 16 The antibody or antigen binding fragment thereof of any of aspects 14-15, wherein the antibody or antigen binding fragment thereof binds human S100A9 protein with a KD of between about 100 nM and about 1 picomolar (pM).
  • a 17 The antibody or antigen binding fragment thereof of any of aspects 14-16, wherein the antibody or antigen binding fragment thereof binds S100A9 protein and an additional SI 00 protein.
  • a 19 The antibody or antigen binding fragment thereof of any of aspects 1-18, wherein the antibody is a blocking antibody.
  • A20 The antibody or antigen binding fragment thereof of aspect 19, wherein the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A4 protein.
  • A22 The antibody or antigen binding fragment thereof of aspect 19, wherein the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A4 protein and S100A9 protein.
  • A23 The antibody or antigen binding fragment thereof of any of aspects 1-22, wherein the antibody is a human antibody, humanized antibody, recombinant antibody, chimeric antibody, an antibody derivative, a veneered antibody, a diabody, a monoclonal antibody, a single domain antibody, or a single chain antibody.
  • A24 The antibody or antigen binding fragment thereof of any of aspects 1-23, wherein the antibody or antigen binding fragment thereof is humanized.
  • A25 The antibody or antigen binding fragment thereof of aspect 24, wherein the humanized antibody is derived from a non-human species.
  • A26 The antibody or antigen binding fragment thereof of aspect 25, wherein the non-human species is rabbit or mouse.
  • A27 The antibody or antigen binding fragment thereof of any of aspects 1-26, wherein the antigen binding fragment is a single chain variable fragment (scFv), F(ab’)2, Fab’, Fab, Fv, or IgG.
  • A28 The antibody of any of aspects 1-27, wherein the antibody is a bispecific antibody comprising a first portion comprising the antibody or antigen binding fragment thereof of any of aspects 1-16, and a second antigen binding domain.
  • A29 The bispecific antibody of aspect 28, wherein the second antigen binding domain comprises a second antigen binding fragment.
  • A30 The bispecific antibody of aspect 28 or 29, wherein the second antigen binding domain comprises a single chain variable fragment (scFv).
  • scFv single chain variable fragment
  • A31 The bispecific antibody of any of aspects 28-30, wherein the second antigen binding domain is fused to the heavy chain C-terminus of the anti-S100A4 antibody portion or the anti- S100A9 antibody portion.
  • A32 The bispecific antibody of any of aspects 28-31, wherein the second antigen binding domain binds transferrin receptor (TfR).
  • TfR transferrin receptor
  • A33 The bispecific antibody of any of aspects 28-32, wherein the second antigen binding domain comprises HCDRs from the heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and LCDRs from the light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • A34 The bispecific antibody of any of aspects 28-33, wherein the second antigen binding domain comprises HCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NOS: 73- 75) and LCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • A35 The bispecific antibody of any of aspects 28-34, wherein the second antigen binding domain comprises a heavy chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and a light chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • A36 The bispecific antibody of any of aspects 28-35, wherein the bispecific antibody crosses the blood-brain barrier when administered to a subject.
  • A37 The bispecific antibody of aspect 36, wherein the administration is systemic.
  • A38 The bispecific antibody of any of aspects 28-37, wherein the bispecific antibody is internalized intracellularly.
  • A40 The bispecific antibody of any of aspects 28-39, wherein the bispecific antibody is internalized intracellularly by tumor cells.
  • A41 The bispecific antibody of any of aspects 28-40, wherein the bispecific antibody is internalized intracellularly by glioblastoma tumor cells.
  • A42 The bispecific antibody of any of aspects 28-41, wherein the bispecific antibody is internalized intracellularly by glioma stem cells.
  • A43 The bispecific antibody of any of aspects 28-42, wherein the bispecific antibody binds intracellular S100A4 and/or S100A9.
  • A44 A polypeptide comprising the antibody or antigen binding fragment of any of aspects 1-27, or a component thereof.
  • a polypeptide comprising at least two antigen binding fragments, wherein at least one antigen binding fragment is the antigen binding fragment of any one of aspects 1-27.
  • polypeptide of aspect 45 wherein the polypeptide is multivalent or wherein the polypeptide is bispecific.
  • A47 The polypeptide of aspect 46, wherein the bispecific polypeptide comprises a first antigen binding fragment and a second antigen binding fragment, wherein the first antigen binding fragment is the antigen binding fragment of any of aspects 1-27.
  • A48 The polypeptide of aspect 46, wherein the second antigen binding fragment binds transferrin receptor (TfR).
  • polypeptide of any of aspects 47-48, wherein the second antigen binding fragment comprises HCDRs from a heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and LCDRs from a light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • A50 The polypeptide of any of aspects 47-49, wherein the second antigen binding fragment comprises HCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NOS: 73-75) and LCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • A51 The polypeptide of any of aspects 47-50, wherein the second antigen binding fragment comprises a heavy chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and a light chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • A52 The polypeptide of any of aspects 47-51, wherein the bispecific polypeptide crosses the blood-brain barrier when administered to a subject.
  • A53 The polypeptide of aspect 52, wherein the administration is systemic.
  • A54 The polypeptide of any of aspects 47-53, wherein the bispecific polypeptide is internalized intracellularly.
  • A55 The polypeptide of any of aspects 47-54, wherein the bispecific polypeptide is internalized intracellularly by cells expressing transferrin receptor.
  • A56 The polypeptide of any of aspects 47-55, wherein the bispecific polypeptide is internalized intracellularly by tumor cells.
  • A57 The polypeptide of any of aspects 47-56, wherein the bispecific polypeptide is internalized intracellularly by glioblastoma tumor cells.
  • A58 The polypeptide of any of aspects 47-57, wherein the bispecific polypeptide is internalized intracellularly by glioma stem cells.
  • a composition comprising the antibody or antigen binding fragment thereof of any of aspects 1-43, or the polypeptide of any of aspects 44-59.
  • composition of aspect 60 wherein the composition is formulated for administration via parenteral, intravenous, subcutaneous, intramuscular, or intranasal administration.
  • A62 One or more nucleic acids encoding the antibody or antigen binding fragment thereof of any of aspects 1-43, or the polypeptide of any of aspects 44-59.
  • A63 A nucleic acid encoding an antibody heavy chain, wherein the nucleic acid has at least 70%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity to one of SEQ ID NOS: 8, 22, 36, 50, and 64.
  • A64 A nucleic acid encoding an antibody light chain, wherein the nucleic acid has at least 70%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity to one of SEQ ID NOS: 9, 23, 37, 51, and 65.
  • A65 A vector comprising the nucleic acid(s) of any one of aspects 63-64.
  • A66 A host cell comprising the nucleic acid(s) of any one of aspects 63-64 or the vector of aspect 65.
  • a method of making an antibody, antigen binding fragment thereof, or polypeptide comprising culturing the host cell of aspect 66 under conditions that allow the host cell to express the antibody, antigen binding fragment thereof, or polypeptide.
  • A68 The method of aspect 67, wherein the method further comprising isolating the expressed antibody, antigen binding fragment thereof, or polypeptide.
  • a pharmaceutical composition comprising the antibody or antigen binding fragment thereof of any of aspects 1-43, or the polypeptide of any of aspects 44-59, and a pharmaceutically acceptable carrier or excipient.
  • a method of treating or preventing a disease, disorder, or condition in a subject comprising administering to the subject a therapeutically effective amount of the antibody or antigen binding fragment thereof of any of aspects 1-43, the polypeptide of any of aspects 44- 59, the composition of any of aspects 60-61, the nucleic acid(s) of any of aspects 62-64, the vector of aspect 65, the host cell of aspect 66, or the pharmaceutical composition of aspect 69.
  • A71 The method of aspect 70, wherein the disease, disorder, or condition is an autoimmune disease or a chronic inflammatory disease.
  • A72 The method of aspect 70, wherein the disease, disorder, or condition is rheumatoid arthritis, fibrosis, psoriasis, atherosclerosis, or cellular stress.
  • A73 The method of aspect 70, wherein the disease, disorder, or condition is cancer and/or metastasis thereof.
  • A74 The method of aspect 73, wherein the cancer expresses S100A4 and/or S100A9.
  • A75 The method of any of aspects 70, 73, and 74, wherein the subject has been determined to have a cancer that expresses S100A4 and/or S100A9.
  • A76 The method of any of aspects 73-75, wherein the cancer is glioblastoma.
  • A77 The method of any of aspects 73-75, wherein the cancer is breast cancer.
  • A78 The method of any of aspects 70-77, wherein the method comprises administering to the subject the bispecific polypeptide of any of aspects 28-43.
  • A79 The method of any of aspects 70-78, wherein the administration is systemic.
  • A80 The method of any of aspects 70-78, wherein the administration is intratumoral.
  • A81 The method of any of aspects 70-78, wherein the subject is human.
  • A82 The method of any of aspects 70-78, wherein the subject is administered an additional therapeutic.
  • A83 The method of aspect 82, wherein the additional therapeutic comprises a therapeutic for treating cancer.
  • the method of aspect 82 or 83, wherein the additional therapeutic is a checkpoint inhibitor.
  • A85. Use of the antibody or antigen binding fragment thereof of any of aspects 1-43, the polypeptide of any of aspects 44-59, the composition of any of aspects 60-61, the nucleic acid(s) of any of aspects 62-64, the vector of aspect 65, the host cell of aspect 66, or the pharmaceutical composition of aspect 69, in the manufacture of a medicament for treating or preventing a disease, disorder, or condition in a subject, wherein the disease, disorder, or condition is an autoimmune disease, chronic inflammatory disease, or cancer and/or metastasis thereof.
  • a method for evaluating a biological sample comprising contacting the biological sample with the antibody or antigen binding fragment thereof of any of aspects 1- 43, or the polypeptide of any of aspects 44-59.
  • A87 The method of aspect 86, wherein the method further comprises incubating the sample under conditions that allow for the binding of the antibody or antigen binding fragment thereof, or the polypeptide, to an antigen in the sample.
  • A88 The method of any of aspects 86-87, wherein the method comprises detecting the binding of the antigen in the sample to the antibody or antigen binding fragment thereof, or the polypeptide, optionally wherein the antigen is an S100A4 protein and/or an S100A9 protein.
  • A89 The method of any of aspects 86-88, wherein the method comprises determining the presence, abundance, and/or location of S100A4 protein and/or S100A9 protein in the sample.
  • a method of treating or preventing a disease, disorder, or condition in a subject comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of any of the antibodies listed in Table 1.
  • A91 A method of treating or preventing a disease, disorder, or condition in a subject, the method comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of the antibody S100A4-11.
  • a method of treating or preventing a disease, disorder, or condition in a subject comprising administering to a subject a therapeutic agent comprising the antibody or antigen binding fragment thereof of any of aspects 1-43, the polypeptide of any of aspects 44- 59, the composition of any of aspects 60-61, the nucleic acid(s) of any of aspects 62-64, the vector of aspect 65, the host cell of aspect 66, or the pharmaceutical composition of aspect 69.
  • A93 The method of any of aspects 90-92, wherein the disease, disorder, or condition is an autoimmune disease, or chronic inflammatory disease.
  • A94 The method of any of aspects 90-92, wherein the disease, disorder, or condition is cancer and/or metastasis thereof.
  • A95 The method of any of aspects 90-94, wherein the cancer is breast cancer or glioblastoma.
  • A96 The method of aspect 94 or 95, wherein the cancer expresses S100A4 and/or S100A9.
  • An anti-S100A4 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • S100A4-1 S
  • An anti-S100A9 antibody or antigen binding fragment thereof comprising: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3, wherein the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • S100A4-1 S
  • a bispecific antibody comprising a first antigen binding fragment capable of binding S100A4 and a second antigen binding fragment capable of binding transferrin receptor (TfR), wherein the first antigen binding fragment comprises the heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49), and the second antigen binding fragment comprises the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • TfR transferrin receptor
  • a bispecific antibody comprising: a first portion comprising an anti-S100A4 antibody comprising heavy chain complementarity determining regions (HCDRs) and light chain complementarity determining regions (LCDRs) set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49), and a second portion comprising an anti-transferrin receptor (TfR) antigen binding fragment comprising the HCDRs and LCDRs set forth in mTfR-4 (SEQ ID NOS: 73-76, DDN, and SEQ ID NO: 77).
  • HCDRs heavy chain complementarity determining regions
  • LCDRs light chain complementarity determining regions set forth in S100A4-11
  • TfR anti-transferrin receptor
  • FIGS. 1A-B show determination of S100A4 mAb bindings to human S100A4 protein using ELISA.
  • FIG. 1A S100A4 mAbs bind to human S100A4 protein (recombinantly expressed in HEK293 cells, Sinobiologicals). Expression medium containing mAbs were diluted in PBS at 1 :5 ratio of expression medium to PBS before adding to S 100A4 protein (Sino Biologicals) coated 96-well high binding plates.
  • FIG. IB Purified A4- 11 binding affinity in a concentration titration ELISA and A4-19 mAb binding affinity measured using ELISA.
  • FIG. 2 shows S 100A4 mAb binding affinity (KD , k on , k o ff rate) measurements using Octet instrument. Kinetic binding sensorgrams of S100A4 mAbs are shown and concentrations of S 100A4 (as analyte) used for fitting and calculation of KD are indicated in each graphs. Each mAb name is indicated on the top of each graph.
  • FIGS. 3A-B show epitope grouping using competition binning method with Octet instrument using protein A biosensors.
  • FIG. 3A A diagram shows steps for sequential binding of mAbl-S100A4-mAb2, as sandwich format for competition binding of S100A4.
  • FIG. 3B Pair- wise competition binding, ‘+’ for no competition binding and for competitive binding to S100A4.
  • FIG. 4 shows binding properties of S100A4 antibodies to other S100 family members and mouse S100A4 protein cross reactivity assay. Binding of S100A4 monoclonal antibodies to other SI 00 family member proteins and mouse S100A4 protein (mS100A4) were assayed using ELISA at 1 , 5, or 20 pg/ml antibody concentrations and S 100A member proteins were coated at 2pg/ml in 96 well high binding plates. Antibody binding signals were detected using anti-human antibody with HRP conjugation (Jackson ImmunoResearch). TMB substrate was used for absorbance (OD450) measurements.
  • FIGS. 5A-B show a functional screen for S100A4 blocking antibodies using the chick dorsal root ganglion neurite outgrowth assay.
  • Dorsal root ganglia were harvested from 7- day-old chicken embryos and cultured with soluble S100A4 protein.
  • IgG and rabbit 114 monoclonal S100A4 antibodies against human S100A4 protein were mixed with exogenous S100A4 and collagen matrix and cultured for 3 days.
  • DRG were fixed and stained with P3 - Tubulin antibody to measure the lengths of the neurites growth (FIG. 5A). Seven S100A4 antibody clones was showed that the reduction in neurite outgrowth enhanced by soluble S100A4 protein (FIG. 5B).
  • FIGS. 6A-D show results from experiments determining the effect of anti-S100A4 monoclonal antibody treatment on lung metastasis in MMTV-PyMT, an exemplary mouse model of breast cancer.
  • FIG. 6A shows the timeline of treatment with control IgG or anti- S100A4 antibodies, and harvesting and analysis of samples.
  • FIG. 6B shows the total number of lung nodules in the lung tissue in animals treated with control IgG or the indicated anti- S100A4 antibody.
  • FIG. 6C shows representative images of lungs from different treatment groups, fixed in Bouin’s solution.
  • FIG. 6D shows H&E staining and polyomavirus middle T antibody staining in lung metastatic nodules from representative IgG control and S100A4-11 antibody treated mice.
  • FIGS. 7A-C show results from experiments to determine the effect of anti-S 100A4 monoclonal antibody treatment on lung metastasis in 4T1, an exemplary mouse model of breast cancer.
  • FIG. 7A shows the timeline of treatment with control IgG or anti-S 100A4 antibodies, and harvesting and analysis of samples.
  • FIG. 7B shows the total number of lung nodules in the lung tissue in animals treated with control IgG or the indicated anti-S 100A4 antibody.
  • FIG. 7C shows representative images of lungs from the indicated treatment groups. Scale bar represents 5mm. The Kruskal- Wallis test was applied for statistical analysis (* P ⁇ 0.05).
  • FIGS. 8A-K show results from experiments assessing immune cells following administration of anti-S 100A4 antibodies in MMTV-PyMT mice.
  • FIG. 8A shows exemplary flow cytometry plots following IgG or S100A4-11 administration. Proportions of cells expressing indicated markers are shown for blood (FIGS. 8B-8C), breast tumor (FIGS. 8D- G) and lung metastases (FIGS. 8H-K) are shown. Ordinary one-way ANOVA was applied for statistical analysis. * P ⁇ 0.05; ** P ⁇ 0.01; *** P ⁇ 0.001.
  • FIGS. 9A-G show results from experiments assessing macrophages following administration of anti-S 100A4 antibodies in 4T1 (FIGS. 9A-D) and MMTV-PyMT (FIGS. 9E-G) mice.
  • FIG. 9A and FIG. 9B show reduction of CD 163+ (FIG. 9A) and CD206+ (FIG. 9B) macrophages in 4T1 breast tumor.
  • FIG. 9C shows flow cytometry analysis of breast tumor tissues.
  • FIG. 9D shows immunofluorescence images of tissue following IgG or S100A4-11 administration.
  • FIG. 9E shows immunofluorescence images of tissue in MMTV-PyMT breast tumor to assess CD 163+ and CD206+ macrophages following IgG or S100A4-11 administration.
  • FIG. 9F and FIG. 9G show flow cytometry analysis of breast tumor tissues. Ordinary one-way ANOVA analysis was applied (* P ⁇ 0.05).
  • FIGS. 10A-N show results from experiments assessing the effect of anti-S 100A4 monoclonal antibody treatment on the pre-metastatic niche in the lung.
  • FIG. 10A shows infiltrating PMN-MDSC cell frequency in the lungs of 4T1 tumor bearing mice, compared to BALB/c control, at an early time point (day 14, prior to presence of detectable macro metastases).
  • FIGS. 10B-D show S100a8 (FIG. 10B), S100a9 (FIG. 10C), and S100a4 (FIG. 10D) mRNA expression in the lung in indicated mice.
  • FIG. 10E shows PMN-MDSC frequency in the lungs of control or S100A4-11 treated 4Tl-tumor bearing mice at day 14.
  • FIG. 10F-H show S100a8 (FIG. 10F), S100a9 (FIG. 10G), and S100a4 (FIG. 10H) expression levels.
  • FIG. 101 shows immunofluorescence analysis of Ly6G+S100A8+ and Ly6G+S100A9+ cells in the lung of IgG vs. S100A4-11 treated 4T1 tumor bearing mice.
  • FIGS. 10J -M show quantified frequencies of cells according to indicated expression in lungs of indicated mice, including percentage of S100A8+ out of Ly6g+ cells (FIG. 10J), S100A9+ out of Ly6g+ cells (FIG. 10K), S100A8+/Ly6g+ out of total cells (FIG.
  • FIG. 10L shows immunohistochemical analysis with an antibody against MPO (myeloperoxidase), a neutrophil activation marker, in lung tissue of IgG or S100A4-11 treated mice. Arrows point to MPO+ cells. Immunofluorescence analyses were conducted from lungs of three mice per treatment group, and three paraffin sections from each mouse. More than 1,500 cells total cells were analyzed per treatment group.
  • MPO myeloperoxidase
  • FIG. ION shows immunohistochemical analysis with an antibody against MPO (myeloperoxidase), a neutrophil activation marker, in lung tissue of IgG or S100A4-11 treated mice. Arrows point to MPO+ cells. Immunofluorescence analyses were conducted from lungs of three mice per treatment group, and three paraffin sections from each mouse. More than 1,500 cells total cells were analyzed per treatment group.
  • FIGS. 11A-I show results from experiments assessing the effect of anti-S100A4 monoclonal antibody treatment on chemokine and cytokine expression in the pre-metastatic lung.
  • FIG. 11A shows the antibody treatment schedule and harvesting time point.
  • FIG. 11B shows lung tissue lysates from day 14 4T1 tumor bearing mice were analyzed with a cytokine array.
  • FIG. 11C shows ten statistically significantly expressed proteins that were identified in replicate experiments.
  • FIG. 11D shows immunohistochemical analysis of MMP9, in the lungs of S100A4-11 treated mice and IgG controls.
  • FIGS. 11E-F show expression levels of MMP9 protein as assessed by western blot analysis (FIG.
  • FIG. 11G shows immunofluorescence images following Ly6g and MMP9 double staining to identify Ly6g+MMP+ double-positive cells in control and S100A4-11 treated lungs.
  • FIG. 11H shows quantification of the Ly6g+MMP+ double-positive cells. The study had three mice per treatment group and analyzed three paraffin sections.
  • FIG. HI shows a working model of how S100A4-11 antibody treatment blocks priming of the lung niche by suppressing granulocyte (PMN-MDSC and neutrophils) infiltration and MMP9 expression in the lung, based on the described experiments and data.
  • PMN-MDSC and neutrophils granulocyte
  • FIGS. 12A-H show results from experiments assessing the effect of anti-S100A4 monoclonal antibody treatment on T cell distribution in multiple organs in the 4T1 model.
  • FIGS. 12A-B show T cell distribution in 4T1 blood (FIG. 12A) and spleen (FIG. 12B).
  • FIGS. 12C-E show T cell distributions in 4T1 tumor for CD3+ (FIG. 12C), CD4+ (FIG. 12D), and CD8+ (FIG. 12E) T cells.
  • FIGS. 12F-H show T cell distributions in 4T1 lung metastases for CD3+ (FIG. 12F), CD4+ (FIG. 12G), and CD8+ (FIG. 12H) T cells.
  • Ordinary one-way ANOVA was applied for statistical analysis. (*** P ⁇ 0.001).
  • FIGS. 13A-H show results from experiments to assess the effect of anti-S 100A4 monoclonal antibody treatment on T cell distribution in multiple organs in the MMTV-PyMT model.
  • FIGS. 13A-B show T cell distribution in blood (FIG. 13A) and spleen (FIG. 13B).
  • FIGS. 13C-E show T cell distributions in tumor for CD3+ (FIG. 13C), CD4+ (FIG. 13D), and CD8+ (FIG. 13E) T cells.
  • FIGS. 13F-H show T cell distributions in lung metastases for CD3+ (FIG. 13F), CD4+ (FIG. 13G), and CD8+ (FIG. 13H) T cells.
  • Statistical analysis was performed using ordinary one-way ANOVA. (*** P ⁇ 0.001).
  • FIGS. 14A-F show results from experiments to assess the effect of S100A4-11 treatment on PD-1 expression on the T cells in the blood of 4T1 (FIGS. 14A-C) and MMTV- PyMT (FIGS. 14D-F) mice.
  • FIGS. 14A-C show the percentage PD-1+ cells out of CD3+ (FIG. 14A), CD4+ (FIG. 14B), or CD8+ (FIG. 14C) T cells in 4T1 blood.
  • FIGS. 14D-F show the percentage PD-1+ cells out of CD3+ (FIG. 14D), CD4+ (FIG. 14E), or CD8+ (FIG. 14F) T cells in MMTV-PyMT blood.
  • FIGS. 15A-D show results from experiments assessing systemic administration of a bispecific anti-S100A4/anti-TfR (BsA) antibody in a glioblastoma mouse model.
  • FIG. 15A representative double immunofluorescence 20x confocal microscopy imaging of a mouse glioma (x5459) tumor region in brain stained with polyclonal S100A4 antibody, anti-human Fc conjugated Alexa Fluor 594 antibody, and DAPI at 24 hours post treatment with S100A4- 11 antibody or BsA antibody. Scale bar: 100 pm.
  • FIG. 15A representative double immunofluorescence 20x confocal microscopy imaging of a mouse glioma (x5459) tumor region in brain stained with polyclonal S100A4 antibody, anti-human Fc conjugated Alexa Fluor 594 antibody, and DAPI at 24 hours post treatment with S100A4- 11 antibody or BsA antibody. Scale bar: 100 pm.
  • FIG. 15A representative double
  • FIG. 15B lOOx confocal microscopy imaging of x5459 tumor region in brain. Z-stack was taken and presented as a maximum intensity projection 3 side slice image.
  • FIG. 15C Representative immunofluorescence image of x5459 murine intracranial glioma stained with a SOX2 antibody (green). Scale bar: 100 pm.
  • FIG. 16A-D show results from experiments using a bi-valent S100A4 antibody (BsA).
  • FIG. 16A Bi-valent S100A4 antibody.
  • FIG. 16B-C Representative IF confocal images of mouse x5459 glioma stained for S100A4 and Human IgG at 24 hours post treatment with S100A4 monoclonal or BsA antibody.
  • Panel c shows 3side compressed Z-stacks from confocal images with XY and XZ plane view of slice shown on the side (co-expression in orange).
  • BsA has human Fc region and detected with anti-human Fc.
  • FIG. 16C BsA and mAb concentration in serum and brain post treatment as measured by ELISA.
  • FIG. 17A-D show results from experiments using BsA.
  • FIG. 17A Representative 20x confocal IF of BsA and IgG treated endpoint x5459 tumors.
  • FIG. 17C and FIG. 17D UMAP representation of intratumor CD45+ CDl lb+ myeloid cells and CD45+ CD 11b- lymphocytes from spectral flow cytometry data, with respective scaled heatmap of protein expression by cluster.
  • FIG. 18A-D show results from experiments using BsA.
  • FIG. 18A Representative lOOx confocal IF of BsA and IgG treated endpoint x5459 tumors
  • FIG. 18C Representative 20x confocal immunofluorescence microscopy (Z stack) of BsA and IgG treated endpoint x5459 tumors
  • FIG. 18D Sphere formation assay. 3000 cells plated per well in tumor stem cell media at 1 cell/pL concentration, 3 technical replicates/group. Cells treated with 100 ng/mL of IgG, mAb, or BsA. At day 7, spheres were counted to determine % sphere forming cells.
  • FIG. 19A-C shows results from experiments using BsA.
  • FIG. 19A Gene set enrichment analysis (GSEA) for hallmark gene sets of differentially expressed genes from bulk RNAseq of IgG and BsA treated x5459 tumors.
  • FIG. 19B GSEA for Biocarta gene sets.
  • FIG. 19C Survival curve of B6 mice (males and females) orthotopically injected with x5459 tumor cells.
  • GSEA Gene set enrichment analysis
  • Cancer is a major cause of death worldwide. Due to earlier detection and effective treatment, overall survival for some cancers, such as breast and colon cancer, has increased significantly in the last decade. However, only limited progress has been made to treat metastatic diseases which account for ⁇ 90% of cancer-related deaths (Fares et al. Molecular principles of metastasis: a hallmark of cancer revisited. Signal Transduct Target Ther. 2020;5(l):28; Steeg et al. Metastasis: a therapeutic target for cancer. Nat Clin Pract Oncol. 2008;5(4):206-19).
  • tumor cells During the metastatic process, primary tumor cells leave the original primary tumor, intravasate into blood vessel, survive and migrate in circulation, extravasate into secondary tissue, and arrest in capillary bed and proliferate. Once in the target organ, tumor cells must overcome short nutrient supply and escape host immune surveillance. To facilitate this, cancer cells mobilize immune cells such as neutrophils to prime the target metastatic organ to prepare the pre-metastatic niche.
  • S100A4 also known as mestasin and fibroblast specific protein 1 (FSP1), is an important member of the S100 protein family, and mediator of metastasis in multiple cancers.
  • S100A4 promotes epithelial-mesenchymal transition, angiogenesis, cancer metastasis and sternness in multiple cancer types, including breast, brain, and colorectal cancer.
  • S100A4 expression in immune cells promotes immune suppressive phenotypes and high levels of S100A4 expression is associated with poor survival in many human cancers (Ismail et al. S100A4 Elevation Empowers Expression of Metastasis Effector Molecules in Human Breast Cancer. Cancer Res. 2017;77(3):780-9; Chow et al.
  • S100A4 Is a Biomarker and Regulator of Glioma Stem Cells That Is Critical for Mesenchymal Transition in Glioblastoma. Cancer Res. 2017;77(19):5360-73; Cho et al. Overexpression of S100A4 is closely associated with progression of colorectal cancer. World J Gastroenterol. 2005;l l(31):4852-6; Gongoil et al. Prognostic significance of calcium-binding protein S100A4 in colorectal cancer. Gastroenterology . 2002 ;123(5):1478-84).
  • the inventors discovered a panel of monoclonal antibodies (mAbs) that target S100A4 and neutralize S100A4 function in vivo. In some cases, the mAbs also targeted S100A9. The mAbs showed modulation of the premetastatic niche and tumor immune microenvironment, and increased antitumor immune activities in in vivo tumor models. The data suggest the utility of the antibodies in the development of therapies for treating and/or preventing cancer or metastasis thereof.
  • antibodies and antigen binding fragments thereof that bind to human S100A4, and related methods and compositions.
  • the antibodies and antigen binding fragments thereof also bind to S100A9.
  • S100A4/S100A9 dual targeting antibodies or antigen binding fragments thereof.
  • the antibodies, antigen binding fragments thereof, and polypeptides described herein can be used in connection with any of the methods described herein to target either or both proteins, or may act in specific instances to target either or both proteins.
  • a method of treating or preventing a disease, disorder, or condition in a subject comprising administering the antibody or antigen binding fragment thereof.
  • the disease, disorder, or condition can be any that is associated with and/or modulated by S100A4 and/or S100A9.
  • the disease, disorder, or condition is cancer and/or metastasis thereof.
  • the disease, disorder, or condition is an autoimmune disease or chronic inflammatory disease.
  • A, B, and/or C includes: A alone, B alone, C alone, a combination of A and B, a combination of A and C, a combination of B and C, or a combination of A, B, and C.
  • A, B, and/or C includes: A alone, B alone, C alone, a combination of A and B, a combination of A and C, a combination of B and C, or a combination of A, B, and C.
  • “and/or” operates as an inclusive or.
  • compositions and methods for their use can “comprise,” “consist essentially of,” or “consist of’ any of the ingredients or steps disclosed throughout the specification. Compositions and methods “consisting essentially of’ any of the ingredients or steps disclosed limits the scope of the claim to the specified materials or steps which do not materially affect the basic and novel characteristic of the claimed invention.
  • the subject of the herein disclosed methods is a vertebrate, e.g., a mammal.
  • the subject of the herein disclosed methods can be a human, non-human primate, horse, pig, rabbit, dog, sheep, goat, cow, cat, guinea pig or rodent.
  • the subject is a human.
  • the term does not denote a particular age or sex. Thus, adult and newborn subjects, as well as fetuses, whether male or female, are intended to be covered.
  • a patient refers to a subject afflicted with a disease or disorder.
  • patient includes human and veterinary subjects.
  • Ranges may be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, also specifically contemplated and considered disclosed is the range from the one particular value and/or to the other particular value unless the context specifically indicates otherwise. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another, specifically contemplated aspect that should be considered disclosed unless the context specifically indicates otherwise. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint unless the context specifically indicates otherwise.
  • the percentage type for the lower limit value is the same as for the upper limit value of the given percentage range.
  • the percentage range of “0.01 to 0.5% w/w” means “0.01% w/w to 0.5% w/w.”
  • a number value with one or more decimal places can be rounded to the nearest whole number using standard rounding guidelines, i.e., round up if the number being rounded is 5, 6, 7, 8, or 9; and round down if the number being rounded is 0, 1, 2, 3, or 4. For example, 0.42 can be rounded to 0.4.
  • coding sequence refers to a sequence which encodes a particular protein or “encoding nucleic acid,” denotes a nucleic acid sequence which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vitro or in vivo when placed under the control of (operably linked to) appropriate regulatory sequences.
  • the boundaries of the coding sequence are determined by a start codon at the 5' (amino) terminus and a translation stop codon at the 3' (carboxy) terminus.
  • a coding sequence can include, but is not limited to, cDNA from prokaryotic or eukaryotic mRNA, genomic DNA sequences from prokaryotic or eukaryotic DNA, and even synthetic DNA sequences.
  • the term “conservative substitution” refers to replacement of one amino acid by a biologically, chemically or structurally similar residue.
  • Biologically similar means that the substitution does not destroy a biological activity.
  • Structurally similar means that the amino acids have side chains with similar length, such as alanine, glycine and serine or a similar size.
  • Chemical similarity means that the residues have the same charge or are both hydrophilic or hydrophobic.
  • Particular examples include the substitution of a hydrophobic residue, such as isoleucine, valine, leucine or methionine with another, or the substitution of one polar residue for another, such as the substitution of arginine for lysine, glutamic acid for aspartic acid or glutamine for asparagine, serine for threonine, and the like.
  • Particular examples of conservative substitutions include the substitution of a hydrophobic residue such as isoleucine, valine, leucine or methionine for one another, the substitution of a polar residue for another, such as the substitution of arginine for lysine, glutamic acid for aspartic acid, or glutamine for asparagine, and the like.
  • Conservative amino acid substitutions typically include, for example, substitutions within the following groups: glycine, alanine, valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
  • a “conservative substitution” also includes the use of a substituted amino acid in place of an unsubstituted parent amino acid.
  • expression control sequence means a nucleic acid sequence that directs transcription of a nucleic acid.
  • An expression control sequence can be a promoter, such as a constitutive or an inducible promoter, or an enhancer.
  • the expression control sequence is operably linked to the nucleic acid sequence to be transcribed.
  • an “effective dosage” or “effective amount” of drug, compound, or pharmaceutical composition is an amount sufficient to affect any one or more beneficial or desired results.
  • an effective amount prevents, alleviates and/or ameliorates at least one sign and/or symptom of a disease.
  • beneficial or desired results include eliminating or reducing the risk, lessening the severity, or delaying the outset of the disease, including biochemical, histological and/or a behavioral symptom of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease.
  • beneficial or desired results include clinical results such as reducing at least one sign and/or symptom of a disease, disorder or condition, decreasing the dose of other medications required to treat the disease, enhancing the effect of another medication, and/or delaying the progression of the disease of patients.
  • An effective dosage can be administered in one or more administrations.
  • an effective dosage of drug, compound, or pharmaceutical composition is an amount sufficient to accomplish prophylactic or therapeutic treatment either directly or indirectly.
  • an effective dosage of a drug, compound, or pharmaceutical composition may or may not be achieved in conjunction with another drug, compound, or pharmaceutical composition.
  • an “effective dosage” may be considered in the context of administering one or more therapeutic agents, and a single agent may be considered to be given in an effective amount if, in conjunction with one or more other agents, a desirable result may be or is achieved.
  • the term “functional” can refer to a biological molecule in a form in which it exhibits a property and/or activity by which it is characterized.
  • a biological molecule may have two functions (i.e., bifunctional) or many functions (i.e., multifunctional).
  • the term “homologous” or “homology” can refer to two or more reference entities (e.g., nucleotide or polypeptide sequences) that share at least partial identity over a given region or fragment. For example, when an amino acid position in two peptides is occupied by identical amino acids, the peptides are homologous at that position.
  • a homologous peptide will retain activity or function associated with the unmodified or reference peptide and the modified peptide will generally have an amino acid sequence “substantially homologous” with the amino acid sequence of the unmodified sequence.
  • substantially homology or “substantial similarity,” means that when optimally aligned with appropriate insertions or deletions with another polypeptide, nucleic acid (or its complementary strand) or fragment thereof, there is sequence identity in at least about 95% to 99% of the sequence.
  • the extent of homology (identity) between two sequences can be ascertained using computer program or mathematical algorithm. Such algorithms that calculate percent sequence homology (or identity) generally account for sequence gaps and mismatches over the comparison region or area. Exemplary programs and algorithms are provided below.
  • host cell can be used interchangeably and mean an individual cell or cell culture that can be or has been a recipient for vector(s) for incorporation of polynucleotide inserts.
  • Host cells include “transformants,” “transformed cells,” and “transduced cells,” which include the primary transformed or transduced cell and progeny derived therefrom without regard to the number of passages.
  • Host cell progeny may not necessarily be completely identical (in morphology or in genomic DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation.
  • a host cell includes cells transfected and/or transformed in vivo with a polynucleotide of this invention (e.g., a polynucleotide encoding an amino acid sequence of an anti-S100A4 antibody).
  • identity can refer to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., DNA molecules and/or RNA molecules) and/or between polypeptide molecules. “Identity” measures the percent of identical matches between two or more sequences with gap alignments addressed by a particular mathematical model of computer programs (i.e. “algorithms”).
  • polymeric molecules are considered to be “substantially identical” to one another if their sequences are at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or 99% identical.
  • the term “specifically binds” can refer to binding with a dissociation constant (KD) of less than 100 nanomolar (nM).
  • Calculation of the percent identity of two nucleic acid or polypeptide sequences can be performed by aligning the two sequences for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second sequence for optimal alignment and non-identical sequences can be disregarded for comparison purposes).
  • the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the length of a reference sequence. The nucleotides at corresponding positions are then compared.
  • the molecules are identical at that position.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST/.
  • Other alignment programs include MegAlign® program in the Lasergene® suite of bioinformatics software (DNASTAR®, Inc., Madison, WI).
  • FASTA is Another alignment algorithm.
  • GCG Genetics Computing Group
  • Other techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc. Of particular interest are alignment programs that permit gaps in the sequence.
  • the BestFit program using the local homology algorithm of Smith and Waterman (1981, Advances in Applied Mathematics 2: 482-489) to determine sequence identity.
  • the gap generation penalty will generally range from 1 to 5, usually 2 to 4 and in some aspects will be 3.
  • the gap extension penalty will generally range from about 0.01 to 0.20 and in some instances will be 0.10.
  • the program has default parameters determined by the sequences inputted to be compared.
  • the sequence identity is determined using the default parameters determined by the program. This program is available also from Genetics Computing Group (GCG) package, from Madison, WI, USA.
  • GCG Genetics Computing Group
  • FastDB is described in Current Methods in Sequence Comparison and Analysis, Macromolecule Sequencing and Synthesis, Selected Methods and Applications, pp. 127-149, 1988, Alan R. Liss, Inc. Percent sequence identity is calculated by FastDB based upon the following parameters: Mismatch Penalty: 1.00; Gap Penalty: 1.00; Gap Size Penalty: 0.33; and Joining Penalty: 30.0.
  • similarity is a related concept, but in contrast to “identity,” refers to a measure of similarity which includes both identical matches and conservative substitution matches. Since conservative substitutions apply to polypeptides and not nucleic acid molecules, similarity only applies to polypeptide sequence comparisons. If two polypeptide sequences have, for example, 10 out of 20 identical amino acids, and the remainder are all nonconservative substitutions, then the percent identity and similarity would both be 50%. If in the same example, there are 5 more positions where there are conservative substitutions, then the percent identity remains 50%, but the percent similarity would be 75% (15 out of 20). Therefore, in cases where there are conservative substitutions, the degree of similarity between two polypeptide sequences will be higher than the percent identity between those two sequences.
  • the terms “increase,” improve,” “decrease” or “reduce” can refer to values that are relative to a baseline measurement, such as a measurement in the same individual prior to initiation of treatment described herein, or a measurement in a control individual (or multiple control individuals) in the absence of the treatment described herein.
  • a “control individual” is an individual afflicted with the same form of disease or injury as an individual being treated.
  • a “control individual” is an individual that is not afflicted with the same form of disease or injury as an individual being treated.
  • the term “isolated molecule” (where the molecule is, for example, a polypeptide, a polynucleotide, or an antibody or antigen-binding fragment thereof) means a molecule that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) is substantially free of other molecules from the same species (3) is expressed by a cell from a different species, or (4) does not occur in nature.
  • a molecule that is chemically synthesized, or expressed in a cellular system different from the cell from which it naturally originates will be “isolated” from its naturally associated components.
  • a molecule also may be rendered substantially free of naturally associated components by isolation, using purification techniques well known in the art.
  • Molecule purity or homogeneity may be assayed by a number of means well known in the art.
  • the purity of a polypeptide sample may be assayed using polyacrylamide gel electrophoresis and staining of the gel to visualize the polypeptide using techniques well known in the art.
  • higher resolution may be provided by using HPLC or other means well known in the art for purification.
  • the term “residue” means a position in a protein and its associated amino acid identity.
  • asparagine 297 also referred to as Asn297, also referred to as N297
  • Asn297 also referred to as N297
  • N297 is a residue in a human antibody IgGl.
  • the term “subject” means a mammal, more preferably, a human. Mammals also include, but are not limited to, farm animals (e.g., cows, pigs, horses, chickens, etc.), pets, primates, horses, dogs, cats, mice and rats.
  • a subject is a patient.
  • a subject is at risk for a disease, disorder or condition.
  • a subject is a patient who has a disease, disorder or condition as described herein.
  • a subject e.g., a patient has or is suspected of having cancer.
  • substantially pure means an object species is the predominant species present (i.e., on a molar basis it is more abundant than any other individual species in the composition), and preferably a substantially purified fraction is a composition wherein the object species (e.g., a glycoprotein, including an antibody or receptor) comprises at least about 50 percent (on a molar basis) of all macromolecular species present.
  • object species e.g., a glycoprotein, including an antibody or receptor
  • a substantially pure composition will comprise more than about 80 percent of all macromolecular species present in the composition, more preferably more than about 85%, 90%, 95%, and 99%.
  • the object species is purified to essential homogeneity (contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species.
  • a substantially pure material is at least 50% pure (i.e., free from contaminants), more preferably, at least 90% pure, more preferably, at least 95% pure, yet more preferably, at least 98% pure, and most preferably, at least 99% pure.
  • Polypeptide or antibody “fragments” or “portions” according to the invention may be made by truncation, e.g. by removal of one or more amino acids from the N and/or C- terminal ends of a polypeptide.
  • One, 2, 3, 4, 5, up to 10, up to 20, up to 30, up to 40 or more amino acids may be removed from the N and/or C terminus in this way. Fragments may also be generated by one or more internal deletions.
  • nucleic acid sequence and “nucleotide sequence,” refer interchangeably to any molecule composed of or comprising nucleotides.
  • a nucleic acid may be an oligonucleotide or a polynucleotide.
  • a nucleotide sequence may be a DNA or RNA (e.g., genomic DNA, cDNA, antisense DNA, mRNA, tRNA, rRNA, etc.).
  • a nucleotide sequence may be chemically modified or artificial.
  • Nucleotide sequences include peptide nucleic acids (PNA), mopholinos and locked nucleic acids (LNA), as well as glycol nucleic acids (GNA) and threose nucleic acids (TNA). Each of these sequences is distinguished from naturally- occurring DNA or RNA by changes to the backbone of the molecule. Also, phoshorothioate nucleotides may be used.
  • deoxynucleotide analogs include methylphosphonates, phosphoramidates, phosphorodithioates, N3’-P5’-phosphoramidates, and oligoribonucleotide phosphorothioates and their 2’-0-allyl analogs and 2’-0-methylribonucleotide methylphosphonates which may be used in a nucleotide sequence of the disclosure.
  • nucleic acid construct refers to a non-naturally occurring nucleic acid molecule resulting from the use of recombinant DNA technology (e.g., a recombinant nucleic acid).
  • a nucleic acid construct is a nucleic acid molecule, either single or double stranded, which has been modified to contain segments of nucleic acid sequences, which are combined and arranged in a manner not found in nature.
  • a nucleic acid construct may be a “vector” (e.g., a plasmid), that is, a nucleic acid molecule designed to deliver exogenously created DNA into a host cell.
  • operably linked can refer to a linkage of polynucleotide (or polypeptide) elements in a functional relationship.
  • a nucleic acid is operably linked when it is placed into a functional relationship with another nucleic acid sequence.
  • a promoter or other transcription regulatory sequence e.g., an enhancer
  • operably linked means that the nucleic acid sequences being linked are contiguous.
  • operably linked does not mean that the nucleic acid sequences are contiguously linked, rather intervening sequences are between those nucleic acid sequences that are linked.
  • polynucleotide (also referred to herein as a “nucleic acid molecule”) refers to a sequence of nucleotides connected by phosphodiester linkages. Polynucleotides are presented herein in the direction from the 5’ to the 3’ direction.
  • a polynucleotide of the present disclosure can be a deoxyribonucleic acid (DNA) molecule or ribonucleic acid (RNA) molecule and refers to all forms of a nucleic acid such as, double stranded molecules, single stranded molecules, small or short hairpin RNA (shRNA), micro RNA, small or short interfering RNA (siRNA), trans- splicing RNA, antisense RNA.
  • a polynucleotide is a DNA molecule, that molecule can be a gene, a cDNA, an antisense molecule or a fragment of any of the foregoing molecules.
  • Nucleotide bases are indicated herein by a single letter code: adenine (A), guanine (G), thymine (T), cytosine (C), inosine (I) and uracil (U).
  • a polynucleotide of the present disclosure can be prepared using standard techniques well known to one of skill in the art.
  • polypeptide As used herein, the terms “polypeptide,” “protein” and “peptide” encoded by a polynucleotide (nucleic acid sequence or nucleotide sequence) refer to full-length native sequences, as with naturally occurring proteins, as well as functional subsequences, modified forms or sequence variants so long as the subsequence, modified form or variant retains some degree of functionality of the native full-length protein.
  • prevention refers to delay of onset, and/or reduction in frequency and/or severity of at least one sign and/or symptom of a particular disease, disorder or condition. In some aspects, prevention is assessed on a population basis such that an agent is considered to “prevent” a particular disease, disorder or condition if a statistically significant decrease in the development, frequency and/or intensity of one or more symptoms of the disease, disorder or condition is observed in a population susceptible to the disease, disorder or condition. Prevention may be considered complete when onset of disease, disorder or condition has been delayed for a predefined period of time.
  • the term “recombinant,” refers to a vector, polynucleotide, polypeptide or cell that is the product of various combinations of cloning, restriction or ligation steps (e.g. relating to a polynucleotide or polypeptide comprised therein), and/or other procedures that result in a construct that is distinct from a product found in nature.
  • the terms “treat” or “treatment” means to administer a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and/or reduces incidence of one or more symptoms, features and/or causes of a particular disease, disorder and/or condition (e.g., cancer).
  • beneficial or desired clinical results include decreased extent of damage from the disease, decreased duration of the disease, and/or reduction in the number, extent, or duration of a symptom related to the disease.
  • the term includes the administration of a compound or agent of the present invention to prevent or delay the onset of a symptom, complication, or biochemical indicia of a disease, alleviating a symptom or arresting or inhibiting further development of a disease, condition, or disorder.
  • Treatment may be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of a clinical or subclinical symptom thereof) or therapeutic suppression or alleviation of a symptom after the manifestation of the disease.
  • the term does not include prophylactic administration (i.e, the term does not include preventing or delaying the onset of the disease or preventing the manifestation of a clinical or subclinical symptom thereof).
  • the disease, condition or disorder is cancer.
  • aspects of the disclosure relate to antibodies, antigen binding fragments thereof, or polypeptides capable of specifically binding to an S100A4 protein.
  • the antibodies, antigen binding fragments thereof, or polypeptides may be capable of binding S100A9 protein.
  • S100A4 is a gene that encodes the S100A4 protein (in humans, also known as
  • S100-A4 Calvasculin; Metastasin; Placental calcium-binding protein; Protein Mtsl; S100 calcium-binding protein A4; Fibroblast Specific Protein 1).
  • An exemplary human S100A4 protein comprises the amino acid sequence: MACPLEKALDVMVSTFHKYSGKEGDKFKLNKSELKELLTRELPSFLGKRTDEAAFQ KLMSNLDSNRDNEVDFQEYCVFLSCIAMMCNEFFEGFPDKQPRKK, and is set forth in SEQ ID NO: 78.
  • S100A4 is a calcium-binding protein that plays a role in various intracellular and extracellular processes including motility, angiogenesis, cell differentiation, apoptosis, and autophagy. S100A4 plays various roles, including affecting cancer stem cell maintenance, regulation of mesenchymal transition, cytokine production and immune cell migration.
  • S100A9 is a gene that encodes S100A9 protein (in humans, also known as
  • Calgranulin-B Calprotectin L1H subunit; Leukocyte LI complex heavy chain; Migration inhibitory factor-related protein 14 (MRP-14; pl4); S100 calcium-binding protein A9).
  • An exemplary human S100A9 protein comprises the amino acid sequence: MTCKMSQLERNIETIINTFHQYSVKLGHPDTLNQGEFKELVRKDLQNFLKKENKNEK VIEHIMEDLDTNADKQLSFEEFIMLMARLTWASHEKMHEGDEGPGHHHKPGLGEGT P, and is set forth in SEQ ID NO: 79.
  • S100A9 plays various roles, including in regulation of inflammatory processes.
  • an antibody or antigen binding fragment thereof is specific for and/or binds to S100A4 (e.g., the antibody is an anti-S100A4 antibody).
  • the antibody or antigen binding fragment thereof comprises: a) heavy chain complementarity determining regions (HCDRs) HCDR1, HCDR2, and HCDR3; and b) light chain complementarity determining regions (LCDRs) LCDR1, LCDR2, and LCDR3.
  • the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4- 19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63), or sequences having at least 80% sequence identity thereto.
  • S100A4-1 SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7
  • S100A4-5 SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21
  • S100A4-9 SEQ ID NOS: 31-34, AAS,
  • the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • S100A4-1 SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7
  • S100A4-5 SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21
  • S100A4-9 SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35
  • S100A4-11
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in: S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7); S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21); S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35); S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49); or S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively are set forth in S100A4-1 (SEQ ID NOS: 3-6, KAS, and SEQ ID NO: 7). In some aspects, the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-5 (SEQ ID NOS: 17-20, KAS, and SEQ ID NO: 21).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively are set forth in S100A4-9 (SEQ ID NOS: 31-34, AAS, and SEQ ID NO: 35). In some aspects, the amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-11 (SEQ ID NOS: 45-48, KAS, and SEQ ID NO: 49).
  • amino acid sequences of the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, are set forth in S100A4-19 (SEQ ID NOS: 59-62, KAS, and SEQ ID NO: 63).
  • the antibody or antigen binding fragment thereof comprises a heavy chain variable region and a light chain variable region, respectively, comprising the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4- 11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58), or sequences having at least 70%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity thereto.
  • the heavy chain variable region and light chain variable region respectively, comprise the amino acid sequences set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58).
  • amino acid sequences of the heavy chain variable region and light chain variable region are set forth in: S100A4-1 (SEQ ID NOS: 1 and 2); S100A4-5 (SEQ ID NOS: 15 and 16); S100A4-9 (SEQ ID NOS: 29 and 30); S100A4-11 (SEQ ID NOS: 43 and 44); or S100A4-19 (SEQ ID NOS: 57 and 58).
  • amino acid sequences of the heavy chain variable region and light chain variable region, respectively are set forth in S100A4-1 (SEQ ID NOS: 1 and 2).
  • the amino acid sequences of the heavy chain variable region and light chain variable region, respectively are set forth in S100A4-5 (SEQ ID NOS: 15 and 16). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-9 (SEQ ID NOS: 29 and 30). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-11 (SEQ ID NOS: 43 and 44). In some aspects, the amino acid sequences of the heavy chain variable region and light chain variable region, respectively, are set forth in S100A4-19 (SEQ ID NOS: 57 and 58). In some aspects, CDRs (e.g.
  • the HCDRs and LCDRs of the antibodies and antigen binding fragments provided herein can be identified from the heavy chain and light chain of any of the anti-S100A4 antibodies provided herein, using any suitable method. For example, various methods are known in the art for determining the CDRs of antibodies based on antibody amino acid sequences (e.g. heavy chain variable region and light chain variable region sequences), as described herein. Other elements of the antibodies (e.g. framework regions) can also be identified using standard analysis methods. In some aspects, the term “respectively,” when referring to listed elements such as CDRs and corresponding listed sequences, denotes that the order of the listed range of sequences corresponds to the order of the listed CDRs.
  • the HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, and LCDR3, respectively, comprise the amino acid sequences set forth in: SEQ ID NOS:3-8” means that HCDR1 comprises the amino acid sequence set forth in SEQ ID NO:3, HCDR2 comprises the amino acid sequence set forth in SEQ ID NO:4, and so forth.
  • HCDR1 comprises the amino acid sequence set forth in SEQ ID NO:3
  • HCDR2 comprises the amino acid sequence set forth in SEQ ID NO:4, and so forth.
  • one skilled in the art would also readily recognize based on the disclosure provided herein which of the listed sequences correspond to which of the listed elements, since the sequences are designated (e.g. in Table 1) as specific elements (e.g. HCDR1, HCDR2, and so on).
  • antibodies and related molecules such antigen binding fragments of the antibodies, and polypeptides comprising the antigen binding fragments, that bind to S100A4.
  • the antibody or antigen binding fragment thereof specifically binds to S100A4 protein.
  • the antibody or antigen binding fragment thereof specifically binds to human S100A4 protein.
  • the antibody or antigen binding fragment thereof binds to human S 100A4 protein with a higher binding affinity than to S100A4 protein from another species, such as mouse S100A4 protein.
  • the antibody or antigen binding fragment thereof binds human S100A4 protein with a dissociation constant (KD) of less than 100 nanomolar (nM), less than 10 nM, less than 5 nM, or less than 1 nM. In some aspects, the antibody or antigen binding fragment thereof binds human S100A4 protein with a KD of between about 100 nM and about 1 picomolar (pM). In some aspects, the antibody or antigen binding fragment thereof binds human S100A4 protein with a KD of at or about 1 nanomolar (nM).
  • KD dissociation constant
  • the anti-S100A4 antibody or antigen binding fragment thereof is cross-reactive with S100A9.
  • the anti-S100A4 antibody binds or is capable of binding S100A4 and S100A9.
  • the anti-S100A4 antibody recognizes and/or is specific for both S100A4 and S100A9.
  • the antibody may provide a therapeutic effect by binding S100A4 and/or S100A9.
  • the antibody is a blocking antibody.
  • a blocking antibody is an antibody that binds to a target molecule and prevents the target molecule from interacting with other molecules and/or prevents the endogenous action of the target molecule.
  • a blocking antibody does not stimulate an immune reaction against the target molecule.
  • the antibody or antigen binding fragment thereof blocks, inhibits, or modifies the function of S100A4 protein.
  • the antibody or antigen binding fragment thereof binds to and inhibits the activity of SI 00 A4 protein, such as in vitro or in vivo in a subject.
  • inhibiting the activity of S100A4 by administration of the antibody or antigen binding fragment thereof can treat or prevent cancer or metastasis thereof.
  • the antibody or antigen binding fragment thereof blocks, inhibits, or modifies the function of S100A9 protein.
  • the antibody or antigen binding fragment thereof binds to and inhibits the activity of S100A9 protein, such as in vitro or in vivo in a subject.
  • inhibiting the activity of S100A9 by administration of the antibody or antigen binding fragment thereof can treat or prevent cancer or metastasis thereof.
  • the antibody is a human antibody, humanized antibody, recombinant antibody, chimeric antibody, an antibody derivative, a veneered antibody, a diabody, a monoclonal antibody, a single domain antibody, or a single chain antibody.
  • the antibody or antigen binding fragment thereof is humanized.
  • the humanized antibody can be derived from any suitable non-human species, such as rabbit or mouse.
  • a monoclonal antibody against a human protein can be developed in a non-human animal (e.g. rabbit or mouse) by immunizing the animal with the protein (e.g. S 100A4 or S 100A9) and isolating monoclonal antibodies that react with the protein.
  • the amino acid sequences of the antibody can be determined, and portions of the antibody sequence (e.g. constant regions) can be modified to reflect sequences present in human antibodies. Such modifications generally preserve the specificity of the antibody to its target, while reducing the possibility of an immune reaction against the antibody when administered to a human subject. Any suitable methods for humanizing antibodies are known and can be readily carried out by one having skill in the art.
  • antigen binding fragments of the antibodies provided herein such as an antigen binding fragment of an antibody that binds S100A4. Any suitable antigen binding fragment of an antibody may be used.
  • the antigen binding fragment of the antibody is a single chain variable fragment (scFv), F(ab’)2, Fab’, Fab, Fv, or IgG.
  • polypeptides such as polypeptides comprising one or more of the antibodies or antigen binding fragments thereof described herein.
  • the polypeptide comprises at least two antigen binding fragments, wherein each antigen binding fragment is independently selected from any of the antigen binding fragments provided herein.
  • the polypeptide can be multivalent and/or bispecific.
  • the polypeptide is multivalent.
  • the multivalent polypeptide can comprise two or more different antigen binding fragments, each being from a different antibody.
  • the polypeptide is bispecific.
  • the bispecific polypeptide can comprise two different antigen binding fragments, each being from a different antibody.
  • the polypeptide can be trispecific.
  • the multivalent or bispecific antibody comprises at least one antigen binding fragment that binds S100A4.
  • the multivalent or bispecific antibody comprises at least one antigen binding fragment that binds an epitope that is not from S 100A4.
  • the bispecific antibody comprises an antigen binding fragment that binds S100A4 and an antigen binding fragment that binds an epitope from a different protein.
  • bispecific and multivalent polypeptides and/or engineered antibodies may have increased specificity, affinity, or therapeutic effectiveness (e.g. for blocking the activity of S100A4), or ability to localize to specific tissues, sites, tumors, and microenvironments.
  • ADCs antibody-drug conjugates
  • the antibody-drug conjugates provided herein can comprise any of the polypeptides, antibodies or antigen-binding fragments thereof, multivalent antibodies, or bispecific antibodies provided herein.
  • a bispecific antibody that binds S100A4 and Transferrin Receptor (TfR), i.e. a bispecific anti-S 100A4/TfR antibody (also referred to as BsA in the Examples).
  • TfR Transferrin Receptor
  • the bispecific antibody comprises a first portion comprising any anti-S 100A4 antibody or anti-S 100A9 antibody described herein, and a second portion that binds a different protein.
  • the second portion can be fused to the first portion.
  • the second portion can be an antigen binding domain, such as a single-chain variable fragment (scFv) fused to the heavy chain C-terminus of the anti-S 100A4 antibody or the anti-S 100A9 antibody.
  • the second portion binds TfR.
  • the second portion is an anti-TfR scFv fused to the heavy chain C-terminus of the anti- S100A4 antibody or the anti-S 100A9 antibody.
  • the antibody comprises (i) an antigen binding fragment that binds S100A4 or S100A9, and (ii) an antigen binding fragment that binds TfR.
  • the bispecific anti-S 100A4/TfR antibody or the bispecific anti- S100A9/TfR antibody is capable of crossing the blood-brain barrier (BBB).
  • BBB blood-brain barrier
  • systemic administration of the antibody can result in localization of the antibody to brain tissue.
  • crossing the BBB and localization of the antibody in brain tissue provides therapeutic utility.
  • localization to brain tissue can allow the antibody to have therapeutic utility in treating conditions affecting the brain, such as brain cancer, such as glioblastoma.
  • a method of treating brain cancer, such as glioblastoma comprising administration of the bispecific anti-S100A4/TfR antibody.
  • the bispecific anti-S100A4/TfR antibody or the bispecific anti-S100A9/TfR antibody is also capable of uptake into cells, such as cells expressing transferrin receptor.
  • the bispecific anti-S100A4/TfR antibody is internalized into tumor cells, such as glioblastoma cells, which may include glioma stem cells.
  • the bispecific antibody can bind to and inhibit activity of S100A4 protein or S100A9 protein intracellularly. Such intracellular delivery may further enhance the therapeutic effect of the bispecific antibody.
  • TfR antibody or antigen binding fragment thereof may be used in connection with the compositions and methods provided herein, including in the bispecific anti-S100A4/TfR antibody or the bispecific anti-S100A9/TfR antibody described above and in Example 8.
  • Suitable anti-TfR antibodies and antigen binding fragments thereof are described, for example, in WO2023039611A2, which is incorporated by reference herein in its entirety.
  • the TfR antibody or antigen binding fragment thereof can comprise any of the sequences set forth in Tables 2-5.
  • the TfR antibody or antigen binding fragement thereof can comprise a heavy chain sequence set forth in Table 2 and a light chain sequence set forth in Table 3, or HCDRs and LCDRs therefrom, such as the HCDRs and LCDRs set forth in Tables 4 and 5, respectively.
  • the heavy chain and light chain are from the same antibody source (e.g. shown as “(mAb Source)” in Tables 2-5).
  • the TfR antibody or antigen binding fragment thereof comprises HCDRs from a heavy chain amino acid sequence set forth in Table 2 and LCDRs from a light chain amino acid sequence set forth in Table 3, wherein the heavy chain and light chain amino acid sequences are from the same antibody source.
  • the TfR antibody or antigen binding fragment thereof comprises HCDRs from the heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and LCDRs from the light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • the TfR antibody or antigen binding fragment thereof comprises HCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NOS: 73-75) and LCDRs comprising the sequences set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • the TfR antibody or antigen binding fragment thereof comprises a heavy chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and a light chain comprising the amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72).
  • compositions comprising any of the antibodies, antigen binding fragments thereof, or polypeptides provided herein.
  • the composition is a pharmaceutical composition.
  • the composition comprises a pharmaceutical excipient.
  • the composition is formulated for administration to a subject.
  • the composition is formulated for administration to a subject via parenteral, intravenous, subcutaneous, intramuscular, or intranasal administration.
  • nucleic acids such as one or more nucleic acids encoding any of the antibody or antigen binding fragments or polypeptides provided herein.
  • the nucleic acid encodes an antibody heavy chain.
  • the nucleic acid has at least 70%, 80%, 85%, 90%, 95%, 99%, or 100% (or any derivable range therein) sequence identity to one of SEQ ID NOS: 8, 22, 36, 50, and 64.
  • the nucleic acid encodes an antibody light chain.
  • the nucleic acid has at least 70%, 80%, 85%, 90%, 95%, 99%, or 100% (or any derivable range therein) sequence identity to one of SEQ ID NOS: 9, 23, 37, 51, and 65.
  • provided herein is a vector comprising any of the nucleic acids provided herein.
  • a host cell comprising any of the nucleic acids or vectors provided herein.
  • a method of making an antibody, antigen binding fragment thereof, or polypeptide comprising culturing the host cell under conditions that allow the host cell to express the antibody, antigen binding fragment thereof, or polypeptide. The method can further comprise isolating the expressed antibody, antigen binding fragment thereof, or polypeptide.
  • the compositions provided herein can be used as or in connection with a method of treating or preventing a disease, disorder, or condition in a subject.
  • the method comprises administering to the subject a therapeutically effective amount of any antibody, antigen binding fragment thereof, polypeptide, composition, pharmaceutical composition, nucleic acid(s), vectors, or host cell provided herein.
  • the disease, disorder, or condition is cancer and/or metastasis thereof.
  • the antibody or antigen binding fragment thereof binds and/or inhibits the activity of S100A4 or S100A9, thereby treating the cancer and/or preventing metastasis of the cancer.
  • the cancer cells express S100A4.
  • the cancer is breast cancer.
  • the cancer is glioblastoma. In some aspects, the subject is human. In some aspects, the cancer expresses S100A4. In some aspects, the subject has been determined to have a cancer that expresses S100A4. In some aspects, the cancer expresses S100A9. In some aspects, the subject has been determined to have a cancer that expresses S100A9. In some aspects, the cancer does not need to be a cancer expressing S100A4 and/or S100A9. For example, the survival and progression of certain cancers may be facilitated by expression of S100A4 and/or S100A9 in non-cancer cells. Thus, the compositions and methods described herein can also find utility in treating cancers not expressing S100A4 and/or S100A9.
  • the subject has been diagnosed with cancer. In some aspects, the subject has been determined to be at risk for cancer or cancer metastasis. In some aspects, the subject has previously been treated for cancer. In some aspects, the cancer has been determined to be resistant to the previous treatment. In some aspects, the cancer is breast cancer. In some aspects, the cancer is glioblastoma. In some aspects, the subject is human.
  • S 100 proteins have diverse roles in health and disease, exhibit both intracellular and extracellular activity, exhibit cell- and tissue-specific expression, and are involved in a wide range of biological processes including proliferation, migration, invasion, differentiation.
  • S100 proteins such as S100A4 and S100A9 may be involved in disease.
  • elevated extracellular S100 proteins can promote pathological inflammatory responses, which can result, for example, in autoimmune conditions and inflammatory disorders.
  • S100 proteins can play important roles in cancer.
  • compositions provided herein including the anti-S100A4 antibodies and antigen-binding fragments thereof, may be used to prevent, ameliorate, or treat various diseases, conditions, and disorders.
  • methods of treating a disease, disorder or condition such as by administration of the anti-S100A4 antibodies and antigen-binding fragments thereof provided herein. Any suitable disease, condition, or disorder is envisioned in connection with the compositions and methods.
  • compositions and methods may be used to modulate immune cell trafficking and/or migration.
  • the methods may be used to modulate immune responses, such as by activating or suppressing an immune response.
  • Activating an immune response may be useful, for example, in the treatment of cancers.
  • Suppressing an immune response may be useful, for example, in the treatment of autoimmune disease or chronic inflammatory disease.
  • the disease, condition, or disorder is cancer.
  • the disease, condition, or disorder is cancer metastasis.
  • the cancer can be a solid cancer (e.g. tumor).
  • the cancer is a cancer of the blood or immune system.
  • the cancer is metastatic.
  • the cancer is refractory.
  • the cancer can be selected from the list consisting of: lung cancer, breast cancer, pancreatic cancer, colon cancer, colorectal cancer, metastatic colorectal cancer, lymphoma, leukemia, acute lymphoblastic leukemia, prostate cancer, liver cancer, hepatocellular cancer, ovarian cancer, renal cell cancer, stomach cancer, gastric cancer, skin cancer, and melanoma.
  • the cancer is breast cancer.
  • the cancer is brain cancer.
  • the cancer is glioblastoma.
  • the disease, condition, or disorder is an autoimmune disease.
  • the disease, condition, or disorder is an inflammatory condition or disease.
  • the disease, condition, or disorder is chronic inflammatory disease.
  • the disease, condition, or disorder can be selected from the list consisting of: arthritis (e.g. rheumatoid arthritis, spondyloarthritis, osteoarthritis), psoriasis, Chron’s disease, colitis, bacterial colitis, fibrosis, sclerosis, systemic sclerosis, lupus, systemic lupus erythematosus, and colon inflammation.
  • the disease, condition, or disorder is atherosclerosis.
  • the disease, condition, or disorder is chronic cellular stress.
  • the antibody or antigen binding fragment thereof can be used in a combination therapy.
  • the subject is administered an additional therapeutic in combination with the antibody or antigen binding fragment thereof.
  • the additional therapeutic can comprise a therapeutic for treating cancer, for example by a different mechanism than blocking S100A4 or S100A9 activity. Combination therapy may improve the therapeutic effectiveness of the method, for example in comparison to administering either therapeutic alone.
  • the additional therapeutic may be any suitable therapeutic for treating cancer, and may be selected according to the type of cancer and needs of the subject by a person skilled in the art.
  • the additional therapeutic is a checkpoint inhibitor.
  • a method for evaluating a biological sample such as for the presence, abundance, and/or location of S 100A4 protein and/or S 100A9 protein. Any suitable method of using the compositions provided herein to evaluate a sample and/or detect the protein in a sample may be used, and various such methods are readily available to one skilled in the art.
  • the method comprises contacting the biological sample with any antibody, antigen binding fragment thereof, or polypeptide provided herein, such as those that bind S100A4 protein or S100A9 protein.
  • the antibody or antigen binding fragment thereof, or the polypeptide is operatively linked to a detectable label.
  • the method further comprises incubating the sample under conditions that allow for the binding of the antibody or antigen binding fragment thereof, or the polypeptide, to antigens (e.g. S100A4 or S100A9 protein antigens) in the sample.
  • the method comprises detecting the binding of an antigen to the antibody or antigen binding fragment thereof, or the polypeptide.
  • the method comprises determining the presence, abundance, and/or location of S100A4 and/or SI 00A9 protein in the sample.
  • the samples is from a human subject.
  • the method can be used in connection with diagnosing the subject, and/or evaluating cells in the subject (e.g. cancer cells or suspected cancer cells from the subject). The diagnosis or evaluation may be based on the determination of the presence, abundance, and/or location of S100A4 and/or S100A9 protein in the sample, and may be made in connection with one or more additional characteristics of the sample or subject.
  • a method of treating, or preventing metastasis of, a cancer comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of any of the antibodies listed in Table 1.
  • the antibody or antigen binding fragment thereof may be or be from any one of the antibodies: S100A4-1, S100A4-5, S100A4-9, S100A4-11, or S100A4-19.
  • a method of treating, or preventing metastasis of, a cancer the method comprising administering to a subject a therapeutic agent comprising an antibody or antigen binding fragment thereof of the antibody S100A4-11.
  • provided herein is a method of treating, or preventing metastasis of, a cancer, the method comprising administering to a subject a therapeutic agent comprising any antibody or antigen binding fragment thereof, polypeptide, composition, nucleic acid(s), vector, host cell, or pharmaceutical composition provided herein.
  • the antibody is S100A4-11.
  • the antigen binding fragment is from the antibody S100A4-11.
  • the cancer is breast cancer or glioblastoma.
  • aspects of the disclosure relate to antibodies, antigen binding fragments thereof, or polypeptides capable of specifically binding to an S100A4 protein.
  • antibody refers to an intact immunoglobulin of any isotype, or a fragment thereof that can compete with the intact antibody for specific binding to the target antigen, and includes chimeric, humanized, fully human, and bispecific antibodies.
  • antibody or “immunoglobulin” are used interchangeably and refer to any of several classes of structurally related proteins that function as part of the immune response of an animal, including IgG, IgD, IgE, IgA, IgM, and related proteins, as well as polypeptides comprising antibody CDR domains that retain antigen-binding activity.
  • antigen refers to a molecule or a portion of a molecule capable of being bound by a selective binding agent, such as an antibody.
  • An antigen may possess one or more epitopes that are capable of interacting with different antibodies.
  • epitope includes any region or portion of molecule capable eliciting an immune response by binding to an immunoglobulin or to a T-cell receptor.
  • Epitope determinants may include chemically active surface groups such as amino acids, sugar side chains, phosphoryl or sulfonyl groups, and may have specific three-dimensional structural characteristics and/or specific charge characteristics.
  • antibodies specific for a particular target antigen will preferentially recognize an epitope on the target antigen within a complex mixture.
  • epitope regions of a given polypeptide can be identified using many different epitope mapping techniques are well known in the art, including: x-ray crystallography, nuclear magnetic resonance spectroscopy, site-directed mutagenesis mapping, protein display arrays, see, e.g., Epitope Mapping Protocols, (Johan Rockberg and Johan Nilvebrant, Ed., 2018) Humana Press, New York, N.Y. Such techniques are known in the art and described in, e.g., U.S. Pat. No. 4,708,871; Geysen et al. Proc. Natl. Acad. Sci. USA 81:3998-4002 (1984); Geysen et al. Proc. Natl.
  • antigenic regions of proteins can also be predicted and identified using standard antigenicity and hydropathy plots.
  • immunogenic sequence means a molecule that includes an amino acid sequence of at least one epitope such that the molecule is capable of stimulating the production of antibodies in an appropriate host.
  • immunogenic composition means a composition that comprises at least one immunogenic molecule (e.g., an antigen or carbohydrate).
  • an intact antibody is generally composed of two full-length heavy chains and two full-length light chains, but in some instances may include fewer chains, such as antibodies naturally occurring in camelids that may comprise only heavy chains.
  • Antibodies as disclosed herein may be derived solely from a single source or may be “chimeric,” that is, different portions of the antibody may be derived from two different antibodies.
  • the variable or CDR regions may be derived from a rat or murine source, while the constant region is derived from a different animal source, such as a human.
  • the antibodies or binding fragments may be produced in hybridomas, by recombinant DNA techniques, or by enzymatic or chemical cleavage of intact antibodies.
  • the term “antibody” includes derivatives, variants, fragments, and muteins thereof, examples of which are described below (Sela-Culang et al., Front Immunol. 2013; 4: 302; 2013).
  • the term “light chain” includes a full-length light chain and fragments thereof having sufficient variable region sequence to confer binding specificity.
  • a full-length light chain has a molecular weight of around 25,000 Daltons and includes a variable region domain (abbreviated herein as VL), and a constant region domain (abbreviated herein as CL).
  • VL variable region domain
  • CL constant region domain
  • VL fragment means a fragment of the light chain of a monoclonal antibody that includes all or part of the light chain variable region, including CDRs.
  • a VL fragment can further include light chain constant region sequences.
  • the variable region domain of the light chain is at the amino-terminus of the polypeptide.
  • the term “heavy chain” includes a full-length heavy chain and fragments thereof having sufficient variable region sequence to confer binding specificity.
  • a full-length heavy chain has a molecular weight of around 50,000 Daltons and includes a variable region domain (abbreviated herein as VH), and three constant region domains (abbreviated herein as CHI, CH2, and CH3).
  • VH variable region domain
  • CHI constant region domain
  • CH2 constant region domains
  • VH fragment means a fragment of the heavy chain of a monoclonal antibody that includes all or part of the heavy chain variable region, including CDRs.
  • a VH fragment can further include heavy chain constant region sequences. The number of heavy chain constant region domains will depend on the isotype.
  • the VH domain is at the amino-terminus of the polypeptide, and the CH domains are at the carboxy-terminus, with the CH3 being closest to the — COOH end.
  • the isotype of an antibody can be IgM, IgD, IgG, IgA, or IgE and is defined by the heavy chains present of which there are five classifications: mu (p), delta (5), gamma (y), alpha (a), or epsilon (a) chains, respectively.
  • IgG has several subtypes, including, but not limited to, IgGl, IgG2, IgG3, and IgG4.
  • IgM subtypes include IgMl and IgM2.
  • IgA subtypes include IgAl and IgA2.
  • Antibodies can be whole immunoglobulins of any isotype or classification, chimeric antibodies, or hybrid antibodies with specificity to two or more antigens. They may also be fragments (e.g., F(ab')2, Fab', Fab, Fv, and the like), including hybrid fragments.
  • An immunoglobulin also includes natural, synthetic, or genetically engineered proteins that act like an antibody by binding to specific antigens to form a complex.
  • the term antibody includes genetically engineered or otherwise modified forms of immunoglobulins.
  • the term “monomer” means an antibody containing only one Ig unit. Monomers are the basic functional units of antibodies.
  • the term “dimer” means an antibody containing two Ig units attached to one another via constant domains of the antibody heavy chains (the Fc, or fragment crystallizable, region). The complex may be stabilized by a joining (J) chain protein.
  • the term “multimer” means an antibody containing more than two Ig units attached to one another via constant domains of the antibody heavy chains (the Fc region). The complex may be stabilized by a joining (J) chain protein.
  • bivalent antibody means an antibody that comprises two antigenbinding sites.
  • the two binding sites may have the same antigen specificities or they may be bispecific, meaning the two antigen-binding sites have different antigen specificities.
  • Bispecific antibodies are a class of antibodies that have two paratopes with different binding sites for two or more distinct epitopes.
  • bispecific antibodies can be biparatopic, wherein a bispecific antibody may specifically recognize a different epitope from the same antigen.
  • bispecific antibodies can be constructed from a pair of different single domain antibodies termed “nanobodies”. Single domain antibodies are sourced and modified from cartilaginous fish and camelids. Nanobodies can be joined together by a linker using techniques typical to a person skilled in the art; such methods for selection and joining of nanobodies are described in PCT Publication No. WO2015044386A1, No. W02010037838A2, and Bever et al., Anal Chem. 86:7875-7882 (2014), each of which are specifically incorporated herein by reference in their entirety.
  • Bispecific antibodies can be constructed as: a whole IgG, Fab '2, Fab 'PEG, a diabody, or alternatively as scFv. Diabodies and scFvs can be constructed without an Fc region, using only variable domains, potentially reducing the effects of anti-idiotypic reaction. Bispecific antibodies may be produced by a variety of methods including, but not limited to, fusion of hybridomas or linking of Fab' fragments. See, e.g., Songsivilai and Lachmann, Clin. Exp. Immunol. 79:315-321 (1990); Kostelny et al., J. Immunol. 148:1547-1553 (1992), each of which are specifically incorporated by reference in their entirety.
  • the antigen-binding domain may be multispecific or hetero specific by multimerizing with VH and VL region pairs that bind a different antigen.
  • the antibody may bind to, or interact with, (a) a cell surface antigen, (b) an Fc receptor on the surface of an effector cell, or (c) at least one other component.
  • aspects may include, but are not limited to, bispecific, trispecific, tetraspecific, and other multispecific antibodies or antigen-binding fragments thereof that are directed to epitopes and to other targets, such as Fc receptors on effector cells.
  • multispecific antibodies can be used and directly linked via a short flexible polypeptide chain, using routine methods known in the art.
  • diabodies that are bivalent, bispecific antibodies in which the VH and VL domains are expressed on a single polypeptide chain, and utilize a linker that is too short to allow for pairing between domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain creating two antigen binding sites.
  • the linker functionality is applicable for aspects of triabodies, tetrabodies, and higher order antibody multimers, (see, e.g., Hollinger et al., Proc Natl. Acad. Sci. USA 90:6444-6448 (1993); Polijak et al., Structure 2:1121-1123 (1994); Todorovska et al., J. Immunol. Methods 248:47-66 (2001)).
  • Bispecific diabodies as opposed to bispecific whole antibodies, may also be advantageous because they can be readily constructed and expressed in E. coli.
  • Diabodies (and other polypeptides such as antibody fragments) of appropriate binding specificities can be readily selected using phage display (WO94/13804) from libraries. If one arm of the diabody is kept constant, for instance, with a specificity directed against a protein, then a library can be made where the other arm is varied and an antibody of appropriate specificity selected.
  • Bispecific whole antibodies may be made by alternative engineering methods as described in Ridgeway et al., (Protein Eng., 9:616-621, 1996) and Krah et al., (N Biotechnol. 39:167-173, 2017), each of which is hereby incorporated by reference in their entirety.
  • Heteroconjugate antibodies are composed of two covalently linked monoclonal antibodies with different specificities. See, e.g., U.S. Patent No. 6,010,902, incorporated herein by reference in its entirety.
  • the part of the Fv fragment of an antibody molecule that binds with high specificity to the epitope of the antigen may be referred to herein as the “paratope.”
  • the paratope consists of the amino acid residues that make contact with the epitope of an antigen to facilitate antigen recognition.
  • Each of the two Fv fragments of an antibody is composed of the two variable domains, VH and VL, in dimerized configuration.
  • the primary structure of each of the variable domains includes three hypervariable loops separated by, and flanked by, Framework Regions (FR).
  • the hypervariable loops are the regions of highest primary sequences variability among the antibody molecules from any mammal.
  • hypervariable loop is sometimes used interchangeably with the term “Complementarity Determining Region (CDR).”
  • CDR Complementarity Determining Region
  • the length of the hypervariable loops (or CDRs) varies between antibody molecules.
  • the framework regions of all antibody molecules from a given mammal have high primary sequence similarity /consensus.
  • the consensus of framework regions can be used by one skilled in the art to identify both the framework regions and the hypervariable loops (or CDRs) which are interspersed among the framework regions.
  • the hypervariable loops are given identifying names which distinguish their position within the polypeptide, and on which domain they occur.
  • CDRs in the VL domain are identified as LI, L2, and L3, with LI occurring at the most distal end and L3 occurring closest to the CL domain.
  • the CDRs may also be given the names CDR-L1, CDR-L2, and CDR-L3, or LCDR1, LCDR2, and LCDR3.
  • the L3 (CDR-L3) is generally the region of highest variability among all antibody molecules produced by a given organism.
  • the CDRs are regions of the polypeptide chain arranged linearly in the primary structure, and separated from each other by Framework Regions.
  • the amino terminal (N- terminal) end of the VL chain is named FR1.
  • the region identified as FR2 occurs between LI and L2 hypervariable loops.
  • FR3 occurs between L2 and L3 hypervariable loops, and the FR4 region is closest to the CL domain.
  • VH chain which includes three CDRs identified as CDR-H1, CDR-H2 and CDR-H3, or HCDR1, HCDR2, and HCDR3.
  • the majority of amino acid residues in the variable domains, or Fv fragments (VH and VL), are part of the framework regions (approximately 85%).
  • the three dimensional, or tertiary, structure of an antibody molecule is such that the framework regions are more internal to the molecule and provide the majority of the structure, with the CDRs on the external surface of the molecule.
  • affinity matured antibodies are enhanced with one or more modifications in one or more CDRs thereof that result in an improvement in the affinity of the antibody for a target antigen as compared to a parent antibody that does not possess those alteration(s).
  • Certain affinity matured antibodies will have nanomolar or picomolar affinities for the target antigen.
  • Affinity matured antibodies are produced by procedures known in the art, e.g., Marks et al., Bio/Technology 10:779 (1992) describes affinity maturation by VH and VL domain shuffling, random mutagenesis of CDR and/or framework residues employed in phage display is described by Rajpal et al., PNAS. 24: 8466-8471 (2005) and Thie et al., Methods Mol Biol. 525:309-22 (2009) in conjugation with computation methods as demonstrated in Tiller et al., Front. Immunol. 8:986 (2017).
  • Chimeric immunoglobulins are the products of fused genes derived from different species; “humanized” chimeras generally have the framework region (FR) from human immunoglobulins and one or more CDRs are from a non-human source.
  • portions of the heavy and/or light chain are identical or homologous to corresponding sequences from another particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.
  • minimizing the antibody polypeptide sequence from the nonhuman species optimizes chimeric antibody function and reduces immunogenicity.
  • Specific amino acid residues from non-antigen recognizing regions of the non-human antibody are modified to be homologous to corresponding residues in a human antibody or isotype.
  • One example is the “CDR-grafted” antibody, in which an antibody comprises one or more CDRs from a particular species or belonging to a specific antibody class or subclass, while the remainder of the antibody chain(s) is identical or homologous to a corresponding sequence in antibodies derived from another species or belonging to another antibody class or subclass.
  • the V region composed of CDR1, CDR2, and partial CDR3 for both the light and heavy chain variance region from a non-human immunoglobulin are grafted with a human antibody framework region, replacing the naturally occurring antigen receptors of the human antibody with the non-human CDRs.
  • corresponding non-human residues replace framework region residues of the human immunoglobulin.
  • humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody to further refine performance.
  • the humanized antibody may also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • Intrabodies are intracellularly localized immunoglobulins that bind to intracellular antigens as opposed to secreted antibodies, which bind antigens in the extracellular space.
  • Polyclonal antibody preparations typically include different antibodies against different determinants (epitopes).
  • a host such as a rabbit or goat, is immunized with the antigen or antigen fragment, generally with an adjuvant and, if necessary, coupled to a carrier.
  • Antibodies to the antigen are subsequently collected from the sera of the host.
  • the polyclonal antibody can be affinity purified against the antigen rendering it monospecific.
  • Monoclonal antibodies or “mAb” refer to an antibody obtained from a population of homogeneous antibodies from an exclusive parental cell, e.g., the population is identical except for naturally occurring mutations that may be present in minor amounts. Each monoclonal antibody is directed against a single antigenic determinant.
  • antibody fragments such as antibody fragments that bind to an S100A4 protein.
  • the term functional antibody fragment includes antigen-binding fragments of an antibody that retain the ability to specifically bind to an antigen. These fragments are constituted of various arrangements of the variable region heavy chain (VH) and/or light chain (VL); and in some aspects, include constant region heavy chain 1 (CHI) and light chain (CL). In some aspects, they lack the Fc region constituted of heavy chain 2 (CH2) and 3 (CH3) domains.
  • antigen binding fragments and the modifications thereof may include: (i) the Fab fragment type constituted with the VL, VH, CL, and CHI domains; (ii) the Fd fragment type constituted with the VH and CHI domains; (iii) the Fv fragment type constituted with the VH and VL domains; (iv) the single domain fragment type, dAb, (Ward, 1989; McCafferty et al., 1990; Holt et al., 2003) constituted with a single VH or VL domain; (v) isolated complementarity determining region (CDR) regions.
  • CDR complementarity determining region
  • Antigen-binding fragments also include fragments of an antibody that retain exactly, at least, or at most 1, 2, or 3 complementarity determining regions (CDRs) from a light chain variable region. Fusions of CDR-containing sequences to an Fc region (or a CH2 or CH3 region thereof) are included within the scope of this definition including, for example, scFv fused, directly or indirectly, to an Fc region are included herein.
  • CDRs complementarity determining regions
  • Fab fragment means a monovalent antigen-binding fragment of an antibody containing the VL, VH, CL and CHI domains.
  • Fab' fragment means a monovalent antigen-binding fragment of a monoclonal antibody that is larger than a Fab fragment.
  • a Fab' fragment includes the VL, VH, CL and CHI domains and all or part of the hinge region.
  • F(ab')2 fragment means a bivalent antigen-binding fragment of a monoclonal antibody comprising two Fab' fragments linked by a disulfide bridge at the hinge region.
  • An F(ab')2 fragment includes, for example, all or part of the two VH and VL domains, and can further include all or part of the two CL and CHI domains.
  • Fd fragment means a fragment of the heavy chain of a monoclonal antibody, which includes all or part of the VH, including the CDRs.
  • An Fd fragment can further include CHI region sequences.
  • Fv fragment means a monovalent antigen-binding fragment of a monoclonal antibody, including all or part of the VL and VH, and absent of the CL and CHI domains.
  • the VL and VH include, for example, the CDRs.
  • Single-chain antibodies are Fv molecules in which the VL and VH regions have been connected by a flexible linker to form a single polypeptide chain, which forms an antigen-binding fragment. Single chain antibodies are discussed in detail in International Patent Application Publication No. WO 88/01649 and U.S. Pat. Nos. 4,946,778 and 5,260,203, the disclosures of which are herein incorporated by reference.
  • (scFv)2 means bivalent or bispecific sFv polypeptide chains that include oligomerization domains at their C-termini, separated from the sFv by a hinge region (Pack et al. 1992).
  • the oligomerization domain comprises self-associating a- helices, e.g., leucine zippers, which can be further stabilized by additional disulfide bonds.
  • (scFv)2 fragments are also known as “miniantibodies” or “minibodies.”
  • a single domain antibody is an antigen-binding fragment containing only a VH or the VL domain.
  • two or more VH regions are covalently joined with a peptide linker to create a bivalent domain antibody.
  • the two VH regions of a bivalent domain antibody may target the same or different antigens.
  • Fab polypeptides of the disclosure include the Fab antigen binding fragment of an antibody. Unless specifically stated otherwise, the term “Fab” relates to a polypeptide excluding the Fc portion of the antibody. The Fab may be conjugated to a polypeptide comprising other components, such as further antigen binding domains, costimulatory domains, linkers, peptide spacers, transmembrane domains, endodomains, and accessory proteins. Fab polypeptides can be generated using conventional techniques known in the art and are well-described in the literature.
  • An Fc region contains two heavy chain fragments comprising the CH2 and CH3 domains of an antibody.
  • the two heavy chain fragments are held together by two or more disulfide bonds and by hydrophobic interactions of the CH3 domains.
  • the term “Fc polypeptide” as used herein includes native and mutein forms of polypeptides derived from the Fc region of an antibody. Truncated forms of such polypeptides containing the hinge region that promotes dimerization are included.
  • Antigen-binding peptide scaffolds such as complementarity-determining regions (CDRs) are used to generate protein-binding molecules in accordance with the aspects.
  • CDRs complementarity-determining regions
  • a person skilled in the art can determine the type of protein scaffold on which to graft at least one of the CDRs. It is known that scaffolds, optimally, must meet a number of criteria such as: good phylogenetic conservation; known three-dimensional structure; small size; few or no post-transcriptional modifications; and/or be easy to produce, express, and purify. Skerra, J Mol Recognit, 13:167-87 (2000).
  • the protein scaffolds can be sourced from, but not limited to: fibronectin type III FN3 domain (known as “monobodies”), fibronectin type III domain 10, lipocalin, anticalin, Z- domain of protein A of Staphylococcus aureus, thioredoxin A or proteins with a repeated motif such as the “ankyrin repeat”, the “armadillo repeat”, the “leucine -rich repeat” and the “tetratricopeptide repeat”.
  • fibronectin type III FN3 domain known as “monobodies”
  • fibronectin type III domain 10 lipocalin
  • anticalin Z- domain of protein A of Staphylococcus aureus
  • Z- domain of protein A of Staphylococcus aureus thioredoxin A or proteins with a repeated motif such as the “ankyrin repeat”, the “armadillo repeat”, the “leucine -rich repeat” and the “tetratricopeptide repeat”.
  • selective binding agent refers to a molecule that binds to an antigen.
  • Non-limiting examples include antibodies, antigen-binding fragments, scFv, Fab, Fab', F(ab')2, single chain antibodies, peptides, peptide fragments and proteins.
  • binding refers to a direct association between two molecules, due to, for example, covalent, electrostatic, hydrophobic, and ionic and/or hydrogen-bond interactions, including interactions such as salt bridges and water bridges.
  • immunologically reactive means that the selective binding agent or antibody of interest will bind with antigens present in a biological sample.
  • immuno complex refers the combination formed when an antibody or selective binding agent binds to an epitope on an antigen.
  • affinity refers the strength with which an antibody or selective binding agent binds an epitope. In antibody binding reactions, this is expressed as the affinity constant (Ka or ka sometimes referred to as the association constant) for any given antibody or selective binding agent. Affinity is measured as a comparison of the binding strength of the antibody to its antigen relative to the binding strength of the antibody to an unrelated amino acid sequence. Affinity can be expressed as, for example, 20- fold greater binding ability of the antibody to its antigen then to an unrelated amino acid sequence.
  • vidity refers to the resistance of a complex of two or more agents to dissociation after dilution.
  • immunosorbent and “preferentially binds” are used interchangeably herein with respect to antibodies and/or selective binding agent.
  • KD equilibrium dissociation constant
  • koff is the rate of dissociation between the antibody and antigen per unit time, and is related to the concentration of antibody and antigen present in solution in the unbound form at equilibrium.
  • kon is the rate of antibody and antigen association per unit time, and is related to the concentration of the bound antigen-antibody complex at equilibrium.
  • the units used for measuring the KD are mol/L (molarity, or M), or concentration.
  • examples of some experimental methods that can be used to determine the KD value are: enzyme-linked immunosorbent assays (ELISA), isothermal titration calorimetry (ITC), fluorescence anisotropy, surface plasmon resonance (SPR), and affinity capillary electrophoresis (ACE).
  • ELISA enzyme-linked immunosorbent assays
  • ITC isothermal titration calorimetry
  • SPR surface plasmon resonance
  • ACE affinity capillary electrophoresis
  • Antibodies deemed useful in certain aspects may have an affinity constant (Ka) of about, at least about, or at most about 10 6 , 10 7 , 10 8 , 10 9 , or IO 10 M, or any range derivable therein.
  • affinity constant Ka
  • antibodies may have a dissociation constant of about, at least about or at most about 10' 6 , 10' 7 , 10' 8 , 10' 9 , IO' 10 M, or any range derivable therein.
  • the epitope of an antigen is the specific region of the antigen for which an antibody has binding affinity.
  • the epitope is the specific residues (or specified amino acids or protein segment) that the antibody binds with high affinity.
  • An antibody does not necessarily contact every residue within the protein. Nor does every single amino acid substitution or deletion within a protein necessarily affect binding affinity.
  • epitope and antigenic determinant can be used interchangeably to refer to the site on an antigen to which B and/or T cells respond or recognize.
  • Polypeptide epitopes can be formed from both contiguous amino acids and noncontiguous amino acids juxtaposed by tertiary folding of a polypeptide.
  • An epitope typically includes at least 3, and typically 5-10 amino acids in a unique spatial conformation.
  • Epitope specificity of an antibody can be determined in a variety of ways.
  • One approach involves testing a collection of overlapping peptides of 15 amino acids spanning the full sequence of the protein and differing in increments of a small number of amino acids (e.g., 3 to 30 amino acids).
  • the peptides are immobilized in separate wells of a microtiter dish. Immobilization can be accomplished, for example, by biotinylating one terminus of the peptides. This process may affect the antibody affinity for the epitope, therefore different samples of the same peptide can be biotinylated at the N and C terminus and immobilized in separate wells for the purposes of comparison. This is useful for identifying end-specific antibodies.
  • additional peptides can be included terminating at a particular amino acid of interest. This approach is useful for identifying end- specific antibodies to internal fragments. An antibody or antigen-binding fragment is screened for binding to each of the various peptides.
  • the epitope is defined as a segment of amino acids that is common to all peptides to which the antibody shows high affinity binding.
  • the antibodies of the present invention may be modified, such that they are substantially identical to the antibody polypeptide sequences, or fragments thereof, and still bind the epitopes of the present invention.
  • Polypeptide sequences are “substantially identical” when optimally aligned using such programs as Clustal Omega, IGBLAST, GAP or BESTFIT using default gap weights, they share at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, at least 96% sequence identity, at least 97% sequence identity, at least 98% sequence identity, or at least 99% sequence identity or any range therein.
  • amino acid sequences of antibodies or antigen-binding regions thereof are contemplated as being encompassed by the present invention, providing that the variations in the amino acid sequence maintain at least 75%, more preferably at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% and most preferably at least 99% sequence identity.
  • conservative amino acid replacements are contemplated.
  • Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids are generally divided into families based on the chemical nature of the side chain; e.g., acidic (aspartate, glutamate), basic (lysine, arginine, histidine), nonpolar (alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), and uncharged polar (glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine).
  • acidic aspartate, glutamate
  • basic lysine, arginine, histidine
  • nonpolar alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan
  • uncharged polar glycine, asparagine, glutamine, cysteine, serine, thre
  • Standard ELISA, Surface Plasmon Resonance (SPR), or other antibody binding assays can be performed by one skilled in the art to make a quantitative comparison of antigen binging affinity between the unmodified antibody and any polypeptide derivatives with conservative substitutions generated through any of several methods available to one skilled in the art.
  • fragments or analogs of antibodies or immunoglobulin molecules can be readily prepared by those skilled in the art. Preferred amino- and carboxy-termini of fragments or analogs occur near boundaries of functional domains. Structural and functional domains can be identified by comparison of the nucleotide and/or amino acid sequence data to public or proprietary sequence databases. Preferably, computerized comparison methods are used to identify sequence motifs or predicted protein conformation domains that occur in other proteins of known structure and/or function. Standard methods to identify protein sequences that fold into a known three-dimensional structure are available to those skilled in the art; Dill and McCallum., Science 338:1042-1046 (2012).
  • Framework modifications can be made to antibodies to decrease immunogenicity, for example, by “backmutating” one or more framework residues to a corresponding germline sequence.
  • the antigen-binding domain may be multi- specific or multivalent by multimerizing the antigen-binding domain with VH and VL region pairs that bind either the same antigen (multi- valent) or a different antigen (multi- specific).
  • glycosylation variants of antibodies wherein the number and/or type of glycosylation site(s) has been altered compared to the amino acid sequences of the parent polypeptide.
  • Glycosylation of the polypeptides can be altered, for example, by modifying one or more sites of glycosylation within the polypeptide sequence to increase the affinity of the polypeptide for antigen (U.S. Pat. Nos. 5,714,350 and 6,350,861).
  • antibody protein variants comprise a greater or a lesser number of N-linked glycosylation sites than the native antibody.
  • N-linked glycosylation site is characterized by the sequence: Asn-X-Ser or Asn-X-Thr, wherein the amino acid residue designated as X may be any amino acid residue except proline.
  • the substitution of amino acid residues to create this sequence provides a potential new site for the addition of an N-linked carbohydrate chain.
  • substitutions that eliminate or alter this sequence will prevent addition of an N- linked carbohydrate chain present in the native polypeptide.
  • the glycosylation can be reduced by the deletion of an Asn or by substituting the Asn with a different amino acid.
  • one or more new N-linked glycosylation sites are created.
  • Antibodies typically have an N-linked glycosylation site in the Fc region.
  • Additional antibody variants include cysteine variants, wherein one or more cysteine residues in the parent or native amino acid sequence are deleted from or substituted with another amino acid (e.g., serine). Cysteine variants are useful, inter alia, when antibodies must be refolded into a biologically active conformation. Cysteine variants may have fewer cysteine residues than the native antibody and typically have an even number to minimize interactions resulting from unpaired cysteines.
  • the polypeptides can be pegylated to increase biological half-life by reacting the polypeptide with polyethylene glycol (PEG) or a reactive ester or aldehyde derivative of PEG, under conditions in which one or more PEG groups become attached to the polypeptide.
  • PEG polyethylene glycol
  • Polypeptide pegylation may be carried out by an acylation reaction or an alkylation reaction with a reactive PEG molecule (or an analogous reactive water-soluble polymer).
  • Methods for pegylating proteins are known in the art and can be applied to the polypeptides of the invention to obtain PEGylated derivatives of antibodies. See, e.g., EP 0 154 316 and EP 0 401 384.
  • the antibody is conjugated or otherwise linked to transthyretin (TTR) or a TTR variant.
  • TTR or TTR variant can be chemically modified with, for example, a chemical selected from the group consisting of dextran, poly(n-vinyl pyrrolidone), polyethylene glycols, propropylene glycol homopolymers, polypropylene oxide/ethylene oxide co-polymers, polyoxy ethylated polyols, and polyvinyl alcohols.
  • polyethylene glycol is intended to encompass any of the forms of PEG that have been used to derivatize other proteins.
  • the derivatized antibody or fragment thereof may comprise any molecule or substance that imparts a desired property to the antibody or fragment.
  • the derivatized antibody can comprise, for example, a detectable (or labeling) moiety (e.g., a radioactive, colorimetric, antigenic, or enzymatic molecule, or a detectable bead), a molecule that binds to another molecule (e.g., biotin or streptavidin), a therapeutic or diagnostic moiety (e.g., a radioactive, cytotoxic, or pharmaceutically active moiety), or a molecule that increases the suitability of the antibody for a particular use (e.g., administration to a subject, such as a human subject, or other in vivo or in vitro uses).
  • a detectable (or labeling) moiety e.g., a radioactive, colorimetric, antigenic, or enzymatic molecule, or a detectable bead
  • an antibody or an immunological portion of an antibody can be chemically conjugated to, or expressed as, a fusion protein with other proteins.
  • polypeptides may be chemically modified by conjugating or fusing the polypeptide to serum protein, such as human serum albumin, to increase half-life of the resulting molecule. See, e.g., EP 0322094 and EP 0486525.
  • the polypeptides may be conjugated to a diagnostic agent and used diagnostically, for example, to monitor the development or progression of a disease and determine the efficacy of a given treatment regimen.
  • the polypeptides may also be conjugated to a therapeutic agent to provide a therapy in combination with the therapeutic effect of the polypeptide.
  • Additional suitable conjugated molecules include ribonuclease (RNase), DNase I, an antisense nucleic acid, an inhibitory RNA molecule such as a siRNA molecule, an immuno stimulatory nucleic acid, aptamers, ribozymes, triplex forming molecules, and external guide sequences.
  • RNase ribonuclease
  • DNase I an antisense nucleic acid
  • an inhibitory RNA molecule such as a siRNA molecule
  • an immuno stimulatory nucleic acid aptamers
  • ribozymes triplex forming molecules
  • the functional nucleic acid molecules may act as effectors, inhibitors, modulators, and stimulators of a specific activity possessed by a target molecule, or the functional nucleic acid molecules may possess a de novo activity independent of any other molecules.
  • antibodies and antibody-like molecules that are linked to at least one agent to form an antibody conjugate or payload.
  • it is conventional to link or covalently bind or complex at least one desired molecule or moiety.
  • a molecule or moiety may be, but is not limited to, at least one effector or reporter molecule.
  • Effector molecules comprise molecules having a desired activity, e.g., cytotoxic activity.
  • Non-limiting examples of effector molecules include toxins, therapeutic enzymes, antibiotics, radiolabeled nucleotides and the like.
  • a reporter molecule is defined as any moiety that may be detected using an assay.
  • Non-limiting examples of reporter molecules that have been conjugated to antibodies include enzymes, radiolabels, haptens, fluorescent labels, phosphorescent molecules, chemiluminescent molecules, chromophores, luminescent molecules, photoaffinity molecules, colored particles, or ligands.
  • disclosed are antibodies, antigen-binding fragments thereof, and other antibody-like molecules that are not conjugated and/or operably linked to another active agent.
  • the antibodies and antibody-like molecules are not conjugated (i.e. not linked to another active agent, such as any of the molecules described above) to achieve a desired effect.
  • antibody conjugates are those conjugates in which the antibody is linked to a detectable label.
  • Detectable labels are compounds and/or elements that can be detected due to their specific functional properties, and/or chemical characteristics, the use of which allows the antibody to be detected, and/or further quantified if desired.
  • detectable labels include, but not limited to, radioactive isotopes, fluorescers, semiconductor nanocrystals, chemiluminescers, chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, dyes, metal ions, metal sols, ligands (e.g., biotin, streptavidin or haptens) and the like.
  • Labels are, but not limited to, horseradish peroxidase (HRP), fluorescein, FITC, rhodamine, dansyl, umbelliferone, dimethyl acridinium ester (DMAE), Texas red, luminol, NADPH and a- or P-galactosidase.
  • Antibody conjugates include those intended primarily for use in vitro, where the antibody is linked to a secondary binding ligand and/or to an enzyme to generate a colored product upon contact with a chromogenic substrate.
  • suitable enzymes include, but are not limited to, urease, alkaline phosphatase, (horseradish) hydrogen peroxidase, or glucose oxidase.
  • Preferred secondary binding ligands are biotin and/or avidin and streptavidin compounds.
  • the uses of such labels is well known to those of skill in the art and are described, for example, in U.S. Patents 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241; each incorporated herein by reference.
  • Molecules containing azido groups may also be used to form covalent bonds to proteins through reactive nitrene intermediates that are generated by low intensity ultraviolet light (Potter & Haley, 1983).
  • contemplated are immunoconjugates comprising an antibody or antigen-binding fragment thereof conjugated to a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active tox
  • the immunoconjugate can be provided in the form of a fusion protein.
  • an antibody may be conjugated to various therapeutic substances in order to target the cell surface antigen.
  • conjugated agents include, but are not limited to, metal chelate complexes, drugs, toxins and other effector molecules, such as cytokines, lymphokines, chemokines, immunomodulators, radiosensitizers, asparaginase, carboranes, and radioactive halogens.
  • an antibody is conjugated to one or more drug moieties (D) through a linker (L).
  • the ADC may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including: (1) reaction of a nucleophilic group of an antibody with a bivalent linker reagent, to form Ab-L, via a covalent bond, followed by reaction with a drug moiety D; and (2) reaction of a nucleophilic group of a drug moiety with a bivalent linker reagent, to form D-L, via a covalent bond, followed by reaction with the nucleophilic group of an antibody.
  • Antibody drug conjugates may also be produced by modification of the antibody to introduce electrophilic moieties, which can react with nucleophilic substituents on the linker reagent or drug.
  • a fusion protein comprising the antibody and cytotoxic agent may be made, e.g., by recombinant techniques or peptide synthesis.
  • the length of DNA may comprise respective regions encoding the two portions of the conjugate either adjacent one another or separated by a region encoding a linker peptide which does not destroy the desired properties of the conjugate.
  • the antibody may be conjugated to a “receptor” (such as streptavidin) for utilization in tumor or cancer cell pre-targeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) which is conjugated to a cytotoxic agent (e.g., a radionucleotide).
  • a receptor such as streptavidin
  • a ligand e.g., avidin
  • cytotoxic agent e.g., a radionucleotide
  • Examples of an antibody-drug conjugates known to a person skilled in the art are pro-drugs useful for the local delivery of cytotoxic or cytostatic agents, i.e. drugs to kill or inhibit tumor cells in the treatment of cancer (Syrigos and Epenetos, Anticancer Res. 19:605- 614 (1999); Niculescu-Duvaz and Springer, Adv. Drg. Del. Rev. 26:151-172 (1997); U.S. Pat. No. 4,975,278).
  • ADC include covalent or aggregative conjugates of antibodies, or antigen-binding fragments thereof, with other proteins or polypeptides, such as by expression of recombinant fusion proteins comprising heterologous polypeptides fused to the N-terminus or C-terminus of an antibody polypeptide.
  • the conjugated peptide may be a heterologous signal (or leader) polypeptide, e.g., the yeast alpha-factor leader, or a peptide such as an epitope tag (e.g., V5-His).
  • Antibody-containing fusion proteins may comprise peptides added to facilitate purification or identification of the antibody (e.g., poly- His).
  • An antibody polypeptide also can be linked to the FLAG® (Sigma- Aldrich, St. Louis, Mo.) peptide as described in Hopp et al., Bio/Technology 6:1204 (1988), and U.S. Pat. No. 5,011,912.
  • Oligomers that contain one or more antibody polypeptides may be employed as antagonists. Oligomers may be in the form of covalently linked or non-covalently linked dimers, trimers, or higher oligomers. Oligomers comprising two or more antibody polypeptides are contemplated for use. Other oligomers include heterodimers, homotrimers, hetero trimers, homo tetramers, hetero tetramers, etc.
  • oligomers comprise multiple antibody polypeptides joined via covalent or non-covalent interactions between peptide moieties fused to the antibody polypeptides.
  • Such peptides may be peptide linkers (spacers), or peptides that have the property of promoting oligomerization.
  • Leucine zippers and certain polypeptides derived from antibodies are among the peptides that can promote oligomerization of antibody polypeptides attached thereto, as described in more detail below.
  • attachment methods involve the use of a metal chelate complex employing, for example, an organic chelating agent such a diethylenetriaminepentaacetic acid anhydride (DTPA); ethylenetriaminetetraacetic acid; N- chloro-p-toluenesulfonamide; and/or tetrachloro-3 -6 -diphenylglycouril-3 attached to the antibody (U.S. Patent Nos. 4,472,509 and 4,938,948, each incorporated herein by reference).
  • DTPA diethylenetriaminepentaacetic acid anhydride
  • ethylenetriaminetetraacetic acid ethylenetriaminetetraacetic acid
  • N- chloro-p-toluenesulfonamide N- chloro-p-toluenesulfonamide
  • tetrachloro-3 -6 -diphenylglycouril-3 attached to the antibody
  • Monoclonal antibodies may also be reacted with an enzyme in the presence of a coupling agent such as glutaraldehyde or periodate.
  • Conjugates may also be made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HC1), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis-azido compounds (such as bis(p-azidobenzoyl)hexanediamine), bis- diazonium derivatives (such as bos(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1,5-
  • derivatization of immunoglobulins by selectively introducing sulfhydryl groups in the Fc region of an immunoglobulin, using reaction conditions that do not alter the antibody combining site, are contemplated.
  • Antibody conjugates produced according to this methodology are disclosed to exhibit improved longevity, specificity, and sensitivity (U.S. Pat. No. 5,196,066, incorporated herein by reference).
  • Site-specific attachment of effector or reporter molecules, wherein the reporter or effector molecule is conjugated to a carbohydrate residue in the Fc region has also been disclosed in the literature (O’Shannessy et al., 1987).
  • antibodies may be polyclonal or monoclonal antibody preparations, monospecific antisera, human antibodies, hybrid or chimeric antibodies, such as humanized antibodies, altered antibodies, F(ab')2 fragments, Fab fragments, Fv fragments, single-domain antibodies, dimeric or trimeric antibody fragment constructs, minibodies, or functional fragments thereof which bind to the antigen in question.
  • polypeptides, peptides, and proteins and immunogenic fragments thereof for use in various aspects can also be synthesized in solution or on a solid support in accordance with conventional techniques. See, for example, Stewart and Young, (1984); Tam et al, (1983); Merrifield, (1986); and Barany and Merrifield (1979), each incorporated herein by reference.
  • a polyclonal antibody is prepared by immunizing an animal with an antigen or a portion thereof and collecting antisera from that immunized animal.
  • the antigen may be altered compared to an antigen sequence found in nature.
  • a variant or altered antigenic peptide or polypeptide is employed to generate antibodies.
  • Inocula are typically prepared by dispersing the antigenic composition in a physiologically tolerable diluent to form an aqueous composition.
  • Antisera is subsequently collected by methods known in the arts, and the serum may be used as-is for various applications or else the desired antibody fraction may be purified by well-known methods, such as affinity chromatography (Harlow and Lane, Antibodies: A Laboratory Manual 1988).
  • Myeloma cell lines suited for use in hybridoma- producing fusion procedures preferably are non-antibody-producing and have high fusion efficiency and enzyme deficiencies that render then incapable of growing in certain selective media that support the growth of only the desired fused cells (hybridomas).
  • the fusion partner includes a property that allows selection of the resulting hybridomas using specific media.
  • fusion partners can be hypoxanthine/aminopterin/thymidine (HAT)-sensitive.
  • Methods for generating hybrids of antibody-producing spleen or lymph node cells and myeloma cells usually comprise mixing somatic cells with myeloma cells in the presence of an agent or agents (chemical or electrical) that promote the fusion of cell membranes.
  • hybridomas selection of hybridomas can be performed by culturing the cells by singleclone dilution in microtiter plates, followed by testing the individual clonal supernatants (after two to three weeks) for the desired reactivity. Fusion procedures for making hybridomas, immunization protocols, and techniques for isolation of immunized splenocytes for fusion are known in the art.
  • SLAM lymphocyte antibody method
  • Monoclonal antibodies may be further purified using filtration, centrifugation, and various chromatographic methods such as HPLC or affinity chromatography.
  • Monoclonal antibodies may be further screened or optimized for properties relating to specificity, avidity, half-life, immunogenicity, binding association, binding disassociation, or overall functional properties relative to being a treatment for infection.
  • monoclonal antibodies may have alterations in the amino acid sequence of CDRs, including insertions, deletions, or substitutions with a conserved or non-conserved amino acid.
  • the immunogenicity of a particular immunogen composition can be enhanced by the use of non-specific stimulators of the immune response, known as adjuvants.
  • adjuvants that may be used in accordance with aspects include, but are not limited to, IL-1, IL-2, IL-4, IL-7, IL- 12, -interferon, GMCSP, BCG, aluminum hydroxide, MDP compounds, such as thur- MDP and nor-MDP, CGP (MTP-PE), lipid A, and monophosphoryl lipid A (MPL).
  • Exemplary adjuvants may include complete Freund’s adjuvant (a non-specific stimulator of the immune response containing killed Mycobacterium tuberculosis), incomplete Freund’s adjuvants, and/or aluminum hydroxide adjuvant.
  • BRM biologic response modifiers
  • Cimetidine CCM; 1200 mg/d
  • CYP Cyclophosphamide
  • cytokines such as P-interferon, IL-2, or IL- 12, or genes encoding proteins involved in immune helper functions, such as B-7.
  • a phage-display system can be used to expand antibody molecule populations in vitro.
  • human antibodies may be produced in a non-human transgenic animal, e.g., a transgenic mouse capable of producing multiple isotypes of human antibodies to protein (e.g., IgG, IgA, and/or IgE) by undergoing V-D-J recombination and isotype switching. Accordingly, this aspect applies to antibodies, antibody fragments, and pharmaceutical compositions thereof, but also non-human transgenic animals, B-cells, host cells, and hybridomas that produce monoclonal antibodies.
  • Applications of human antibodies include, but are not limited to, detect a cell expressing an anticipated protein, either in vivo or in vitro, pharmaceutical preparations containing the antibodies of the present invention, and methods of treating disorders by administering the antibodies.
  • Fully human antibodies can be produced by immunizing transgenic animals (usually mice) that are capable of producing a repertoire of human antibodies in the absence of endogenous immunoglobulin production.
  • Antigens for this purpose typically have six or more contiguous amino acids, and optionally are conjugated to a carrier, such as a hapten.
  • a carrier such as a hapten.
  • transgenic animals are produced by incapacitating the endogenous mouse immunoglobulin loci encoding the mouse heavy and light immunoglobulin chains therein, and inserting into the mouse genome large fragments of human genome DNA containing loci that encode human heavy and light chain proteins. Partially modified animals, which have less than the full complement of human immunoglobulin loci, are then crossbred to obtain an animal having all of the desired immune system modifications. When administered an immunogen, these transgenic animals produce antibodies that are immuno specific for the immunogen but have human rather than murine amino acid sequences, including the variable regions. For further details of such methods, see, for example, International Patent Application Publication Nos.
  • mice described above contain a human immunoglobulin gene minilocus that encodes unrearranged human heavy (p and y) and K light chain immunoglobulin sequences, together with targeted mutations that inactivate the endogenous p and K chain loci (Lonberg et al., Nature 368:856-859 (1994)). Accordingly, the mice exhibit reduced expression of mouse IgM or K chains and in response to immunization, the introduced human heavy and light chain transgenes undergo class switching and somatic mutation to generate high affinity human IgG K monoclonal antibodies (Lonberg et al., supra; Lonberg and Huszar, Intern. Ref. Immunol.
  • HuMAb mice The preparation of HuMAb mice is described in detail in Taylor et al., Nucl. Acids Res. 20:6287-6295 (1992); Chen et al., Int. Immunol. 5:647-656 (1993); Tuaillon et al., J. Immunol. 152:2912-2920 (1994); Lonberg et al., supra; Lonberg, Handbook of Exp. Pharmacol. 113:49-101 (1994); Taylor et al., Int. Immunol. 6:579-591 (1994); Lonberg and Huszar, Intern. Ref.
  • WO 93/1227; WO 92/22646; and WO 92/03918 the disclosures of all of which are hereby incorporated by reference in their entirety for all purposes.
  • Technologies utilized for producing human antibodies in these transgenic mice are disclosed also in WO 98/24893, and Mendez et al., Nat. Genetics 15:146-156 (1997), which are herein incorporated by reference. Lor example, the HCo7 and HCol2 transgenic mice strains can be used to generate human antibodies.
  • antigen-specific humanized monoclonal antibodies with the desired specificity can be produced and selected from the transgenic mice such as those described above.
  • Such antibodies may be cloned and expressed using a suitable vector and host cell, or the antibodies can be harvested from cultured hybridoma cells.
  • Lully human antibodies can also be derived from phage-display libraries (as disclosed in Hoogenboom et al., J. Mol. Biol. 227:381 (1991); and Marks et al., J. Mol. Biol. 222:581 (1991)).
  • phage-display libraries as disclosed in Hoogenboom et al., J. Mol. Biol. 227:381 (1991); and Marks et al., J. Mol. Biol. 222:581 (1991).
  • One such technique is described in International Patent Application Publication No. WO 99/10494 (herein incorporated by reference), which describes the isolation of high affinity and functional agonistic antibodies for MPL- and m
  • Antibody fragments that retain the ability to recognize the antigen of interest will also find use herein.
  • a number of antibody fragments are known in the art that comprise antigen-binding sites capable of exhibiting immunological binding properties of an intact antibody molecule and can be subsequently modified by methods known in the arts. Lunctional fragments, including only the variable regions of the heavy and light chains, can also be produced using standard techniques such as recombinant production or preferential proteolytic cleavage of immunoglobulin molecules. These fragments are known as Fv. See, e.g., Inbar et ak, Proc. Nat. Acad. Sci. USA 69:2659-2662 (1972); Hochman et al., Biochem. 15:2706-2710 (1976); and Ehrlich et al., Biochem. 19:4091-4096 (1980).
  • Single-chain variable fragments may be prepared by fusing DNA encoding a peptide linker between DNAs encoding the two variable domain polypeptides (VL and VH).
  • scFvs can form antigen-binding monomers, or they can form multimers (e.g., dimers, trimers, or tetramers), depending on the length of a flexible linker between the two variable domains (Kortt et al., Prot. Eng. 10:423 (1997); Kort et al., Biomol. Eng. 18:95-108 (2001)).
  • VL- and VH-comprising polypeptides By combining different VL- and VH-comprising polypeptides, one can form multimeric scFvs that bind to different epitopes (Kriangkum et al., Biomol. Eng. 18:31-40 (2001)). Antigen-binding fragments are typically produced by recombinant DNA methods known to those skilled in the art.
  • the two domains of the Fv fragment, VL and VH are coded for by separate genes, they can be joined using recombinant methods by a synthetic linker that enables them to be made as a single chain polypeptide (known as single chain Fv (sFv or scFv); see e.g., Bird et al., Science 242:423-426 (1988); and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988).
  • Design criteria include determining the appropriate length to span the distance between the C-terminus of one chain and the N-terminus of the other, wherein the linker is generally formed from small hydrophilic amino acid residues that do not tend to coil or form secondary structures.
  • Suitable linkers generally comprise polypeptide chains of alternating sets of glycine and serine residues, and may include glutamic acid and lysine residues inserted to enhance solubility.
  • Antigen-binding fragments are screened for utility in the same manner as intact antibodies. Such fragments include those obtained by amino-terminal and/or carboxy-terminal deletions, where the remaining amino acid sequence is substantially identical to the corresponding positions in the naturally occurring sequence deduced, for example, from a full- length cDNA sequence.
  • Antibodies may also be generated using peptide analogs of the epitopic determinants disclosed herein, which may consist of non-peptide compounds having properties analogous to those of the template peptide. These types of non-peptide compound are termed “peptide mimetics” or “peptidomimetics”. Fauchere, J. Adv. Drug Res. 15:29 (1986); Veber and Freidinger TINS p. 392 (1985); and Evans et al., J. Med. Chem. 30:1229 (1987). Liu et al.
  • ABSiPs antibody like binding peptidomimetics
  • These analogs can be peptides, non-peptides or combinations of peptide and non-peptide regions. Fauchere, Adv. Drug Res. 15:29 (1986); Veber and Freidiner, TINS p. 392 (1985); and Evans et al., J. Med. Chem. 30: 1229 (1987), which are incorporated herein by reference in their entirety for any purpose.
  • Peptide mimetics that are structurally similar to therapeutically useful peptides may be used to produce a similar therapeutic or prophylactic effect.
  • Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type may be used in certain aspects of the invention to generate more stable proteins.
  • constrained peptides comprising a consensus sequence or a substantially identical consensus sequence variation may be generated by methods known in the art (Rizo and Gierasch, Ann. Rev. Biochem. 61:387 (1992), incorporated herein by reference), for example, by adding internal cysteine residues capable of forming intramolecular disulfide bridges which cyclize the peptide.
  • a phage display library can be used to improve the immunological binding affinity of the Fab molecules using known techniques. See, e.g., Figini et al., J. Mol. Biol. 239:68 (1994).
  • the coding sequences for the heavy and light chain portions of the Fab molecules selected from the phage display library can be isolated or synthesized and cloned into any suitable vector or replicon for expression. Any suitable expression system can be used.
  • nucleic acid molecule encoding antibody polypeptides e.g., heavy or light chain, variable domain only, or full-length. These may be generated by methods known in the art, e.g., isolated from B cells of animals such as mice or rabbits that have been immunized and isolated, phage display, expressed in any suitable recombinant expression system and allowed to assemble to form antibody molecules.
  • the nucleic acid molecules may be used to express large quantities of recombinant antibodies or to produce chimeric antibodies, single chain antibodies, immunoadhesins, diabodies, mutated antibodies, and other antibody derivatives. If the nucleic acid molecules are derived from a non-human, non-transgenic animal, the nucleic acid molecules may be used for antibody humanization.
  • contemplated are expression vectors comprising a nucleic acid molecule encoding a polypeptide of the desired sequence or a portion thereof (e.g., a fragment containing one or more CDRs or one or more variable region domains).
  • Expression vectors comprising the nucleic acid molecules may encode the heavy chain, light chain, or the antigenbinding portion thereof.
  • expression vectors comprising nucleic acid molecules may encode fusion proteins, modified antibodies, antibody fragments, and probes thereof.
  • vectors and expression vectors may contain nucleic acid sequences that serve other functions as well.
  • DNAs encoding partial or full-length light and heavy chains are inserted into expression vectors such that the gene area is operatively linked to transcriptional and translational control sequences.
  • expression vectors used in any of the host cells contain sequences for plasmid or virus maintenance and for cloning and expression of exogenous nucleotide sequences.
  • flanking sequences typically include one or more of the following operatively linked nucleotide sequences: a promoter, one or more enhancer sequences, an origin of replication, a transcriptional termination sequence, a complete intron sequence containing a donor and acceptor splice site, a sequence encoding a leader sequence for polypeptide secretion, a ribosome binding site, a polyadenylation sequence, a polylinker region for inserting the nucleic acid encoding the polypeptide to be expressed, and a selectable marker element.
  • a promoter one or more enhancer sequences
  • an origin of replication a transcriptional termination sequence
  • a complete intron sequence containing a donor and acceptor splice site a sequence encoding a leader sequence for polypeptide secretion
  • ribosome binding site a sequence encoding a leader sequence for polypeptide secretion
  • polyadenylation sequence a polylinker region for inserting the nucleic acid encoding the polypeptid
  • Prokaryote- and/or eukaryote-based systems can be employed for use with an aspect to produce nucleic acid sequences, or their cognate polypeptides, proteins and peptides.
  • Commercially and widely available systems include in but are not limited to bacterial, mammalian, yeast, and insect cell systems.
  • Different host cells have characteristic and specific mechanisms for the post- translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.
  • Those skilled in the art are able to express a vector to produce a nucleic acid sequence or its cognate polypeptide, protein, or peptide using an appropriate expression system.
  • nucleic acid delivery to effect expression of compositions are anticipated to include virtually any method by which a nucleic acid (e.g., DNA, including viral and nonviral vectors) can be introduced into a cell, a tissue or an organism, as described herein or as would be known to one of ordinary skill in the art.
  • a nucleic acid e.g., DNA, including viral and nonviral vectors
  • Such methods include, but are not limited to, direct delivery of DNA such as by injection (U.S. Patents 5,994,624,5,981,274, 5,945,100, 5,780,448, 5,736,524, 5,702,932, 5,656,610, 5,589,466 and 5,580,859, each incorporated herein by reference), including microinjection (Harland and Weintraub, 1985; U.S.
  • Patent 5,789,215 incorporated herein by reference
  • electroporation U.S. Patent No. 5,384,253, incorporated herein by reference
  • calcium phosphate precipitation Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al., 1990
  • DEAE dextran followed by polyethylene glycol
  • direct sonic loading Fechheimer et al., 1987
  • liposome mediated transfection Nicolau and Sene, 1982; Fraley et al., 1979; Nicolau et al., 1987; Wong et al., 1980; Kaneda et al., 1989; Kato et al., 1991
  • microprojectile bombardment PCT Application Nos.
  • contemplated are the use of host cells into which a recombinant expression vector has been introduced.
  • Antibodies can be expressed in a variety of cell types.
  • An expression construct encoding an antibody can be transfected into cells according to a variety of methods known in the art.
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. Some vectors may employ control sequences that allow it to be replicated and/or expressed in both prokaryotic and eukaryotic cells.
  • the antibody expression construct can be placed under control of a promoter that is linked to T-cell activation, such as one that is controlled by NFAT- 1 or NF-KB, both of which are transcription factors that can be activated upon T-cell activation.
  • Control of antibody expression allows T cells, such as tumor- targeting T cells, to sense their surroundings and perform real-time modulation of cytokine signaling, both in the T cells themselves and in surrounding endogenous immune cells.
  • T cells such as tumor- targeting T cells, to sense their surroundings and perform real-time modulation of cytokine signaling, both in the T cells themselves and in surrounding endogenous immune cells.
  • T cells such as tumor- targeting T cells
  • cytokine signaling both in the T cells themselves and in surrounding endogenous immune cells.
  • One of skill in the art would understand the conditions under which to incubate host cells to maintain them and to permit replication of a vector. Also understood and known are techniques and conditions that would allow large-scale production of vectors, as well as production of the nucleic acids
  • a selectable marker e.g., for resistance to antibiotics
  • Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die), among other methods known in the arts.
  • nucleic acid molecule encoding either or both of the entire heavy and light chains of an antibody or the variable regions thereof may be obtained from any source that produces antibodies. Methods of isolating mRNA encoding an antibody are well known in the art. See e.g., Sambrook et al., supra. The sequences of human heavy and light chain constant region genes are also known in the art. See, e.g., Kabat et al., 1991, supra. Nucleic acid molecules encoding the full-length heavy and/or light chains may then be expressed in a cell into which they have been introduced and the antibody isolated. VI. ANTIBODIES, ANTIGEN BINDING FRAGMENTS, AND POLYPEPTIDES
  • a “protein” or “polypeptide” refers to a molecule comprising at least five amino acid residues.
  • wild-type refers to the endogenous version of a molecule that occurs naturally in an organism.
  • wild-type versions of a protein or polypeptide are employed, however, in many aspects of the disclosure, a modified protein or polypeptide is employed to generate an immune response.
  • a “modified protein” or “modified polypeptide” or a “variant” refers to a protein or polypeptide whose chemical structure, particularly its amino acid sequence, is altered with respect to the wild-type protein or polypeptide.
  • a modified/variant protein or polypeptide has at least one modified activity or function (recognizing that proteins or polypeptides may have multiple activities or functions). It is specifically contemplated that a modified/variant protein or polypeptide may be altered with respect to one activity or function yet retain a wild- type activity or function in other respects, such as immunogenicity.
  • the term polypeptide also includes an antibody fragment described herein as well as antibody domains, such as HCDR1, HCDR2, HCDR3, LCDR1, LCDR2, LCDR3, HFR1, HFR2, HFR3, HFR4, LFR1, LFR2, LFR3, LFR4, VH, VL, CH, or CL.
  • a protein is specifically mentioned herein, it is in general a reference to a native (wild-type) or recombinant (modified) protein or, optionally, a protein in which any signal sequence has been removed.
  • the protein may be isolated directly from the organism of which it is native, produced by recombinant DNA/exogenous expression methods, or produced by solid-phase peptide synthesis (SPPS) or other in vitro methods.
  • SPPS solid-phase peptide synthesis
  • recombinant may be used in conjunction with a polypeptide or the name of a specific polypeptide, and this generally refers to a polypeptide produced from a nucleic acid molecule that has been manipulated in vitro or that is a replication product of such a molecule.
  • an antibody, antigen binding fragment, protein or polypeptide may comprise, but is not limited to, 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,
  • polypeptides may be mutated by truncation, rendering them shorter than their corresponding wild-type form, also, they might be altered by fusing or conjugating a heterologous protein or polypeptide sequence with a particular function (e.g., for targeting or localization, for enhanced immunogenicity, for purification purposes, etc.).
  • domain refers to any distinct functional or structural unit of a protein or polypeptide, and generally refers to a sequence of amino acids with a structure or function recognizable by one skilled in the art.
  • the antibody, antigen binding fragment, polypeptides, proteins, or polynucleotides encoding such polypeptides or proteins of the disclosure may include 1, 2, 3, 4, 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, or 50 (or any derivable range therein) or more variant amino acids or nucleic acid substitutions or be at least 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
  • the antibody, antigen binding fragment, protein, or polypeptide may comprise amino acids 1 to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, , 22, 23, 24, 25, 26, 27, 28 29, 30, 31, 32. , 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,, 47, 48, 49, 50, 51, 52, 53 54, 55, 56, 57. , 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70,, 72, 73, 74, 75, 76, 77, 78 79, 80, 81, 82.
  • the antibody, antigen binding fragment, or polypeptide may comprise 1, 2, 3, 4, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 11
  • the antibody, antigen binding fragment, protein, or polypeptide may comprise at least, at most, or exactly 1, 2, 3, 4, 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, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
  • nucleic acid molecule comprising amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids, amino acids
  • a polypeptide (e.g., antibody, antibody fragment, Fab, etc.) of the disclosure comprises a CDR that is at least 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100% identical (or any range derivable therein) in sequence to one of SEQ ID NOS: 1-191.
  • a polypeptide comprises 1, 2, and/or 3 CDRs from one of SEQ ID NOS: 1-191.
  • the CDR may be one that has been determined by Kabat, IMGT, or Chothia.
  • a polypeptide may have CDRs that have 1, 2, and/or 3 amino acid changes (e.g., addition of 1 or 2 amino acids, deletions of 1 or 2 amino acids, substitution) with respect to these 1, 2, or 3 CDRs.
  • a polypeptide comprises additionally or alternatively, an amino acid sequence that is at least 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99, or 100% identical or homologous to the amino acid sequence of the variable region that is not a CDR sequence, i.e., the variable region framework.
  • the CDRs are CDR1, CDR2, and CDR3.
  • a polypeptide may have CDRs that have 1, 2, and/or 3 amino acid changes (e.g., addition of 1 or 2 amino acids, deletions of 1 or 2 amino acids, substitution) with respect to CDR1, CDR2, or CDR3.
  • the CDRs of any of SEQ ID NOS: 1-191 may further comprise 1, 2, 3, 4, 5, or 6 additional amino acids at the amino or carboxy terminus of the CDR,
  • the additional amino acids may be from the heavy and/or light chain framework regions of any of SEQ ID NOS: 1-191, that are shown as immediately adjacent to the CDRs.
  • aspects relate to polypeptides comprising an HCDR1 (i.e., CDR-H1), HCDR2 (i.e., CDR-H2), HCDR3 (i.e., CDR-H3), LCDR1 (i.e., CDR-L1), LCDR2 (i.e., CDR-L2), and/or LCDR3 (i.e., CDR-L3) with at least or at most or exactly 1, 2, 3, 4, 5, 6 or 7 amino acids at the amino end of the CDR or at the carboxy end of the CDR, wherein the additional amino acids are the 1, 2, 3, 4, 5, 6, or 7 amino acids of Table 1 or any of SEQ ID NOS:1-191 that are shown as immediately adjacent to the CDRs.
  • HCDR1 i.e., CDR-H1
  • HCDR2 i.e., CDR-H2
  • HCDR3 i.e., CDR-H3
  • LCDR1 i.e., CDR-L1
  • antibodies comprising one or more CDRs, wherein the CDR is a fragment of Table 1 or any of SEQ ID NOS: 1-191 and wherein the fragment lacks 1, 2, 3, 4, or 5 amino acids from the amino or carboxy end of the CDR.
  • the CDR may lack one, 2, 3, 4, 5, 6, or 7 amino acids from the carboxy end and may further comprise 1, 2, 3, 4, 5, 6, 7, or 8 amino acids from the framework region of the amino end of the CDR.
  • the CDR may lack one, 2, 3, 4, 5, 6, or 7 amino acids from the amino end and may further comprise 1, 2, 3, 4, 5, 6, 7, or 8 amino acids from the framework region of the carboxy end of the CDR.
  • an antibody may be alternatively or additionally humanized in regions outside the CDR(s) and/or variable region(s).
  • a polypeptide comprises additionally or alternatively, an amino acid sequence that is at least 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99, or 100% identical or homologous to the amino acid sequence of the variable region that is not a CDR sequence, i.e., the variable region framework.
  • a polypeptide or protein comprises 1, 2, 3, 4, 5, or 6 CDRs from either or both of the light and heavy variable regions of Table 1 or any of SEQ ID NOS:1-191, and 1, 2, 3, 4, 5, or 6 CDRs may have 1, 2, and/or 3 amino acid changes with respect to these CDRs.
  • parts or all of the antibody sequence outside the variable region have been humanized.
  • a protein may comprise one or more polypeptides.
  • a protein may contain one or two polypeptides similar to a heavy chain polypeptide and/or 1 or 2 polypeptides similar to a light chain polypeptide.
  • nucleotide as well as the protein, polypeptide, and peptide sequences for various genes have been previously disclosed, and may be found in the recognized computerized databases.
  • Two commonly used databases are the National Center for Biotechnology Information’s Genbank and GenPept databases (on the World Wide Web at ncbi.nlm.nih.gov/) and The Universal Protein Resource (UniProt; on the World Wide Web at uniprot.org).
  • Genbank and GenPept databases on the World Wide Web at ncbi.nlm.nih.gov/
  • the Universal Protein Resource UniProt; on the World Wide Web at uniprot.org.
  • the coding regions for these genes may be amplified and/or expressed using the techniques disclosed herein or as would be known to those of ordinary skill in the art.
  • compositions of the disclosure can comprise any suitable concentration of protein.
  • concentration of protein in a composition can be about, at least about or at most about 0.001, 0.010, 0.050, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10.0 mg/ml or more (or any range derivable therein).
  • Antibody, and antigen binding fragment, and polypeptide aspects are shown below in the following tables.
  • Table 1 S100A4 monoclonal antibody sequences
  • Table 2 Amino Acid sequences of anti-TfR antibody heavy (H) chains
  • amino acid subunits of a protein may be substituted for other amino acids in a protein or polypeptide sequence with or without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein’ s functional activity, certain amino acid substitutions can be made in a protein sequence and in its corresponding DNA coding sequence, and nevertheless produce a protein with similar or desirable properties. It is thus contemplated by the inventors that various changes may be made in the DNA sequences of genes which encode proteins without appreciable loss of their biological utility or activity.
  • the term “functionally equivalent codon” is used herein to refer to codons that encode the same amino acid, such as the six different codons for arginine. Also considered are “neutral substitutions” or “neutral mutations” which refers to a change in the codon or codons that encode biologically equivalent amino acids.
  • Amino acid sequence variants of the disclosure can be substitutional, insertional, or deletion variants.
  • a variation in a polypeptide of the disclosure may affect 1, 2, 3, 4, 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, or more non-contiguous or contiguous amino acids of the protein or polypeptide, as compared to wild-type.
  • a variant can comprise an amino acid sequence that is at least 50%, 60%, 70%, 80%, or 90%, including all values and ranges there between, identical to any sequence provided or referenced herein.
  • a variant can include 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more substitute amino acids.
  • amino acid and nucleic acid sequences may include additional residues, such as additional N- or C-terminal amino acids, or 5' or 3' sequences, respectively, and yet still be essentially identical as set forth in one of the sequences disclosed herein, so long as the sequence meets the criteria set forth above, including the maintenance of biological protein activity where protein expression is concerned.
  • the addition of terminal sequences particularly applies to nucleic acid sequences that may, for example, include various non-coding sequences flanking either of the 5' or 3' portions of the coding region.
  • Deletion variants typically lack one or more residues of the native or wild type protein. Individual residues can be deleted or a number of contiguous amino acids can be deleted. A stop codon may be introduced (by substitution or insertion) into an encoding nucleic acid sequence to generate a truncated protein.
  • Insertional mutants typically involve the addition of amino acid residues at a nonterminal point in the polypeptide. This may include the insertion of one or more amino acid residues. Terminal additions may also be generated and can include fusion proteins which are multimers or concatemers of one or more peptides or polypeptides described or referenced herein.
  • Substitutional variants typically contain the exchange of one amino acid for another at one or more sites within the protein or polypeptide, and may be designed to modulate one or more properties of the polypeptide, with or without the loss of other functions or properties. Substitutions may be conservative, that is, one amino acid is replaced with one of similar chemical properties. “Conservative amino acid substitutions” may involve exchange of a member of one amino acid class with another member of the same class.
  • Conservative substitutions are well known in the art and include, for example, the changes of: alanine to serine; arginine to lysine; asparagine to glutamine or histidine; aspartate to glutamate; cysteine to serine; glutamine to asparagine; glutamate to aspartate; glycine to proline; histidine to asparagine or glutamine; isoleucine to leucine or valine; leucine to valine or isoleucine; lysine to arginine; methionine to leucine or isoleucine; phenylalanine to tyrosine, leucine or methionine; serine to threonine; threonine to serine; tryptophan to tyrosine; tyrosine to tryptophan or phenylalanine; and valine to isoleucine or leucine.
  • Conservative amino acid substitutions may encompass non-naturally occurring amino acid residues, which
  • substitutions may be “non-conservative”, such that a function or activity of the polypeptide is affected.
  • Non-conservative changes typically involve substituting an amino acid residue with one that is chemically dissimilar, such as a polar or charged amino acid for a nonpolar or uncharged amino acid, and vice versa.
  • Non-conservative substitutions may involve the exchange of a member of one of the amino acid classes for a member from another class.
  • polypeptides as set forth herein using well-known techniques.
  • One skilled in the art may identify suitable areas of the molecule that may be changed without destroying activity by targeting regions not believed to be important for activity.
  • the skilled artisan will also be able to identify amino acid residues and portions of the molecules that are conserved among similar proteins or polypeptides.
  • areas that may be important for biological activity or for structure may be subject to conservative amino acid substitutions without significantly altering the biological activity or without adversely affecting the protein or polypeptide structure.
  • hydropathy index of amino acids may be considered.
  • the hydropathy profile of a protein is calculated by assigning each amino acid a numerical value (“hydropathy index”) and then repetitively averaging these values along the peptide chain.
  • Each amino acid has been assigned a value based on its hydrophobicity and charge characteristics.
  • the importance of the hydropathy amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte et al., J.
  • hydrophilicity values have been assigned to these amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0+1); glutamate (+3.0+1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (—0.4); proline (-0.5+1); alanine ( _ 0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); and tryptophan (-3.4).
  • the substitution of amino acids whose hydrophilicity values are within +2 are included, in other aspects, those which are within +1 are included, and in still other aspects, those within +0.5 are included.
  • One skilled in the art can also analyze the three-dimensional structure and amino acid sequence in relation to that structure in similar proteins or polypeptides. In view of such information, one skilled in the art may predict the alignment of amino acid residues of an antibody with respect to its three-dimensional structure. One skilled in the art may choose not to make changes to amino acid residues predicted to be on the surface of the protein, since such residues may be involved in important interactions with other molecules. Moreover, one skilled in the art may generate test variants containing a single amino acid substitution at each desired amino acid residue.
  • amino acid substitutions are made that: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming protein complexes, (4) alter ligand or antigen binding affinities, and/or (5) confer or modify other physicochemical or functional properties on such polypeptides.
  • conservative amino acid substitutions may be made in the naturally occurring sequence. Substitutions can be made in that portion of the antibody that lies outside the domain(s) forming intermolecular contacts. In such aspects, conservative amino acid substitutions can be used that do not substantially change the structural characteristics of the protein or polypeptide (e.g., one or more replacement amino acids that do not disrupt the secondary structure that characterizes the native antibody).
  • nucleic acid sequences can exist in a variety of instances such as: isolated segments and recombinant vectors of incorporated sequences or recombinant polynucleotides encoding peptides and polypeptides of the disclosure, or a fragment, derivative, mutein, or variant thereof, polynucleotides sufficient for use as hybridization probes, PCR primers or sequencing primers for identifying, analyzing, mutating or amplifying a polynucleotide encoding a polypeptide, anti-sense nucleic acids for inhibiting expression of a polynucleotide, and complementary sequences of the foregoing described herein.
  • nucleic acids encoding fusion proteins that include these peptides are also provided.
  • the nucleic acids can be single-stranded or double- stranded and can comprise RNA and/or DNA nucleotides and artificial variants thereof (e.g., peptide nucleic acids).
  • polynucleotide refers to a nucleic acid molecule that either is recombinant or has been isolated from total genomic nucleic acid. Included within the term “polynucleotide” are oligonucleotides (nucleic acids 100 residues or less in length), recombinant vectors, including, for example, plasmids, cosmids, phage, viruses, and the like. Polynucleotides include, in certain aspects, regulatory sequences, isolated substantially away from their naturally occurring genes or protein encoding sequences.
  • Polynucleotides may be single- stranded (coding or antisense) or double- stranded, and may be RNA, DNA (genomic, cDNA or synthetic), analogs thereof, or a combination thereof. Additional coding or noncoding sequences may, but need not, be present within a polynucleotide.
  • the term “gene,” “polynucleotide,” or “nucleic acid” is used to refer to a nucleic acid that encodes a protein, polypeptide, or peptide (including any sequences required for proper transcription, post-translational modification, or localization). As will be understood by those in the art, this term encompasses genomic sequences, expression cassettes, cDNA sequences, and smaller engineered nucleic acid segments that express, or may be adapted to express, proteins, polypeptides, domains, peptides, fusion proteins, and mutants.
  • a nucleic acid encoding all or part of a polypeptide may contain a contiguous nucleic acid sequence encoding all or a portion of such a polypeptide. It also is contemplated that a particular polypeptide may be encoded by nucleic acids containing variations having slightly different nucleic acid sequences but, nonetheless, encode the same or substantially similar protein.
  • polynucleotide variants having substantial identity to the sequences disclosed herein; those comprising at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% or higher sequence identity, including all values and ranges there between, compared to a polynucleotide sequence provided herein using the methods described herein (e.g., BLAST analysis using standard parameters).
  • the isolated polynucleotide will comprise a nucleotide sequence encoding a polypeptide that has at least 90%, preferably 95% and above, identity to an amino acid sequence described herein, over the entire length of the sequence; or a nucleotide sequence complementary to said isolated polynucleotide.
  • nucleic acid segments regardless of the length of the coding sequence itself, may be combined with other nucleic acid sequences, such as promoters, poly adenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably.
  • the nucleic acids can be any length.
  • nucleic acid fragments of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant nucleic acid protocol.
  • a nucleic acid sequence may encode a polypeptide sequence with additional heterologous coding sequences, for example to allow for purification of the polypeptide, transport, secretion, post-translational modification, or for therapeutic benefits such as targeting or efficacy.
  • a tag or other heterologous polypeptide may be added to the modified polypeptide-encoding sequence, wherein “heterologous” refers to a polypeptide that is not the same as the modified polypeptide.
  • Nucleic acids can hybridize, e.g. to other nucleic acids, under particular hybridization conditions. Methods for hybridizing nucleic acids are well known in the art. See, e.g., Current Protocols in Molecular Biology, John Wiley and Sons, N.Y. (1989), 6.3.1-6.3.6. As defined herein, a moderately stringent hybridization condition uses a prewashing solution containing 5x sodium chloride/sodium citrate (SSC), 0.5% SDS, 1.0 mM EDTA (pH 8.0), hybridization buffer of about 50% formamide, 6xSSC, and a hybridization temperature of 55° C.
  • SSC sodium chloride/sodium citrate
  • pH 8.0 0.5%
  • hybridization buffer of about 50% formamide
  • 6xSSC 6xSSC
  • a hybridization temperature 55° C.
  • a stringent hybridization condition hybridizes in 6xSSC at 45° C., followed by one or more washes in O.lxSSC, 0.2% SDS at 68° C.
  • nucleic acids comprising nucleotide sequence that are at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% identical to each other typically remain hybridized to each other.
  • Changes can be introduced by mutation into a nucleic acid, thereby leading to changes in the amino acid sequence of a polypeptide (e.g., an antigenic peptide or polypeptide) that it encodes. Mutations can be introduced using any technique known in the art. In one aspect, one or more particular amino acid residues are changed using, for example, a site- directed mutagenesis protocol. In another aspect, one or more randomly selected residues are changed using, for example, a random mutagenesis protocol. However it is made, a mutant polypeptide can be expressed and screened for a desired property. [0246] Mutations can be introduced into a nucleic acid without significantly altering the biological activity of a polypeptide that it encodes.
  • one or more mutations can be introduced into a nucleic acid that selectively changes the biological activity of a polypeptide that it encodes. See, eg., Romain Studer et al., Biochem. J. 449:581-594 (2013).
  • the mutation can quantitatively or qualitatively change the biological activity. Examples of quantitative changes include increasing, reducing or eliminating the activity. Examples of qualitative changes include altering the antigen specificity of an antibody.
  • nucleic acid molecules are suitable for use as primers or hybridization probes for the detection of nucleic acid sequences.
  • a nucleic acid molecule can comprise only a portion of a nucleic acid sequence encoding a full-length polypeptide, for example, a fragment that can be used as a probe or primer or a fragment encoding an active portion of a given polypeptide.
  • the nucleic acid molecules may be used as probes or PCR primers for specific nucleic acid sequences.
  • a nucleic acid molecule probe may be used in diagnostic methods or a nucleic acid molecule PCR primer may be used to amplify regions of DNA that could be used, inter alia, to isolate nucleic acid sequences for use in producing the engineered cells of the disclosure.
  • the nucleic acid molecules are oligonucleotides.
  • Probes based on the desired sequence of a nucleic acid can be used to detect the nucleic acid or similar nucleic acids, for example, transcripts encoding a polypeptide of interest.
  • the probe can comprise a label group, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used to identify a cell that expresses the polypeptide.
  • nucleic acid molecule encoding polypeptides, antibodies, or antigen binding fragments of the disclosure.
  • the nucleic acid molecules may be used to express large quantities of polypeptides. If the nucleic acid molecules are derived from a non- human, non-transgenic animal, the nucleic acid molecules may be used for humanization of the antibody or TCR genes.
  • contemplated are expression vectors comprising a nucleic acid molecule encoding a polypeptide of the desired sequence or a portion thereof (e.g., a fragment containing one or more CDRs or one or more variable region domains).
  • Expression vectors comprising the nucleic acid molecules may encode the heavy chain, light chain, or the antigenbinding portion thereof.
  • expression vectors comprising nucleic acid molecules may encode fusion proteins, modified antibodies, antibody heavy and/or light chain, antibody fragments, and probes thereof.
  • vectors and expression vectors may contain nucleic acid sequences that serve other functions as well.
  • DNAs encoding the polypeptides or peptides are inserted into expression vectors such that the gene area is operatively linked to transcriptional and translational control sequences.
  • expression vectors used in any of the host cells contain sequences for plasmid or virus maintenance and for cloning and expression of exogenous nucleotide sequences.
  • sequences collectively referred to as “flanking sequences” typically include one or more of the following operatively linked nucleotide sequences: a promoter, one or more enhancer sequences, an origin of replication, a transcriptional termination sequence, a complete intron sequence containing a donor and acceptor splice site, a sequence encoding a leader sequence for polypeptide secretion, a ribosome binding site, a polyadenylation sequence, a polylinker region for inserting the nucleic acid encoding the polypeptide to be expressed, and a selectable marker element.
  • a promoter one or more enhancer sequences
  • an origin of replication a transcriptional termination sequence
  • a complete intron sequence containing a donor and acceptor splice site a sequence encoding a leader sequence for polypeptide secreti
  • Prokaryote- and/or eukaryote-based systems can be employed for use with an aspect to produce nucleic acid sequences, or their cognate polypeptides, proteins and peptides.
  • Commercially and widely available systems include in but are not limited to bacterial, mammalian, yeast, and insect cell systems.
  • Different host cells have characteristic and specific mechanisms for the post- translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed.
  • Those skilled in the art are able to express a vector to produce a nucleic acid sequence or its cognate polypeptide, protein, or peptide using an appropriate expression system.
  • nucleic acid delivery to effect expression of compositions are anticipated to include virtually any method by which a nucleic acid (e.g., DNA, including viral and nonviral vectors) can be introduced into a cell, a tissue or an organism, as described herein or as would be known to one of ordinary skill in the art.
  • a nucleic acid e.g., DNA, including viral and nonviral vectors
  • Such methods include, but are not limited to, direct delivery of DNA such as by injection (U.S. Patents 5,994,624,5,981,274, 5,945,100, 5,780,448, 5,736,524, 5,702,932, 5,656,610, 5,589,466 and 5,580,859, each incorporated herein by reference), including microinjection (Harland and Weintraub, 1985; U.S.
  • Patent 5,789,215 incorporated herein by reference
  • electroporation U.S. Patent No. 5,384,253, incorporated herein by reference
  • calcium phosphate precipitation Graham and Van Der Eb, 1973; Chen and Okayama, 1987; Rippe et al., 1990
  • DEAE dextran followed by polyethylene glycol
  • direct sonic loading Fechheimer et al., 1987
  • liposome mediated transfection Nicolau and Sene, 1982; Fraley et al., 1979; Nicolau et al., 1987; Wong et al., 1980; Kaneda et al., 1989; Kato et al., 1991
  • microprojectile bombardment PCT Application Nos.
  • Other methods include viral transduction, such as gene transfer by lentiviral or retroviral transduction.
  • the present disclosure includes pharmaceutical compositions and methods for treating or preventing a disease, disorder, or condition in a subject in need thereof.
  • the disease, disorder, or condition is cancer and/or metastasis thereof.
  • the cancer may be a cancer expressing S100A4.
  • the cancer is breast cancer or glioblastoma.
  • the subject is human.
  • compositions according to the current disclosure will typically be via any common route. This includes, but is not limited to parenteral, orthotopic, intradermal, subcutaneous, orally, transdermally, intramuscular, intraperitoneal, intraperitoneally, intraorbitally, by implantation, by inhalation, intraventricularly, intrathecal, intranasally or intravenous injection.
  • the administration is systemic.
  • the administration is local administration.
  • the administration is intratumoral.
  • the compositions are delivered, such as injected, directly into the tumor and/or tumor bed.
  • compositions of the present disclosure are administered to a subject intravenously.
  • compositions and therapies of the disclosure are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective.
  • the quantity to be administered depends on the subject to be treated. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner.
  • administrations may be administered at intervals of any suitable length.
  • the administrations may be adiminstered at a range from daily, weekly, monthly, or yearly intervals.
  • pharmaceutically acceptable refers to molecular entities and compositions that do not produce an adverse, allergic, or other untoward reaction when administered to an animal, or human.
  • pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like.
  • compositions of the current disclosure are pharmaceutically acceptable compositions.
  • compositions of the disclosure can be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, or even intraperitoneal routes.
  • parenteral administration e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, or even intraperitoneal routes.
  • such compositions can be prepared as injectables, either as liquid solutions or suspensions and the preparations can also be emulsified.
  • compositions suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil, or aqueous propylene glycol. It also should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • Sterile injectable solutions are prepared by incorporating the active ingredients (e.g., polypeptides of the disclosure) in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization.
  • active ingredients e.g., polypeptides of the disclosure
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
  • An effective amount of a composition is determined based on the intended goal.
  • unit dose or “dosage” refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the composition calculated to produce the desired responses discussed herein in association with its administration, i.e., the appropriate route and regimen.
  • the quantity to be administered depends on the result and/or protection desired. Precise amounts of the composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the subject, route of administration, intended goal of treatment (alleviation of symptoms versus cure), and potency, stability, and toxicity of the particular composition.
  • solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective.
  • the formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above.
  • compositions and related methods of the present disclosure may also be used in combination with the administration of additional therapies such as the additional therapeutics described herein or in combination with other traditional therapeutics known in the art.
  • additional therapies such as the additional therapeutics described herein or in combination with other traditional therapeutics known in the art.
  • the antibody or antigen binding fragment thereof may be part of a combination therapy for treating cancer and/or metastasis thereof.
  • the combination therapy comprises administration of the antibody or antigen binding fragment thereof, and an additional therapeutic.
  • the additional therapeutic can be, for example, a therapeutic for treating the cancer. Any suitable additional therapeutic may be used, and may be selected in accordance with the particular subject and cancer to be treated.
  • the additional therapeutic is a checkpoint inhibitor.
  • Various immune checkpoint inhibitors are known in the art and may be suitable for combining with the antibody or antigen binding fragment thereof.
  • compositions and treatments disclosed herein may precede, be cocurrent with and/or follow another treatment or agent (e.g. the additional therapeutic) by intervals ranging from minutes to weeks.
  • another treatment or agent e.g. the additional therapeutic
  • agents are applied separately to a cell, tissue or organism, one would generally ensure that a significant period of time did not expire between the time of each delivery, such that the therapeutic agents would still be able to exert an advantageously combined effect on the cell, tissue or organism.
  • one may contact the cell, tissue or organism with two, three, four or more agents or treatments substantially simultaneously (i.e., within less than about a minute).
  • one or more therapeutic agents or treatments may be administered or provided within 1 minute, 5 minutes, 10 minutes, 20 minutes, 30 minutes, 45 minutes, 60 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 22 hours, 23 hours, 24 hours, 25 hours, 26 hours, 27 hours, 28 hours, 29 hours, 30 hours, 31 hours, 32 hours, 33 hours, 34 hours, 35 hours, 36 hours, 37 hours, 38 hours, 39 hours, 40 hours, 41 hours, 42 hours, 43 hours, 44 hours, 45 hours, 46 hours, 47 hours, 48 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 1 week, 2 weeks, 3 weeks, 4 hours, 5
  • the treatments may include various “unit doses.”
  • Unit dose is defined as containing a predetermined-quantity of the therapeutic composition.
  • the quantity to be administered, and the particular route and formulation, is within the skill of determination of those in the clinical arts.
  • a unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time.
  • a unit dose comprises a single administrable dose.
  • the quantity to be administered depends on the treatment effect desired.
  • An effective dose is understood to refer to an amount necessary to achieve a particular effect. In the practice in certain aspects, it is contemplated that doses in the range from 10 mg/kg to 200 mg/kg can affect the protective capability of these agents.
  • doses include doses of about 0.1, 0.5, 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, and 200, 300, 400, 500, 1000 pg/kg, mg/kg, pg/day, or mg/day or any range derivable therein.
  • doses can be administered at multiple times during a day, and/or on multiple days, weeks, or months.
  • the therapeutically effective or sufficient amount of the composition e.g.
  • the therapy used is about 0.01 to about 45 mg/kg, about 0.01 to about 40 mg/kg, about 0.01 to about 35 mg/kg, about 0.01 to about 30 mg/kg, about 0.01 to about 25 mg/kg, about 0.01 to about 20 mg/kg, about 0.01 to about 15 mg/kg, about 0.01 to about 10 mg/kg, about 0.01 to about 5 mg/kg, or about 0.01 to about 1 mg/kg (or any range derivable therein) administered daily, for example.
  • a therapy described herein is administered to a subject at a dose of about 100 mg, about 200 mg, about 300 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, about 900 mg, about 1000 mg, about 1100 mg, about 1200 mg, about 1300 mg or about 1400 mg (or any range derivable therein) on day 1 of 21-day cycles.
  • the dose may be administered as a single dose or as multiple doses (e.g., 2 or 3 doses), such as infusions.
  • the progress of this therapy may be monitored by conventional techniques.
  • the effective dose of the pharmaceutical composition is one which can provide a blood level of about 1 pM to 150 pM. In another aspect, the effective dose provides a blood level of about 4 pM to 100 pM.; or about 1 pM to 100 pM; or about 1 pM to 50 pM; or about 1 pM to 40 pM; or about 1 pM to 30 pM; or about 1 pM to 20 pM; or
  • the dose can provide the following blood level of the agent that results from a therapeutic agent being administered to a subject: about, at least about, or at most about 1, 2, 3, 4, 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,
  • the therapeutic agent that is administered to a subject is metabolized in the body to a metabolized therapeutic agent, in which case the blood levels may refer to the amount of that agent.
  • the blood levels discussed herein may refer to the unmetabolized therapeutic agent.
  • Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and may be specific to the treated individual. Factors affecting dose include physical and clinical state of the subject, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance or other therapies a subject may be undergoing.
  • dosage units of pg/kg or mg/kg of body weight can be converted and expressed in comparable concentration units of pg/ml or mM (blood levels), such as 4 pM to 100 pM. It is also understood that uptake is species and organ/tissue dependent. The applicable conversion factors and physiological assumptions to be made concerning uptake and concentration measurement are well-known and would permit those of skill in the art to convert one concentration measurement to another and make reasonable comparisons and conclusions regarding the doses, efficacies and results described herein.
  • compositions of the disclosure are directed to compositions of the disclosure (e.g. anti- S100A4 and/or anti-S100A9 antibodies or antigen binding fragments thereof) and methods for therapeutic use.
  • the compositions of the disclosure may be used for in vivo, in vitro, or ex vivo administration.
  • the route of administration of the composition may be, for example, intratumoral, intravenous, intramuscular, intraperitoneal, subcutaneous, intraarticular, intrasynovial, intrathecal, oral, topical, through inhalation, or through a combination of two or more routes of administration.
  • the disclosed methods comprise administering a cancer therapy to a subject or patient.
  • the cancer therapy comprises a local cancer therapy or a systemic cancer therapy.
  • the cancer therapy excludes a local cancer therapy or a systemic cancer therapy.
  • the cancer therapy comprises an immunotherapy, which may be a checkpoint inhibitor therapy. Any of these cancer therapies may also be excluded. Combinations of these therapies may also be administered.
  • the term “cancer,” as used herein, may be used to describe a solid tumor, metastatic cancer, or non-metastatic cancer.
  • the cancer may originate in the bladder, blood, bone, bone marrow, brain, breast, colon, esophagus, duodenum, small intestine, large intestine, colon, rectum, anus, gum, head, kidney, liver, lung, nasopharynx, neck, ovary, pancreas, prostate, skin, stomach, testis, tongue, or uterus.
  • the cancer is a Stage I cancer.
  • the cancer is a Stage II cancer.
  • the cancer is a Stage III cancer.
  • the cancer is a Stage IV cancer.
  • the cancer may specifically be of the following histological type, though it is not limited to these: neoplasm, malignant; carcinoma; carcinoma, undifferentiated; giant and spindle cell carcinoma; small cell carcinoma; papillary carcinoma; squamous cell carcinoma; lymphoepithelial carcinoma; basal cell carcinoma; pilomatrix carcinoma; transitional cell carcinoma; papillary transitional cell carcinoma; adenocarcinoma; gastrinoma, malignant; cholangiocarcinoma; hepatocellular carcinoma; combined hepatocellular carcinoma and cholangiocarcinoma; trabecular adenocarcinoma; adenoid cystic carcinoma; adenocarcinoma in adenomatous polyp; adenocarcinoma, familial polyposis coli; solid carcinoma; carcinoid tumor, malignant; branchiolo-alveolar adenocarcinoma; papillary adenocarcinoma; chromophobe carcinoma;
  • the cancer is lung cancer. In some aspects, the cancer is non-small cell lung cancer (NSCLC). In some aspects, disclosed are methods for treating cancer originating from the breast. In some aspects, the cancer is breast cancer. In some aspects, the cancer is triple negative breast cancer. In some aspects, the cancer is a recurrent cancer. In some aspects, the cancer is an immunotherapy-resistant cancer.
  • NSCLC non-small cell lung cancer
  • Management regimen refers to a management plan that specifies the type of examination, screening, diagnosis, surveillance, care, and treatment (such as dosage, schedule and/or duration of a treatment) provided to a subject in need thereof (e.g., a subject diagnosed with cancer).
  • the selected treatment regimen can be an aggressive one which is expected to result in the best clinical outcome (e.g., complete cure of the disease) or a more moderate one which may relieve symptoms of the disease yet may result in incomplete cure of the disease.
  • the type of treatment can include administration of the compositions provided herein (e.g. an anti- S100A4 antibody or antigen binding fragment thereof), a surgical intervention, administration of a therapeutic drug, immunotherapy, an exposure to radiation therapy, and/or any combination thereof.
  • the dosage, schedule and duration of treatment can vary, depending on the severity of disease and the selected type of treatment, and those of skill in the art can adjust the type of treatment with the dosage, schedule, and duration of treatment.
  • a cancer treatment may include or exclude any of the cancer treatments described herein.
  • aspects of the disclosure include patients that have been previously treated for a therapy described herein, are currently being treated for a therapy described herein, or have not been treated for a therapy described herein.
  • the patient is one that has been determined to be resistant to a therapy described herein.
  • the patient is one that has been determined to be sensitive to a therapy described herein.
  • a radiotherapy such as ionizing radiation
  • ionizing radiation means radiation comprising particles or photons that have sufficient energy or can produce sufficient energy via nuclear interactions to produce ionization (gain or loss of electrons).
  • ionizing radiation is an x-radiation.
  • Means for delivering x-radiation to a target tissue or cell are well known in the art.
  • the radiotherapy can comprise external radiotherapy, internal radiotherapy, radioimmunotherapy, or intraoperative radiation therapy (IORT).
  • IORT intraoperative radiation therapy
  • the external radiotherapy comprises three-dimensional conformal radiation therapy (3D-CRT), intensity modulated radiation therapy (IMRT), proton beam therapy, image-guided radiation therapy (IGRT), or stereotactic radiation therapy.
  • the internal radiotherapy comprises interstitial brachytherapy, intracavitary brachytherapy, or intraluminal radiation therapy.
  • the radiotherapy is administered to a primary tumor.
  • the amount of ionizing radiation is greater than 20 Gy and is administered in one dose. In some aspects, the amount of ionizing radiation is 18 Gy and is administered in three doses. In some aspects, the amount of ionizing radiation is at least, at most, exactly, or between (inclusive or exclusive) of about 0.5, 1, 2, 4, 6, 8, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 18, 19, 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, 56, 57, 58, 59, or 60 Gy (or any derivable range therein).
  • the ionizing radiation is administered in at least, at most, exactly, or between (inclusive or exclusive) of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 doses (or any derivable range therein).
  • the doses may be about 1, 4, 8, 12, or 24 hours or 1, 2, 3, 4, 5, 6, 7, or 8 days or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, or 16 weeks apart, or any derivable range therein.
  • the amount of radiotherapy administered to a subject may be presented as a total dose of radiotherapy, which is then administered in fractionated doses.
  • the total dose is 50 Gy administered in 10 fractionated doses of 5 Gy each.
  • the total dose is 50-90 Gy, administered in 20-60 fractionated doses of 2-3 Gy each.
  • the total dose of radiation is at least, at most, exactly, or between (inclusive or exclusive) of about 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
  • the total dose is administered in fractionated doses of at least, at most, exactly, or between (inclusive or exclusive) of about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 20, 25, 30, 35, 40, 45, or 50 Gy (or any derivable range therein).
  • At least, at most, exactly, or between (inclusive or exclusive) of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 (or any derivable range therein) fractionated doses are administered per day. In some aspects, at least, at most, exactly, or between (inclusive or exclusive) of 1, 2, 3, 4, 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, or 30 (or any derivable range therein) fractionated doses are administered per week.
  • the methods comprise administration of a cancer immunotherapy.
  • Cancer immunotherapy (sometimes called immuno-oncology, abbreviated IO) is the use of the immune system to treat cancer.
  • Immunotherapies can be categorized as active, passive or hybrid (active and passive). These approaches exploit the fact that cancer cells often have molecules on their surface that can be detected by the immune system, known as tumor- associated antigens (TAAs); they are often proteins or other macromolecules (e.g., carbohydrates).
  • TAAs tumor- associated antigens
  • Passive immunotherapies enhance existing anti-tumor responses and include the use of monoclonal antibodies, lymphocytes, and cytokines.
  • Various immunotherapies are known in the art, and examples are described below.
  • checkpoint inhibitor therapy refers to cancer therapy comprising providing one or more immune checkpoint inhibitors to a subject suffering from or suspected of having cancer.
  • ICT immune checkpoint blockade therapy
  • CBI checkpoint blockade immunotherapy
  • Any suitable checkpoint inhibitor may be used in connection with the methods and compositions described herein.
  • Suitable checkpoint inhibitors may include inhibitors of any of: PD1/PDL1, CTLA4, TIGIT, LY6G, P-selectin, and ICOS. 1. PD-1, PDL1, and PDL2 inhibitors
  • PD -1 can act in the tumor microenvironment where T cells encounter an infection or tumor. Activated T cells upregulate PD-1 and continue to express it in the peripheral tissues. Cytokines such as IFN-gamma induce the expression of PDL1 on epithelial cells and tumor cells. PDL2 is expressed on macrophages and dendritic cells. The main role of PD-1 is to limit the activity of effector T cells in the periphery and prevent excessive damage to the tissues during an immune response. Inhibitors of the disclosure may block one or more functions of PD-1 and/or PDL1 activity.
  • Alternative names for “PD-1” include CD279 and SLEB2.
  • Alternative names for “PDL1” include B7-H1, B7-4, CD274, and B7-H.
  • Alternative names for “PDL2” include B7- DC, Btdc, and CD273.
  • PD-1, PDL1, and PDL2 are human PD-1, PDL1 and PDL2.
  • the PD-1 inhibitor is a molecule that inhibits the binding of PD-1 to its ligand binding partners.
  • the PD-1 ligand binding partners are PDL1 and/or PDL2.
  • a PDL1 inhibitor is a molecule that inhibits the binding of PDL1 to its binding partners.
  • PDL1 binding partners are PD-1 and/or B7- 1.
  • a PDL2 inhibitor is a molecule that inhibits the binding of PDL2 to its binding partners.
  • a PDL2 binding partner is PD-1.
  • the inhibitor may be an antibody, an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
  • Exemplary antibodies are described in U.S. Patent Nos. 8,735,553, 8,354,509, and 8,008,449, all incorporated herein by reference.
  • Other PD-1 inhibitors for use in the methods and compositions provided herein are known in the art such as described in U.S. Patent Application Nos. US2014/0294898, US2014/022021, and US2011/0008369, all incorporated herein by reference.
  • the PD-1 inhibitor is an anti-PD-1 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody).
  • the anti-PD-1 antibody is selected from the group consisting of nivolumab, pembrolizumab, and pidilizumab.
  • the PD-1 inhibitor is an immunoadhesin (e.g., an immunoadhesin comprising an extracellular or PD-1 binding portion of PDL1 or PDL2 fused to a constant region (e.g., an Fc region of an immunoglobulin sequence).
  • the PDL1 inhibitor comprises AMP- 224.
  • Nivolumab also known as MDX-1106-04, MDX-1106, ONO-4538, BMS-936558, and OPDIVO®, is an anti-PD-1 antibody described in W02006/121168.
  • Pembrolizumab also known as MK-3475, Merck 3475, lambrolizumab, KEYTRUDA®, and SCH-900475, is an anti-PD-1 antibody described in W02009/114335.
  • Pidilizumab also known as CT-011, hBAT, or hBAT-1, is an anti-PD-1 antibody described in W02009/101611.
  • AMP-224 also known as B7-DCIg, is a PDL2-Fc fusion soluble receptor described in WO2010/027827 and WO201 1/066342.
  • Additional PD-1 inhibitors include MED 10680, also known as AMP-514, and REGN2810.
  • the immune checkpoint inhibitor is a PDL1 inhibitor such as durvalumab, also known as MEDI4736, atezolizumab, also known as MPDL3280A, avelumab, also known as MSB00010118C, MDX-1105, BMS-936559, or combinations thereof.
  • the immune checkpoint inhibitor is a PDL2 inhibitor such as rHIgM12B7.
  • the inhibitor comprises the heavy and light chain CDRs or VRs of nivolumab, pembrolizumab, or pidilizumab. Accordingly, in one aspect, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of nivolumab, pembrolizumab, or pidilizumab, and the CDR1, CDR2 and CDR3 domains of the VL region of nivolumab, pembrolizumab, or pidilizumab. In another aspect, the antibody competes for binding with and/or binds to the same epitope on PD-1, PDL1, or PDL2 as the above- mentioned antibodies.
  • the antibody has at least, at most, exactly, or between (inclusive or exclusive) of 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies.
  • CTLA-4 cytotoxic T-lymphocyte-associated protein 4
  • CD 152 cytotoxic T-lymphocyte-associated protein 4
  • the complete cDNA sequence of human CTLA-4 has the GENBANK® accession number L15006.
  • CTLA-4 is found on the surface of T cells and acts as an “off’ switch when bound to B7-1 (CD80) or B7-2 (CD86) on the surface of antigen-presenting cells.
  • CTLA4 is a member of the immunoglobulin superfamily that is expressed on the surface of Helper T cells and transmits an inhibitory signal to T cells.
  • CTLA4 is similar to the T-cell co- stimulatory protein, CD28, and both molecules bind to B7-1 and B7-2 on antigen-presenting cells.
  • CTLA-4 transmits an inhibitory signal to T cells, whereas CD28 transmits a stimulatory signal.
  • Intracellular CTLA- 4 is also found in regulatory T cells and may be important to their function. T cell activation through the T cell receptor and CD28 leads to increased expression of CTLA-4, an inhibitory receptor for B7 molecules.
  • Inhibitors of the disclosure may block one or more functions of CTLA-4, B7-1, and/or B7-2 activity. In some aspects, the inhibitor blocks the CTLA-4 and B7-
  • the inhibitor blocks the CTLA-4 and B7-2 interaction.
  • the immune checkpoint inhibitor is an anti-CTLA-4 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
  • an anti-CTLA-4 antibody e.g., a human antibody, a humanized antibody, or a chimeric antibody
  • an antigen binding fragment thereof e.g., an immunoadhesin, a fusion protein, or oligopeptide.
  • Anti-human-CTLA-4 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
  • art recognized anti-CTLA-4 antibodies can be used.
  • the anti- CTLA-4 antibodies disclosed in: US 8,119,129, WO 01/14424, WO 98/42752; WO 00/37504 (CP675,206, also known as tremelimumab; formerly ticilimumab), U.S. Patent No. 6,207,156; Hurwitz et al., 1998; can be used in the methods disclosed herein.
  • the teachings of each of the aforementioned publications are hereby incorporated by reference.
  • Antibodies that compete with any of these art-recognized antibodies for binding to CTLA-4 also can be used.
  • a humanized CTLA-4 antibody is described in International Patent Application No. W02001/014424, W02000/037504, and U.S. Patent No. 8,017,114; all incorporated herein by reference.
  • a further anti-CTLA-4 antibody useful as a checkpoint inhibitor in the methods and compositions of the disclosure is ipilimumab (also known as 10D1, MDX- 010, MDX- 101, and YERVOY®) or antigen binding fragments and variants thereof (see, e.g., WO 01/14424).
  • the inhibitor comprises the heavy and light chain CDRs or VRs of tremelimumab or ipilimumab.
  • the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of tremelimumab or ipilimumab, and the CDR1, CDR2 and CDR3 domains of the VL region of tremelimumab or ipilimumab.
  • the antibody competes for binding with and/or binds to the same epitope on PD-1, B7-1, or B7-
  • the antibody has at least, at most, exactly, or between (inclusive or exclusive) of 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above- mentioned antibodies.
  • LAG3 lymphocyte-activation gene 3
  • CD223 lymphocyte activating 3
  • LAG3 is a member of the immunoglobulin superfamily that is found on the surface of activated T cells, natural killer cells, B cells, and plasmacytoid dendritic cells.
  • LAG3’s main ligand is MHC class II, and it negatively regulates cellular proliferation, activation, and homeostasis of T cells, in a similar fashion to CTLA-4 and PD-1 and has been reported to play a role in Treg suppressive function.
  • LAG3 also helps maintain CD8+ T cells in a tolerogenic state and, working with PD-1, helps maintain CD8 exhaustion during chronic viral infection.
  • LAG3 is also known to be involved in the maturation and activation of dendritic cells.
  • Inhibitors of the disclosure may block one or more functions of LAG3 activity.
  • the immune checkpoint inhibitor is an anti-LAG3 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
  • an anti-LAG3 antibody e.g., a human antibody, a humanized antibody, or a chimeric antibody
  • an antigen binding fragment thereof e.g., an immunoadhesin, a fusion protein, or oligopeptide.
  • Anti-human-LAG3 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
  • art recognized anti-LAG3 antibodies can be used.
  • the anti-LAG3 antibodies can include: GSK2837781, IMP321, FS-118, Sym022, TSR-033, MGD013, BI754111, AVA-017, or GSK2831781.
  • the inhibitor comprises the heavy and light chain CDRs or VRs of an anti-LAG3 antibody. Accordingly, in one aspect, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of an anti-LAG3 antibody, and the CDR1, CDR2 and CDR3 domains of the VL region of an anti-LAG3 antibody. In another aspect, the antibody has at least, at most, exactly, or between (inclusive or exclusive) of 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range therein) variable region amino acid sequence identity with the above-mentioned antibodies.
  • TIM-3 T-cell immunoglobulin and mucin-domain containing-3
  • HAVCR2 hepatitis A virus cellular receptor 2
  • CD366 CD366
  • the complete mRNA sequence of human TIM-3 has the GENBANK® accession number NM_032782.
  • TIM-3 is found on the surface IFNy-producing CD4+ Thl and CD8+ Tel cells.
  • the extracellular region of TIM-3 consists of a membrane distal single variable immunoglobulin domain (IgV) and a glycosylated mucin domain of variable length located closer to the membrane.
  • TIM-3 is an immune checkpoint and, together with other inhibitory receptors including PD-1 and LAG3, it mediates the T-cell exhaustion.
  • TIM-3 has also been shown as a CD4+ Thl -specific cell surface protein that regulates macrophage activation.
  • Inhibitors of the disclosure may block one or more functions of TIM-3 activity.
  • the immune checkpoint inhibitor is an anti-TIM-3 antibody (e.g., a human antibody, a humanized antibody, or a chimeric antibody), an antigen binding fragment thereof, an immunoadhesin, a fusion protein, or oligopeptide.
  • an anti-TIM-3 antibody e.g., a human antibody, a humanized antibody, or a chimeric antibody
  • an antigen binding fragment thereof e.g., an immunoadhesin, a fusion protein, or oligopeptide.
  • Anti-human-TIM-3 antibodies (or VH and/or VL domains derived therefrom) suitable for use in the present methods can be generated using methods well known in the art.
  • art recognized anti-TIM-3 antibodies can be used.
  • anti-TIM-3 antibodies including: MBG453, TSR-022 (also known as cobolimab), and EY3321367 can be used in the methods disclosed herein.
  • MBG453, TSR-022 also known as cobolimab
  • EY3321367 can be used in the methods disclosed herein.
  • These and other anti-TIM-3 antibodies useful in the claimed invention can be found in, for example: US 9,605,070, US 8,841,418, US2015/0218274, and US 2016/0200815.
  • the teachings of each of the aforementioned publications are hereby incorporated by reference.
  • Antibodies that compete with any of these art-recognized antibodies for binding to TIM-3 also can be used.
  • the inhibitor comprises the heavy and light chain CDRs or VRs of an anti-TIM-3 antibody. Accordingly, in one aspect, the inhibitor comprises the CDR1, CDR2, and CDR3 domains of the VH region of an anti-TIM-3 antibody, and the CDR1, CDR2 and CDR3 domains of the VL region of an anti-TIM-3 antibody. In another aspect, the antibody has at least, at most, exactly, or between (inclusive or exclusive) of 70, 75, 80, 85, 90, 95, 97, or 99% (or any derivable range or value therein) variable region amino acid sequence identity with the above-mentioned antibodies.
  • the immunotherapy comprises an inhibitor of a co-stimulatory molecule.
  • the inhibitor comprises an inhibitor of B7-1 (CD80), B7-2 (CD86), CD28, ICOS, 0X40 (TNFRSF4), 4-1BB (CD137; TNFRSF9), CD40L (CD40LG), GITR (TNFRSF18), and combinations thereof.
  • Inhibitors include inhibitory antibodies, polypeptides, compounds, and nucleic acids.
  • compositions such as the antibody, antigen binding fragment thereof, or polypeptides provided herein.
  • Methods for conjugating polypeptides to these agents are known in the art.
  • polypeptides can be labeled with a detectable moiety such as a radioactive atom, a chromophore, a fluorophore, or the like.
  • a detectable moiety such as a radioactive atom, a chromophore, a fluorophore, or the like.
  • Such labeled polypeptides can be used for diagnostic techniques, either in vivo, or in an isolated test sample or in methods described herein.
  • label intends a directly or indirectly detectable compound or composition that is conjugated directly or indirectly to the composition to be detected, e.g., polynucleotide or protein such as an antibody so as to generate a "labeled" composition.
  • the term also includes sequences conjugated to the polynucleotide that will provide a signal upon expression of the inserted sequences, such as green fluorescent protein (GFP) and the like.
  • the label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition that is detectable.
  • the labels can be suitable for small scale detection or more suitable for high-throughput screening.
  • suitable labels include, but are not limited to radioisotopes, fluorochromes, chemiluminescent compounds, dyes, and proteins, including enzymes.
  • the label may be simply detected or it may be quantified.
  • a response that is simply detected generally comprises a response whose existence merely is confirmed, whereas a response that is quantified generally comprises a response having a quantifiable (e.g., numerically reportable) value such as an intensity, polarization, and/or other property.
  • the detectable response may be generated directly using a luminophore or fluorophore associated with an assay component actually involved in binding, or indirectly using a luminophore or fluorophore associated with another (e.g., reporter or indicator) component.
  • luminescent labels that produce signals include, but are not limited to bioluminescence and chemiluminescence. Detectable luminescence response generally comprises a change in, or an occurrence of, a luminescence signal. Suitable methods and luminophores for luminescently labeling assay components are known in the art and described for example in Haugland, Richard P. (1996) Handbook of Fluorescent Probes and Research Chemicals (6. sup. th ed.). Examples of luminescent probes include, but are not limited to, aequorin and luciferases.
  • fluorescent labels include, but are not limited to, fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin, coumarin, methyl-coumarins, pyrene, Malacite green, stilbene, Lucifer Yellow, Cascade Blue.TM., and Texas Red.
  • suitable optical dyes are described in the Haugland, Richard P. (1996) Handbook of Fluorescent Probes and Research Chemicals (6. sup. th ed.).
  • the fluorescent label is functionalized to facilitate covalent attachment to a cellular component present in or on the surface of the cell or tissue such as a cell surface marker.
  • Suitable functional groups include, but not are limited to, isothiocyanate groups, amino groups, haloacetyl groups, maleimides, succinimidyl esters, and sulfonyl halides, all of which may be used to attach the fluorescent label to a second molecule.
  • the choice of the functional group of the fluorescent label will depend on the site of attachment to either a linker, the agent, the marker, or the second labeling agent.
  • Attachment of the fluorescent label may be either directly to the cellular component or compound or alternatively, can be via a linker.
  • Suitable binding pairs for use in indirectly linking the fluorescent label to the intermediate include, but are not limited to, antigens/polypeptides, e.g., rhodamine/anti-rhodamine, biotin/avidin and biotin/strepavidin.
  • haptens such as biotin, which reacts avidin, or dinitrophenol, pyridoxal, and fluorescein, which can react with specific anti-hapten polypeptides. See, Harlow and Lane (1988) supra. XIII. Sample Preparation
  • methods involve obtaining or evaluating a sample from a subject.
  • the sample may include a sample obtained from any source including but not limited to blood, sweat, hair follicle, buccal tissue, tears, menses, feces, or saliva.
  • any medical professional such as a doctor, nurse or medical technician may obtain a biological sample for testing.
  • the biological sample can be obtained without the assistance of a medical professional.
  • a sample may include but is not limited to, tissue, cells, or biological material from cells or derived from cells of a subject.
  • the biological sample may be a heterogeneous or homogeneous population of cells or tissues.
  • the biological sample may be obtained using any method known to the art that can provide a sample suitable for the analytical methods described herein.
  • the sample may be obtained by non-invasive methods including but not limited to: scraping of the skin or cervix, swabbing of the cheek, saliva collection, urine collection, feces collection, collection of menses, tears, or semen.
  • the sample may be obtained by methods known in the art.
  • the samples are obtained by biopsy.
  • the sample is obtained by swabbing, endoscopy, scraping, phlebotomy, or any other methods known in the art.
  • the sample may be obtained, stored, or transported using components of a kit of the present methods.
  • multiple samples may be obtained for diagnosis by the methods described herein.
  • multiple samples such as one or more samples from one tissue type (for example breast tissue) and one or more samples from another specimen (for example serum) may be obtained for diagnosis by the methods.
  • multiple samples such as one or more samples from one tissue type (e.g. breast) and one or more samples from another specimen (e.g. serum) may be obtained at the same or different times. Samples may be obtained at different times are stored and/or analyzed by different methods. For example, a sample may be obtained and analyzed by routine staining methods or any other cytological analysis methods.
  • the biological sample may be obtained by a physician, nurse, or other medical professional such as a medical technician, endocrinologist, cytologist, phlebotomist, radiologist, or a pulmonologist.
  • the medical professional may indicate the appropriate test or assay to perform on the sample.
  • a molecular profiling business may consult on which assays or tests are most appropriately indicated.
  • the patient or subject may obtain a biological sample for testing without the assistance of a medical professional, such as obtaining a whole blood sample, a urine sample, a fecal sample, a buccal sample, or a saliva sample.
  • the sample is obtained by an invasive procedure including but not limited to: biopsy, needle aspiration, endoscopy, or phlebotomy.
  • the method of needle aspiration may further include fine needle aspiration, core needle biopsy, vacuum assisted biopsy, or large core biopsy.
  • multiple samples may be obtained by the methods herein to ensure a sufficient amount of biological material.
  • the sample is a fine needle aspirate of a tumor or suspected tumor or neoplasm.
  • the fine needle aspirate sampling procedure may be guided by the use of an ultrasound, X-ray, or other imaging device.
  • the molecular profiling business may obtain the biological sample from a subject directly, from a medical professional, from a third party, or from a kit provided by a molecular profiling business or a third party.
  • the biological sample may be obtained by the molecular profiling business after the subject, a medical professional, or a third party acquires and sends the biological sample to the molecular profiling business.
  • the molecular profiling business may provide suitable containers, and excipients for storage and transport of the biological sample to the molecular profiling business.
  • a medical professional need not be involved in the initial diagnosis or sample acquisition.
  • An individual may alternatively obtain a sample through the use of an over the counter (OTC) kit.
  • OTC kit may contain a means for obtaining said sample as described herein, a means for storing said sample for inspection, and instructions for proper use of the kit.
  • molecular profiling services are included in the price for purchase of the kit. In other cases, the molecular profiling services are billed separately.
  • a sample suitable for use by the molecular profiling business may be any material containing tissues, cells, nucleic acids, genes, gene fragments, expression products, gene expression products, or gene expression product fragments of an individual to be tested. Methods for determining sample suitability and/or adequacy are provided.
  • the subject may be referred to a specialist such as an oncologist, surgeon, or endocrinologist.
  • the specialist may likewise obtain a biological sample for testing or refer the individual to a testing center or laboratory for submission of the biological sample.
  • the medical professional may refer the subject to a testing center or laboratory for submission of the biological sample.
  • the subject may provide the sample.
  • a molecular profiling business may obtain the sample.
  • the terms “cell,” “cell line,” and “cell culture” may be used interchangeably. All of these terms also include both freshly isolated cells and ex vivo cultured, activated or expanded cells. All of these terms also include their progeny, which is any and all subsequent generations. It is understood that all progeny may not be identical due to deliberate or inadvertent mutations.
  • “host cell” refers to a prokaryotic or eukaryotic cell, and it includes any transformable organism that is capable of replicating a vector or expressing a heterologous gene encoded by a vector. A host cell can, and has been, used as a recipient for vectors or viruses.
  • a host cell may be “transfected” or “transformed,” which refers to a process by which exogenous nucleic acid, such as a recombinant protein-encoding sequence, is transferred or introduced into the host cell.
  • a transformed cell includes the primary subject cell and its progeny.
  • transfection can be carried out on any prokaryotic or eukaryotic cell.
  • electroporation involves transfection of a human cell.
  • electroporation involves transfection of an animal cell.
  • transfection involves transfection of a cell line or a hybrid cell type.
  • the cell or cells being transfected are cancer cells, tumor cells or immortalized cells.
  • tumor, cancer, immortalized cells or cell lines are induced and in other instances tumor, cancer, immortalized cells or cell lines enter their respective state or condition naturally.
  • the cells or cell lines can be A549, B-cells, B16, BHK-21, C2C12, C6, CaCo-2, CAP/, CAP-T, CHO, CHO2, CHO-DG44, CHO-K1, COS-1, Cos-7, CV-1, Dendritic cells, DLD-1, Embryonic Stem (ES) Cell or derivative, H1299, HEK, 293, 293T, 293FT, Hep G2, Hematopoietic Stem Cells, HOS, Huh-7, Induced Pluripotent Stem (iPS) Cell or derivative, Jurkat, K562, L5278Y, LNCaP, MCF7, MDA-MB-231, MDCK, Mesenchymal Cells, Min-6, Monocytic cell, Neuro2a, NIH 3T3, NIH3T3L1, K562, NK-cells, NSO, Panc-1, PC12, PC-3, Peripheral blood cells, Plasma cells, Primary Fibroblasts,
  • the host cell is used for expression of the antibody, antigen binding fragment thereof, or polypeptide.
  • a nucleic acid encoding the antibody can be tranfected into the host cell, which is cultured under conditions such that the host cell expresses the antibody.
  • the expressed antibody can be harvested and/or isolated, and stored or used for any suitable purpose as described herein.
  • engineered receptors comprising any of the polypeptides (e.g. antibodies or antigen binding fragments thereof) provided herein.
  • the receptor is a heterologous antigen receptor.
  • the receptor is a chimeric antigen receptor (CAR).
  • host cells that express any of the polypeptides, antibodies or antigen binding fragments thereof, or receptors provided herein.
  • engineered immune cells e.g.
  • engineered T cells engineered macrophages, or engineered B cells
  • engineered T cells such as anti-S100A4 CAR T cells
  • engineered macrophages such as anti-S100A4 CAR M cells.
  • Chimeric antigen receptors are engineered receptors that combine a new specificity with an immune cell to target a particular antigen, such as one present in cancer cells. Typically, these receptors graft the specificity of a monoclonal antibody onto a T cell. The receptors are called chimeric because they are fused of parts from different sources.
  • CAR- T cell therapy refers to a treatment that uses such transformed cells for therapy (e.g. cancer therapy).
  • the basic principle of CAR-T cell design involves recombinant receptors that combine antigen-binding and T-cell activating functions.
  • CAR-T cells The general premise of CAR-T cells is to artificially generate T-cells targeted to markers found on cancer cells or other useful targets.
  • Scientists can remove T-cells from a person, genetically alter them, and put them back into the patient for them to attack the cancer cells.
  • T cell Once the T cell has been engineered to become a CAR-T cell, it acts as a “living drug”.
  • CAR-T cells create a link between an extracellular ligand recognition domain to an intracellular signaling molecule which in turn activates T cells.
  • the extracellular ligand recognition domain is usually a single-chain variable fragment (scFv).
  • the specificity of CAR-T cells is determined by the choice of molecule that is targeted. XV. Kits
  • kits containing compositions of the disclosure or compositions to implement methods of the disclosure can be used in connection with any of the methods provided herein.
  • kits can be used to detect the presence, abundance, and/or location of S100A4 in a biological sample.
  • the kit may be used for analysis of a biological sample and/or diagnostic purposes.
  • a kit contains, contains at least or contains at most 1, 2, 3, 4, 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, 100, 500, 1,000 or more probes, primers or primer sets, synthetic molecules or inhibitors, or any value or range and combination derivable therein.
  • kits contains one or more antibodies, antigen binding fragments thereof, or polypeptides disclosed herein capable of binding to an S100A4 protein.
  • the kit comprises an enzyme.
  • the kit comprises a substrate for an enzyme.
  • the enzyme and substrate enable the detection of S100A4.
  • Kits may comprise components, which may be individually packaged or placed in a container, such as a tube, bottle, vial, syringe, or other suitable container means. Individual components may also be provided in a kit in concentrated amounts; in some aspects, a component is provided individually in the same concentration as it would be in a solution with other components. Concentrations of components may be provided as lx, 2x, 5x, lOx, or 20x or more.
  • Kits for using compositions of the disclosure for prognostic or diagnostic applications are included as part of the disclosure.
  • negative and/or positive control samples, antibodies, nucleic acids, probes, and/or inhibitors are included in some kit aspects.
  • Kits may further comprise instructions for use.
  • a kit comprises instructions for detecting S100A4 in a sample.
  • S 100A4 is a marker for suppressive immunity and expressed in suppressive myeloid cells and T regulatory cells in different tumor types.
  • Tumor microenvironment of glioma cells implanted in S100a4 (-/-) null mice produced less aggressive gliomas tumors and conferred a significant survival advantage in S100a4-/- mice when comparing with that in wild type mice.
  • the inventors identified a panel of novel monoclonal antibodies (mAbs) that recognize S100A4 and neutralize S100A4 function in mouse tumor models. These mAbs showed modulation of tumor immune microenvironment and increased antitumor immune activities in mouse tumor models. The results support the utility of the antibodies against SI 00 A4 in immunotherapies to reprogramm tumor immune landscape for anticancer treatments, and other indications as provided herein.
  • mAbs against S100A4 were generated by immunization of rabbits (NZW, Charles River) using recombinantly expressed S100A4 protein (Sino Biologicals).
  • Peripheral blood mononuclear cells (PBMCs) were isolated when serum titer reached >10 6 and titers of anti-S100A4 sera were determined by series of dilutions of serum in ELISA for binding on S 100A4 protein coated on 96-well plates (max-sorb plates, Nunc).
  • Single memory B cells were isolated from freshly collected PBMCs using a memory isolation kit (STEMCELLS) and the enriched single memory B cells were plated in 96-well cell culture plates for single B cell culturing.
  • the sorted single B cells were plated in 96-well cell culture plates (Fisher Scientific) and were cultured for 7-10 days in a cell culture incubator with 5% CO2 and 95% humidity in RPMI culture media with 10% FBS and added cytokins.
  • the antibodies in the culture supernatants were assayed for S100A4 bindings.
  • Cells from the positives wells were lysed, total RNA was isolated, and cDNA was synthesized using a superscript reverse transcriptase II (Invitrogen) according to manufacturer’s suggestion.
  • DNA sequences of antibody variable regions from both heavy chains and light chains were amplified by polymerase chain reaction (PCR) using a set of designed primers for human IgG variable sequence PCR amplification.
  • PCR products were cloned into a mammalian expression vector system for sequencing variable regions of each of the antibodies. Variable sequences of both DNA and amino acid sequences are listed in Table 1. CDRs of the anti-S100A4 monoclonal antibodies were identified using the IMGT program (http://www.IMGT.org) and are listed in Table 1, as well as Table 6 and Table 7.
  • the identified anti-S100A4 antibodies included the following clones: S100A4-1, S100A4-5, S100A4-9, S100A4-11, and S100A4-19, which are referred to herein.
  • CDRs Complementary determining regions
  • HCDRs Table 6
  • LCDRs Table 7
  • G;F;ST means G at position 1, F at position 2, and S or T at position 3.
  • Asterisk (*) indicates that there is not necessarily an amino acid at that position.
  • A;G* means A at position 1, and G or no amino acid at position 2.
  • full length rabbit or human chimeric IgGs were expressed using a mammalian expression vector system in human embryonic kidney (HEK293) cells (Invitrogen/Thermo Fisher) for characterization of the mAbs binding functions against S100A4.
  • Antibodies were purified with protein A affinity resin using a fast protein liquid chromatography (FPLC). Purified S100A4 binding antibodies were characterized for their biological properties.
  • Example 2 Determinations of S100A4 monoclonal antibody (mAb) binding affinity using ELISA.
  • Example 3 Binding affinities (KD) of anti-S100A4 monoclonal antibodies determined using Bio-layer interferometry (BLI) based Octet instrument.
  • Pairwise binding competition among anti-S100A4 mAbs was used to determine the binding epitopes of each of the mAbs using Octet instrument and protein A biosensors.
  • Kinetic binding sensorgrams were fitted using a 1:1 binding model and the KD was calculated using the ratio of k o ff/ k on (dissociation rate / association rate).
  • Estimated values of KD for S100A4 mAbs are shown in Table 8.
  • the epitope bins are shown in FIG. 3 using a tandem binding for competition binding to S100A4 with Octet software analysis.
  • mAb clones S100A4-11 and S100A4-10 showed some overlaps in binding epitope as indicated some competition binding, while others showed no clear competitions in binding to S100A4 (FIG. 3B).
  • S100A4 monoclonal antibodies to other family member proteins were assayed using ELISA at 1 , 5, or 20 pg/ml antibody concentrations and S 100A member proteins at 2 pg/ml in 96 well high binding plates (FIG. 4).
  • S100A4-11 and S100A4-19 mAbs showed bindings to several SI 00 family members at 20 pg/ml concentration with the highest binding affinity to S100A4>S100A9>S100B>S100A16 and the lowest for SIOOP and S100A13.
  • the antibodies also showed binding to mouse S100A4 (mS100A4) with a reduced binding affinity in comparison with bindings to human S100A4 (hS100A4).
  • a functional screen for S100A4 antibody blocking activity using the chick dorsal root ganglion neurite outgrowth assay was performed. Soluble S100A4 protein has been shown to induce neurite growth of astrocytes and dorsal route ganglia (DRG) from chick embryos (see, for example, Fang Z et al. Sensory neurite outgrowth on white matter astrocytes is influenced by intracellular and extracellular S100A4 protein. J Neurosci Res. 2006;83(4):619- 26), and effective blocking of S 100A4 can result in reduced neurite growth.
  • Dorsal root ganglia (DRG)s were harvested from 7-day-old chicken embryos and cultured with soluble S100A4 protein.
  • S100A4 mAbs against human S100A4 protein were mixed with exogenous S100A4 with collagen matrix and cultured for 3 days. DRGs were fixed and stained with P3 -Tubulin antibody to measure the lengths of the neurites growth (FIG. 5A). Adding S100A4 antibody in culture showed the reduction in neurite outgrowth and neutralized the enhancing function by soluble S100A4 protein (FIG. 5B). Multiple of the mAbs facilitated suppression of neurite growth, with S100A4-1, S100A4-5, and S100A4-11 showing significant suppression of neurites growth using one-way ANOVA analysis, * P ⁇ 0.05, supporting effective blocking activity by these antibodies.
  • Example 6 Inhibition of cancer metastasis by anti-S100A4 monoclonal antibodies
  • S100A4 antibodies were assessed for ability to suppress metastasis in mouse models of breast cancer.
  • S100A4 antibodies were assessed for ability to suppress spontaneous lung metastasis, using an exemplary mouse breast cancer model (MMTV-PyMT). 6- week-old MMTV-PyMT transgenic female mice were treated with IgG control or one of four different monoclonal antibodies against S100A4 (S100A4-4; S100A4-11; S100A4-12; and S100A4-19), twice per week for 4 weeks. The mice were harvested and assessed for tumor growth and metastasis at approximately at 12-14 weeks of age (FIG. 6A). As shown in FIG. 6B and FIG.
  • FIG. 6C shows staining and polyomavirus middle T antibody staining in lung metastatic nodules from representative IgG control and S100A4-11 antibody treated mice.
  • S100A4 antibodies were assessed for ability to suppress lung metastasis using another exemplary mouse breast cancer model (4T1).
  • T1 mouse breast cancer model
  • FIG. 7A Balb/c female 4 mice were injected with 5x10 4T1 cells to establish breast tumors for 3 days and then treated with control IgG or S100A4 antibodies once a week for 4 weeks. All mice were harvested on day 29 and analyzed. After harvest, total number of lung metastatic nodules were recorded.
  • FIG. 7B and FIG. 7C anti-S100A4 antibodies suppressed lung metastasis in comparison to control IgG, and statistically significant suppression was observed for the antibody S100A4-11.
  • the results support the therapeutic utility of the S100A4 antibodies and antigen binding fragments thereof, including S100A4-11, in the treatment and/or prevention of cancer.
  • the results further support the use of the antibodies and antigen binding fragments thereof for treatment and prevention of breast cancer and breast cancer metastasis.
  • Example 7 Immune modulation by anti-S100A4 monoclonal antibodies in cancer
  • FIGS. 8A-K show M-MDSC and PMN-MDSC were reduced in the blood and lung, respectively, of S100A4-11 antibody treated mice.
  • M-MDSC frequency in the blood was decreased when MMTV-PyMT mice were treated with S100A4-11 antibody (FIGS. 8A-C).
  • FIG. 8D In the primary breast tumor, no significant changes in the total immune cells (FIG. 8D), myeloid cells (FIG. 8E), M-MDSC (FIG. 8F) and PMN-MDSC (FIG. 8G) were detected between IgG and S100A4 antibody treated mice.
  • FIG. 8D total immune cells
  • FIG. 8E myeloid cells
  • M-MDSC FIG. 8F
  • PMN-MDSC FIG. 8G
  • FIGS. 9A-G show the effect of S100A4- 11 treatment on CD 163+ and CD206+ macrophages in breast tumor of 4T1 and MMTV-PyMT mice.
  • S100A4-11 treatment reduced CD163+ (FIG. 9A), but not CD206+ (FIG. 9B), macrophages in the 4T1 breast tumor.
  • Flow cytometry analysis of breast tumor tissues confirmed a significant decrease in CD 163+ macrophages in S100A4-11 antibody treated tumors but no significant change in CD206+ macrophages (FIG. 9C and FIG. 9D).
  • FIGS. 10A-N show S100A4-11 treatment alters the pre- metastatic niche in lung.
  • FIG. 10A shows that at an early time point (day 14, prior to presence of detectable macro metastases), infiltrating PMN-MDSC cell frequency was significantly increased in the lung of 4T1 tumor bearing mice, compared to BAEB/c control.
  • S100a8 (FIG. 10B) and S100a9 (FIG. 10C) mRNA expression in the lung is significantly increased, while S100a4 (FIG. 10D) expression is not significantly increased in 4T1 mammary tumor bearing mice.
  • FIG. 10B shows that at an early time point (day 14, prior to presence of detectable macro metastases), infiltrating PMN-MDSC cell frequency was significantly increased in the lung of 4T1 tumor bearing mice, compared to BAEB/c control.
  • S100a8 (FIG. 10B) and S100a9 (FIG. 10C) mRNA expression in the lung is significantly increased, while S100a4 (FI
  • FIG. 10E shows that PMN-MDSC frequency is significantly reduced in the lung of S10A4-11 treated 4T1 -tumor bearing mice at day 14. Consistently, S100a8 (FIG. 10F), S100a9 (FIG. 10G), and S100a4 (FIG. 10H) expression levels were significantly reduced in the S100A4-11 antibody treated lung, compared to IgG treated.
  • FIG. 101 shows Immunofluorescence analysis of Ly6G+S100A8 and Ly6G+S100A9+ cells in the lung of IgG vs. S100A4-11 treated 4T1 tumor bearing mice. >95% of S100A8 (FIG. 10J) or S100A9 (FIG.
  • IOK IOK expressing cells are Ly6G+ granulocytes.
  • the frequencies of S100a8+/Ly6g+ (FIG.
  • FIG. ION shows Immunohistochemical analysis with an antibody against MPO (myeloperoxidase), a neutrophil activated marker, show decreased MPO+ cells in the S100A4-11 treated lung tissue. Arrows point to MPO+ cells. Immunofluorescence analyses were conducted from lungs of three mice per treatment group, and three paraffin sections from each mouse. More than 1,500 cells total cells were analyzed per treatment group.
  • MPO myeloperoxidase
  • FIGS. 11A-I show S100A4-11 treatment altered chemokine and cytokine expression in the pre-metastatic lung.
  • FIG. 11A shows the S100A4 antibody treatment schedule for the early stage of lung analysis.
  • FIG. 11B shows lung tissue lysates from day 14 4T1 tumor bearing mice were analyzed with a cytokine array.
  • FIG. 11C shows ten statistically significantly expressed proteins were identified in replicate experiments.
  • FIG. 11D shows Immunohistochemical analysis of MMP9, which shows dramatically decreased expression in the lungs of S100A4-11 treated mice, compared with IgG control.
  • FIG. 11G shows a working model of how S100A4-11 antibody treatment blocks priming of the lung niche by suppressing granulocyte (PMN-MDSC and neutrophils) infiltration and MMP9 expression in the lung, based on the described experiments and data.
  • PMN-MDSC and neutrophils granulocyte
  • FIGS. 12A-H show T cell distribution in the multiple organs of the 4T1 model. Compared with tumor-free mice (Balb/c), the total CD3+ T cell frequency was significant decreased in the blood (FIG. 12A) and spleen (FIG. 12B) of 4T1 tumor-carrying mice. However, S 100A4 antibody-treated mice did not exhibit a significant change in total CD3+ T cell frequency, similar to results obtained from the MMTV-PyMT model.
  • FIGS. 13A-H show T cells distribution in the multiple organs of the MMTV-PyMT model.
  • CD3+ T cell frequency was significantly decreased in the blood (FIG. 13A) and spleen (FIG. 13B) of tumor-bearing MMTV-PyMT mice compared to tumor- free mice (FVB).
  • FIG. 13C the total CD3+
  • FIG. 13D the total CD4+
  • FIG. 13D CD8+
  • T cells also did not exhibit dramatic differences among IgG and S100A4 antibody-treated groups.
  • the total CD3+ T cell frequency from lung tissue was not changed by S100A4-11 treatment (FIG. 13F).
  • Average CD4+ T cell frequency trended higher in the S100A4-11 treated group, but no significant differences were observed in comparison with the isotype control group (p 0.3304, FIG. 13G).
  • CD8+ T cells were not altered in comparison to IgG control. The statistical analysis was performed using ordinary one-way ANOVA. (*** P ⁇ 0.001).
  • FIGS. 14A-F show the effect of anti-S100A4 antibody treatment on T cell PD-1 expression in the two models.
  • PD-1 is a protein expressed on T cells that can inhibit T cell activity when bound to PD-1 ligand on tumor cells.
  • S100A4-11 treated animals exhibited significantly suppressed PD-1+ cell fractions in total blood CD3+ T cells (FIG. 14A) and CD4+ T cells (FIG. 14B) in blood, compared with IgG control animals. CD8+ T cells did not exhibit the same effect (FIG. 14C).
  • Example 8 A bispecific anti-S100A4/anti-TfR antibody crosses the blood brain barrier and mediates anti-glioblastoma activity
  • TfR transferrin receptor
  • GBM Glioblastoma
  • Immunotherapy is an emerging and promising treatment modality for GBM.
  • most immunotherapy trials have provided only modest benefit to GBM patients thus far.
  • a significant barrier that limits efficacy of immunotherapy in GBM is the paucity of tumor infiltrating lymphocytes and abundance of immune suppressive myeloid cells.
  • a critical step in enhancing the efficacy of immunotherapy for GBM requires approaches that enhance T cell infiltration and reprogram the myeloid cells to a more pro-inflammatory state.
  • S100A4 is a major regulator of sternness, epithelial-mesenchymal transition, and immunosuppression in glioma stem cells and a critical regulator of immune suppressive myeloid and T cell phenotypes in GBM.
  • S100A4 has both intracellular and extracellular functions, including cytokine-like function. Targeting S100A4 in either glioma cells or stromal cells is sufficient to reprogram the tumor immune landscape and extend survival of glioma bearing mice, indicating that S100A4 is a promising immunotherapy target.
  • BBB blood-brain barrier
  • BsA bispecific anti-S100A4/TfR antibody
  • the exemplary bispecific anti-S100A4/TfR antibody comprised an S100A4 (S100A4-11) antibody (IgG) fused with a TfR antigen binding single chain variable fragment (scFv) at the heavy chain C-terminus.
  • the TfR antigen binding fragment comprised the heavy chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 71) and the light chain amino acid sequence set forth in mTfR-4 (SEQ ID NO: 72), and comprised HCDRs set forth in mTfR- 4 (SEQ ID NOS: 73-75) and LCDRs set forth in mTfR-4 (SEQ ID NO: 76, DDN, and SEQ ID NO: 77).
  • the anti-S100A4 antibody and the bispecific antibody were administered systemically to mice that develop glioma (x5459 mouse glioma model). 24 hours later, brains were harvested and assessed for presence of the administered antibodies (based on detection of Human Fc) and colocalization with S100A4 in glioma tumor regions. As shown in FIG. 15A (top panels), the anti-S100A4 antibody was not detected in the brain, as expected. In contrast, the bispecific anti-S 100A4/TfR antibody (BsA) penetrated the BBB and was detected in glioma tumor regions, and colocalized with S100A4 protein.
  • FIG. 15A top panels
  • BsA bispecific anti-S 100A4/TfR antibody
  • FIG. 15B shows higher magnification (lOOx confocal microscopy imaging) demonstrating absence of the anti-S 100A4 antibody (left) and presence of the bispecific antibody and colocalization with S 100A4 (right) in glioma tumor regions.
  • FIG. 15C shows representative immunofluorescence images of x5459 murine intracranial glioma stained with a SOX2 antibody (green) and DAPI (blue).
  • SOX2 is a marker of tumor sternness in glioblastoma. The results show decreased expression of SOX2 in glioma tumors of animals administered with the bispecific antibody, suggesting that the bispecific antibody is taken up by glioma cells, accumulates intracellularly, and decreases nuclear SOX2 expression.
  • mice treated with BsA exhibited an increased percentage of CD4+ T cells among CD3+ T cells (left panel), and an increased percentage of CD3+/CD4+/PD1+ T cells among live cells within gliomas.
  • the results indicate that the bispecific antibody facilitates increased T cell infiltration and immune remodeling in the glioma tumor.
  • bispecific anti-S 100A4/TfR antibody can cross the blood brain barrier, reduce glioblastoma tumor sternness, increase T cell infiltration, and reprogram the glioblastoma immune landscape.
  • BsA bispecific anti-S 100A4/TfR antibody
  • mouse primary glioma tumorspheres were isolated from spontaneous S100B-vErbB;p53 glioma models.
  • 3422 mouse primary glioma tumorspheres were isolated form spontaneous P53 flox/flox ; Pten flox/flox ; piK3CAH1047R flox/+ glioma models.
  • mice 8-12 week old B6 mice were injected with 10 A 5 x5459 cells intracranially in the striatum.
  • IP intraperitoneally
  • BsA or mAb monoclonal S100A4 antibody.
  • mice were sacrificed and perfused with ice-cold PBS. Tumors were harvested, fixed in 4% PFA for 24 hours, treated with 10-20-30% sucrose gradient, and embedded in OCT medium.
  • mice 8-12 week old B6 mice were intraperitoneally injected with 20 mg/kg BsA or mAb (monoclonal S100A4 antibody). At 4, 24, 48, 96, 168 hours, mice were sacrificed. Blood was harvested via cardiac puncture, followed by perfusion with PBS. After perfusion, brain and other organs were extracted. To collect serum, blood was left to coagulate at room temperature for 20 minutes. Afterwards, blood was centrifuged for 10 minutes at 2000 RCF. Clean serum was collected and stored at -80C for later use. To process the brain for downstream ELISA, brain mass was measured, followed by digestion in RIPA buffer with protease and phosphatase inhibitors. Brain pieces were mechanically dissociated via micro pestles and left rocking at 4C for 1 hour. Afterwards, the digestion mixture was centrifuged at 14000 RCF for 20 minutes to remove debris. The supernatant was collected and stored for ELISA.
  • BsA or mAb monoclonal S100A4 antibody
  • High binding ELISA plates were coated with S 100A4. Afterwards, brain and serum samples were prepared, diluted (1:10 for brain, 1:50 for serum), and incubated for 1 hour.
  • tumors were microdissected from brain sections, cut up with microscissors, and digested for 30 minutes at 37C in a buffer consisting of 20% collagenase/hyaluronidase diluted in accutase. After digestion, the tumor was further mechanically dissociated by pipetting up and down with a P200 pipette. The tumor digest was spun down, washed once in PBS, and resuspended in RBC lysis buffer for 10 minutes on ice to remove RBCs. Afterwards, tumor digests were resuspended in wash media (DMEM/F12 with B27, lx Glutamax, lx Anti-anti). To separate debris, this tumor digests were separated over a 30% percoll gradient (40 minutes, 800 RCF). After washing and counting, isolated cells were used for flow cytometry.
  • wash media DMEM/F12 with B27, lx Glutamax, lx Anti-anti
  • Isolated single cells from tumor digests were blocked in flow cytometry buffer (5% FBS in PBS) with 1:100 TruStain Fc block for 5 minutes, before incubating with pre -prepared antibody cocktail mixture for 40 minutes at 4C. Cells were then washed in PBS twice before incubating in Live Dead Blue stain for 20 minutes at 4C. After washing, cells were fixed and stained for intracellular markers according to the Foxp3 transcription factor staining buffer kit. Cells were then scanned on an FACSymphony A5SE cytometer.
  • sectioned samples underwent de-paraffinization and antigen retrieval using a Tris-EDTA buffer, before being processed in the same manner as OCT embedded samples.
  • OCT embedded samples sectioned slides were blocked in 0.2% Triton X-100, 5% goat or donkey serum, and lx PBS for 1 hour at room temperature. Sectioned slides were then incubated with primary antibody diluted in blocking buffer overnight at 4C. After washing 2 times in PBS, slides were incubated in fluorophore conjugated secondary antibodies diluted in blocking buffer for 30 minutes. After washing twice in PBS, and autofluorescence was quenched and slides were mounted in mounting medium with DAPI using the Vector TrueVIEW Autofluorescence quenching kit. Slides were imaged on a OYLMPUS Fluoview FV3000. Images were segmented and processed using CellProfiler.
  • DMEM F12 + B27+ GlutaMAX
  • TSC medium DMEM: F12 + B27+ GlutaMAX
  • Cultures were dissociated with Accutase and viable cells were seeded at 3,000 cells/well (at a density of 1 cell/uL) in 6-well plates in triplicate with 100 ng/ml of an IgG control, BsA, or an S100A4 mAb. After 7 days, tumorspheres >6 cells in diameter were counted.
  • Example 10 S100A4/TRF-BsA bypasses the BBB and accumulates intracellularly within tumors
  • Example 11 BsA treatment reprograms TME to increase immune cell infiltration
  • CD45+ cell infiltration via IF (FIG. 17A) was measured.
  • CD45 IF revealed that BsA treated tumors had significantly increased numbers of CD45+ immune cells compared to IgG treated counterparts, which was confirmed by quantification of multiple fields from treated tumors (FIG. 17B).
  • Spectral flow cytometry of infiltrating CD45+ immune cells showed a diverse population of lymphocyte and myeloid cell populations (FIG. 17C, D).
  • Example 12 BsA treatment decreases intratumor S100A4 and reduces GSC sternness
  • S100A4 levels were measured via IF from IgG and BsA treated tumors and found markedly decreased S100A4 levels in BsA treated tumors compared to IgG treated tumors (FIG. 18 A, B).
  • Co-staining with CD45 indicated that a majority of S100A4-low cells in BsA treated tumors were CD45- tumor cells, whereas CD45+ cells in BsA treated tumors were still characterized by high S100A4 expression (FIG. 3A).
  • Example 13 BsA treatment increases immune activation and synergizes with aPDl therapy
  • ELISA and IF results reveal that BsA bypasses the blood brain barrier at almost 10- fold the rate of the monoclonal S100A4 antibody and is internalized intracellularly by tumor cells in vivo.
  • BsA concentrations in the brain remain high at up to 1 week posttreatment.
  • Intracellular uptake was significant as it correlated with intracellular depletion of S100A4 in tumor cells.
  • BsA treatment was associated with reprogramming of the TME characterized by increased immune cell infiltration and activation.
  • GBMs are predominantly “immune cold” tumors characterized by low levels of infiltrating lymphocytes and are typically unresponsive to immunotherapy such as immune checkpoint inhibitors.
  • Survival data show that BsA treatment synergizes with anti-PDl therapy to significantly extend survival in aggressive mouse models of GBM, suggesting that BsA treatment converts GBMs to an “immune hot” tumor and sensitize them to checkpoint inhibitors such as anti-PDl therapy.

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Abstract

Selon certains aspects, l'invention concerne des anticorps et des fragments de liaison à l'antigène de ceux-ci qui se lient à S100A4 ou S100A9 humain, et des compositions et des procédés associés. L'invention concerne également des méthodes de traitement et de prévention d'une inflammation, d'une fibrose, d'une athérosclérose et d'un cancer et/ou de métastases associées, par administration des anticorps et des fragments de liaison à l'antigène de ceux-ci à un sujet. Selon certains aspects, les compositions selon l'invention peuvent être utilisées pour une analyse d'échantillon, par exemple pour la détection de S100A4 ou S100A9 dans un échantillon biologique provenant d'un sujet.
PCT/US2025/018586 2024-03-08 2025-03-05 Anticorps anti-s100a et compositions et procédés associés Pending WO2025188905A1 (fr)

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