[go: up one dir, main page]

WO2023278826A2 - Méthodes de sélection de patients atteints d'un cancer du poumon pour un traitement avec des médicaments anti-inflammatoires non stéroïdiens - Google Patents

Méthodes de sélection de patients atteints d'un cancer du poumon pour un traitement avec des médicaments anti-inflammatoires non stéroïdiens Download PDF

Info

Publication number
WO2023278826A2
WO2023278826A2 PCT/US2022/035921 US2022035921W WO2023278826A2 WO 2023278826 A2 WO2023278826 A2 WO 2023278826A2 US 2022035921 W US2022035921 W US 2022035921W WO 2023278826 A2 WO2023278826 A2 WO 2023278826A2
Authority
WO
WIPO (PCT)
Prior art keywords
mmes
effective amount
cancer patient
pcr
intraoperative
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.)
Ceased
Application number
PCT/US2022/035921
Other languages
English (en)
Other versions
WO2023278826A3 (fr
Inventor
Joshua MINCER
Gregory Fischer
Patrick Mccormick
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.)
Memorial Sloan Kettering Cancer Center
Original Assignee
Memorial Sloan Kettering Cancer Center
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 Memorial Sloan Kettering Cancer Center filed Critical Memorial Sloan Kettering Cancer Center
Publication of WO2023278826A2 publication Critical patent/WO2023278826A2/fr
Publication of WO2023278826A3 publication Critical patent/WO2023278826A3/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/185—Acids; Anhydrides, halides or salts thereof, e.g. sulfur acids, imidic, hydrazonic or hydroximic acids
    • A61K31/19—Carboxylic acids, e.g. valproic acid
    • A61K31/192—Carboxylic acids, e.g. valproic acid having aromatic groups, e.g. sulindac, 2-aryl-propionic acids, ethacrynic acid 
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/40—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil
    • A61K31/407—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with one nitrogen as the only ring hetero atom, e.g. sulpiride, succinimide, tolmetin, buflomedil condensed with other heterocyclic ring systems, e.g. ketorolac, physostigmine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/445—Non condensed piperidines, e.g. piperocaine
    • A61K31/4468—Non condensed piperidines, e.g. piperocaine having a nitrogen directly attached in position 4, e.g. clebopride, fentanyl
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present technology relates to methods for determining whether a patient diagnosed with lung cancer and undergoing tumor resection surgery will benefit from treatment with a class of nonsteroidal anti-inflammatory drugs (NSAID) (e.g., carboxylic acid derivative NSAIDs). These methods are based on screening a cancer patient for mutations in MDM2 and/or mutations in the NRF2 signaling pathways. Also disclosed herein are methods for improving survival in lung cancer patients undergoing tumor resection surgery comprising administering to the subject an effective amount of carboxylic acid derivative NxAIDs.
  • NSAID nonsteroidal anti-inflammatory drugs
  • the present disclosure provides a method for selecting a cancer patient undergoing tumor resection surgery for lung cancer for treatment with a carboxylic acid derivative nonsteroidal anti-inflammatory drug (NSAID) comprising (a) determining (i) the absence of mutations in MDM2 or (ii) the absence of mutations in the Nrf2 pathway in a biological sample obtained from the cancer patient; and (b) administering to the cancer patient an effective amount of a carboxylic acid derivative NSAID during the tumor resection surgery.
  • NSAID carboxylic acid derivative nonsteroidal anti-inflammatory drug
  • the biological sample is assayed via next-generation sequencing, PCR, real-time quantitative PCR (qPCR), digital PCR (dPCR), Southern blotting, Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • the biological sample comprises genomic DNA, cDNA, ctDNA, cfDNA, RNA, and/or mRNA.
  • the present disclosure provides a method for prolonging survival of a cancer patient undergoing tumor resection surgery for lung cancer comprising administering to the cancer patient an effective amount of a carboxylic acid derivative NSAID during the tumor resection surgery.
  • mRNA or polypeptide expression and/or activity levels of MDM2, KEAPl and NEE2L2 in a biological sample obtained from the cancer patient are comparable to that observed in a control sample obtained from a healthy subject or a predetermined threshold.
  • mRNA expression levels are detected via real-time quantitative PCR (qPCR), digital PCR (dPCR), Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • polypeptide expression levels are detected via Western blotting, enzyme-linked immunosorbent assays (ELISA), dot blotting, immunohistochemistry, immunofluorescence, immunoprecipitation, Immunoelectrophoresis, or mass-spectrometry.
  • the carboxylic acid derivative NSAID is an acetic acid NSAID or a propionic acid NSAID.
  • the carboxylic acid derivative NSAID include, but are not limited to, ibuprofen, dexibuprofen, naproxen, fenoprofen, ketoprofen, dexketoprofen, flurbiprofen, oxaprozin, loxoprofen, pelubiprofen, zaltoprofen, indomethacin, tolmetin, sulindac, etodolac, ketorolac, diclofenac, aceclofenac, bromfenac, or nabumeton.
  • the carboxylic acid derivative NSAID is administered orally, intravenously, or intramuscularly.
  • the effective amount of the carboxylic acid derivative NSAID is 10 mg-1500 mg. In certain embodiments, the effective amount of the carboxylic acid derivative NSAID is administered as a bolus dose during the tumor resection surgery. In a further embodiment, the carboxylic acid derivative NSAID is administered as a bolus of 0.25 mg/kg- 10 mg/kg. Additionally or alternatively, in some embodiments, the effective amount of the carboxylic acid derivative NSAID is administered intraoperatively and/or postoperatively. The effective amount of the carboxylic acid derivative NSAID may be administered to the cancer patient during closing of an incision.
  • the methods of the present technology further comprises administering to the cancer patient an effective amount of an intraoperative opioid analgesic.
  • intraoperative opioid analgesic include, but are not limited to fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, and sufentanil.
  • the effective amount of the intraoperative opioid analgesic may range from about 1 MME to about 200 MMEs. In certain embodiments, the effective amount of the intraoperative opioid analgesic is about 1 MME to about 20 MMEs, about 20 MMEs to about 45 MMEs, or about 45 MMEs to about 200 MMEs.
  • the effective amount of the intraoperative opioid analgesic is about 1 MME, about 2 MMEs, about 3 MMEs, about 4 MMEs, about 5 MMEs, about 6 MMEs, about 7 MMEs, about 8 MMEs, about 9 MMEs, about 10 MMEs, about 11 MMEs, about 12 MMEs, about 13 MMEs, about 14 MMEs, about 15 MMEs, about 16 MMEs, about 17 MMEs, about 18 MMEs, about 19 MMEs, about 20 MMEs, about 21 MMEs, about 22 MMEs, about 23 MMEs, about 24 MMEs, about 25 MMEs, about 26 MMEs, about 27 MMEs, about 28 MMEs, about 29 MMEs, about 30 MMEs, about 31 MMEs, about 32 MMEs, about 33 MMEs, about 34 MMEs, about 35 MMEs, about 36 MMEs, about 37 MMEs, about 38 MMEs, about 39 MMEs, about 40-45
  • the effective amount of the intraoperative opioid analgesic is administered as a series of bolus doses or as a continuous infusion during the tumor resection surgery. In certain embodiments, the effective amount of the intraoperative opioid analgesic is administered to the cancer patient prior to incision. Additionally or alternatively, in some embodiments, the effective amount of the intraoperative opioid analgesic is administered intravenously.
  • the method further comprises administering to the cancer patient an effective amount of a local anesthetic solution that comprises one or more of lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, or benzocaine, and optionally an opioid.
  • the methods of the present technology further comprise administering to the cancer patient an effective amount of a local anesthetic solution via an epidural catheter before, during and/or after the tumor resection surgery.
  • the effective amount of the local anesthetic solution may range from about 0.05%-4% local anesthetic solution in a volume of 1-10 ml per hour when administered via an epidural catheter.
  • the effective amount of the local anesthetic solution is about 0.05 %, about 0.06 %, about 0.07 %, about 0.08 %, about 0.09 %, about 0.1 %, about 0.15 %, about 0.2 %, about 0.25 %, about 0.3 %, about 0.35 %, about 0.4 %, about 0.45 %, about 0.5 %, about 0.55 %, about 0.6 %, about 0.65 %, about 0.7 %, about 0.75 %, about 0.8 %, about 0.85 %, about 0.9 %, about 0.95 %, about 1.0 %, about 1.1 %, about 1.2 %, about 1.3 %, about 1.4 %, about 1.5 %, about 1.6 %, about 1.7 %, about 1.8 %,
  • the effective amount of the local anesthetic solution is administered as a series of bolus doses or as a continuous infusion during the tumor resection surgery.
  • suitable local anesthetics include, but are not limited to, lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, and benzocaine.
  • the effective amount of the local anesthetic solution may be administered before, during and/or after the tumor resection surgery using any regional anesthesia technique directed at nerves innervating the thorax and chest wall (e.g ., via serratus plane nerve block, intercostal nerve block, or paravertebral block).
  • the effective amount of the local anesthetic solution may range from about 0.05%-4% local anesthetic solution in a volume of 10-40 ml when administered using any regional anesthesia technique directed at nerves innervating the thorax and chest wall (e.g., via serratus plane nerve block, intercostal nerve block, or paravertebral block).
  • the effective amount of the local anesthetic solution is about 0.05 %, about 0.06 %, about 0.07 %, about 0.08 %, about 0.09 %, about 0.1 %, about 0.15 %, about 0.2 %, about 0.25 %, about 0.3 %, about 0.35 %, about 0.4 %, about 0.45 %, about 0.5 %, about 0.55 %, about 0.6 %, about 0.65 %, about 0.7 %, about 0.75 %, about 0.8 %, about 0.85 %, about 0.9 %, about 0.95 %, about 1.0 %, about 1.1 %, about 1.2 %, about 1.3 %, about 1.4 %, about 1.5 %, about 1.6 %, about 1.7 %, about 1.8 %, about 1.9 %, about 2.0 %, about 2.1 %, about 2.2 %, about 2.3 %, about 2.4 %, about 2.5 %, about 2.6 %, about
  • Suitable local anesthetics include, but are not limited to, lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, and benzocaine.
  • the local anesthetic solution may further comprise an opioid (e.g., fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil).
  • an opioid e.g., fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the local anesthetic solution may comprise 0.5 mcg/ml-50 mcg/ml opioid.
  • the local anesthetic solution may comprise about 0.5 mcg/ml, about 0.6 mcg/ml, about 0.7 mcg/ml, about 0.8 mcg/ml, about 0.9 mcg/ml, about 1.0 mcg/ml, about 1.5 mcg/ml, about 2.0 mcg/ml, about 2.5 mcg/ml, about 3.0 mcg/ml, about 3.5 mcg/ml, about 4.0 mcg/ml, about 4.5 mcg/ml, about 5.0 mcg/ml, about 5.5 mcg/ml, about 6.0 mcg/ml, about 6.5 mcg/ml, about 7.0 mcg/ml, about 7.5 mcg/ml, about 8.0 mcg/ml, about 8.5 mcg/ml, about 9.0 mcg/ml, about 10
  • the methods of the present technology further comprise administering to the cancer patient an effective amount of a post- operative opioid analgesic after the tumor resection surgery.
  • post-operative opioid analgesics include, but are not limited to, fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the post- operative opioid analgesic and the intraoperative opioid analgesic are the same opioid analgesic or different opioid analgesics.
  • the effective amount of the post-operative opioid analgesic and the effective amount of the intraoperative opioid analgesic are the same or different. Additionally or alternatively, in some embodiments, the effective amount of the postoperative opioid analgesic is administered to the cancer patient as a bolus of about 0.005 mg to about 100 mg.
  • the effective amount of the post-operative opioid analgesic is administered to the cancer patient as a bolus of about 0.005 mg, about 0.006 mg, about 0.007 mg, about 0.008 mg, about 0.009 mg, about 0.01 mg, about 0.02 mg, about 0.03 mg, about 0.04 mg, about 0.05 mg, about 0.06 mg, about 0.07 mg, about 0.08 mg, about 0.09 mg, about 0.1 mg, about 0.2 mg, about 0.3 mg, about 0.4 mg, about 0.5 mg, about 0.6 mg, about 0.7 mg, about 0.8 mg, about 0.9 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 10-15 mg, about 15-20 mg, about 20-25 mg, about 25-30 mg, about 30-35 mg, about 35-40 mg, about 40-45 mg, about 45-50 mg, about 50-55 mg, about 55-60 mg, about 60-65 mg, about 65-70 mg, about 70
  • the effective amount of the post-operative opioid analgesic may be continuously delivered to the cancer patient at a per hour rate of about 0.01 mg/hr to about 10 mg/hr. In certain embodiments, the effective amount of the post-operative opioid analgesic is continuously delivered to the cancer patient at a per hour rate of about 0.01 mg/hr, about 0.02 mg/hr, about 0.03 mg/hr, about 0.04 mg/hr, about 0.05 mg/hr, about 0.06 mg/hr, about 0.07 mg/hr, about 0.08 mg/hr, about 0.09 mg/hr, about 0.1 mg/hr, about 0.2 mg/hr, about 0.3 mg/hr, about 0.4 mg/hr, about 0.5 mg/hr, about 0.6 mg/hr, about 0.7 mg/hr, about 0.8 mg/hr, about 0.9 mg/hr, about 1 mg/hr, about 1.5 mg/hr, about 2 mg/hr, about 2.5 mg/hr, about 3 mg
  • the effective amount of the post- operative opioid analgesic is administered intravenously, orally, or transdermally.
  • the method further comprises administering to the cancer patient an effective amount of ketamine, precedex, or acetaminophen during the tumor resection surgery.
  • the present disclosure provides a method for selecting a cancer patient undergoing tumor resection surgery for lung cancer for treatment with a NSAID-free intraoperative analgesic comprising (a) (i) detecting the presence of at least one gain of function mutation in MDM2 in a biological sample obtained from the cancer patient, and/or (ii) detecting the presence of one or more mutations that result in elevated activity of Nrf2 pathway in a biological sample obtained from the cancer patient; and (b) administering to the cancer patient an effective amount of a NSAID-free intraoperative analgesic during the tumor resection surgery.
  • the mutations in MDM2 and/or the Nrf2 pathway may be detected via next-generation sequencing, PCR, real-time quantitative PCR (qPCR), digital PCR (dPCR), Southern blotting, Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • qPCR real-time quantitative PCR
  • dPCR digital PCR
  • RT-PCR Reverse transcriptase-PCR
  • FISH fluorescent in situ hybridization
  • the present disclosure provides a method for prolonging survival of a cancer patient undergoing tumor resection surgery for lung cancer comprising administering to the cancer patient an effective amount of a NSAID-free intraoperative analgesic during the tumor resection surgery, wherein mRNA or polypeptide expression and/or activity levels of MDM2 or Nrf2 pathway in a biological sample obtained from the cancer patient are elevated compared to that observed in a control sample obtained from a healthy subject or a predetermined threshold.
  • mRNA expression levels are detected via real-time quantitative PCR (qPCR), digital PCR (dPCR), Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • polypeptide expression levels are detected via Western blotting, enzyme-linked immunosorbent assays (ELISA), dot blotting, immunohistochemistry, immunofluorescence, immunoprecipitation, Immunoelectrophoresis, or mass-spectrometry.
  • NSAID-free intraoperative analgesic is an opioid, or acetaminophen.
  • opioids include, but are not limited to, fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the effective amount of the NSAID-free intraoperative analgesic may be administered as a series of bolus doses, or as a continuous infusion during the tumor resection surgery.
  • the cancer patient exhibits stage I, stage II or stage III lung cancer. Additionally or alternatively, in some embodiments, the cancer patient has been diagnosed with lung adenocarcinoma (LUAD).
  • the histologic subtype of the lung adenocarcinoma may be lepidic, acinar, papillary, micropapillary, solid or unknown.
  • the cancer patient has received an adjuvant therapy.
  • the adjuvant therapy may be chemotherapy, radiation therapy or chemoradiation therapy. Additionally or alternatively, in some embodiments of the methods disclosed herein, the patient is human.
  • the biological sample obtained from the cancer patient comprises biopsied tumor tissue, whole blood, plasma, or serum.
  • FIGs. 1A-1C show Kaplan-Meier curves for recurrence-specific survival (RSS) for patients who did (green) or did not (red) receive ketorolac, for (FIG. 1A) all patients in the cohort, (FIG. IB) patients withNRF2 oncogenic pathway alteration, and (FIG. 1C) patients with MDM2 gene alteration.
  • RSS recurrence-specific survival
  • FIG. ID shows predicted pro- vs. anti-tumour regulation by ketorolac of the six survival- associated gene networks in the TCGA-LUAD external validation cohort; each coloured circle is one survival-associated gene network, and the x-axis (tau) represents the percentile rank of ketorolac in comparison with all other 8558 drugs and small molecules in the Connectivity Map database in terms of predicted strength and direction (pro- vs. anti-tumour) of regulation of each network; blue dotted line represents the 50th percentile and the red line represents the 90th percentile).
  • FIG. IE shows survival curves for patients in the TCGA-LUAD cohort with up- versus downregulation of the survival-associated gene network highlighted by the red circle in FIG.1D.
  • FIG. IF shows predicted antitumour regulation by ketorolac of the highlighted gene network (x-axis tau, as described before), with other drugs commonly used in the treatment of lung adenocarcinoma highlighted for comparison.
  • FIG. 2A shows an analysis of pathway alterations as function of NPA value.
  • FIG. 2B shows an analysis of gene alterations as function of NPA value.
  • FIG.3 shows CONSORT diagram describing the exclusion criteria for the patient cohort.
  • MSK-IMPACTTM Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets.
  • FIG. 4 shows the results of multivariable analysis for RSS and overall survival (OS).
  • Cl confidence interval
  • EvW Elixhauser van Walraven
  • HR hazard ratio
  • MMEs oral morphine milligram equivalents
  • OS overall survival
  • RSS recurrence-specific survival.
  • FIG. 5 shows estimates for interaction terms for ketorolac with the tumour genomic factors for the RSS endpoint. Note that a positive estimate corresponds to a hazard ratio >1 (i.e., worse RSS with genomic factor alteration in the presence of ketorolac), whereas a negative estimate corresponds to a hazard ratio ⁇ 1 (i.e., improved RSS with genomic factor alteration in the presence of ketorolac).
  • FGA fraction genome altered
  • RSS recurrence- specific survival
  • TMB tumor mutational burden.
  • FIG. 6A shows five-year predicted curve for recurrence specific survival in patients with wild-type MDM2 with increasing intraoperative MME dose.
  • RSS recurrence specific survival
  • MME oral morphine milligram equivalents.
  • FIG. 6B shows five-year predicted curve for recurrence specific survival in patients with wild-type NRF2 with increasing intraoperative MME dose.
  • RSS recurrence specific survival
  • MME oral morphine milligram equivalents.
  • the term “about” in reference to a number is generally taken to include numbers that fall within a range of 1%, 5%, or 10% in either direction (greater than or less than) of the number unless otherwise stated or otherwise evident from the context (except where such number would be less than 0% or exceed 100% of a possible value).
  • adapter refers to a short, chemically synthesized, nucleic acid sequence which can be used to ligate to the end of a nucleic acid sequence in order to facilitate attachment to another molecule.
  • the adapter can be single-stranded or double-stranded
  • An adapter can incorporate a short (typically less than 50 base pairs) sequence useful for PCR amplification or sequencing.
  • the “administration” of an agent or drug to a subject includes any route of introducing or delivering to a subject a compound to perform its intended function. Administration can be carried out by any suitable route, including but not limited to, orally, intranasally, parenterally (intravenously, intramuscularly, intraperitoneally, or subcutaneously), rectally, intrathecally, intratumorally or topically. Administration includes self-administration and the administration by another.
  • an “alteration” of a gene or gene product refers to the presence of a mutation or mutations within the gene or gene product, e.g., a mutation, which affects the quantity or activity of the gene or gene product, as compared to the normal or wild-type gene.
  • the genetic alteration can result in changes in the quantity, structure, and/or activity of the gene or gene product in a cancer tissue or cancer cell, as compared to its quantity, structure, and/or activity, in a normal or healthy tissue or cell (e.g., a control).
  • an alteration which is associated with cancer, or predictive of responsiveness to intraoperative analgesics can have an altered nucleotide sequence (e.g., a mutation), amino acid sequence, chromosomal translocation, intra-chromosomal inversion, copy number, expression level, protein level, protein activity, in a cancer tissue or cancer cell, as compared to a normal, healthy tissue or cell.
  • exemplary mutations include, but are not limited to, point mutations (e.g., silent, missense, or nonsense), deletions, insertions, inversions, linking mutations, duplications, translocations, inter- and intra-chromosomal rearrangements Mutations can be present in the coding or non-coding region of the gene.
  • nucleic acid amplification methods are well known to the skilled artisan and include ligase chain reaction (LCR), ligase detection reaction (LDR), ligation followed by Q-replicase amplification, PCR, primer extension, strand displacement amplification (SDA), hyperbranched strand displacement amplification, multiple displacement amplification (MDA), nucleic acid strand-based amplification (NASBA), two-step multiplexed amplifications, rolling circle amplification (RCA), recombinase- polymerase amplification (RPA)(TwistDx, Cambridge, UK), transcription mediated amplification, signal mediated amplification of RNA technology, loop-mediated isothermal amplification of DNA, helicase-dependent amplification, single primer isothermal amplification, and self
  • amplicons Copies of a particular nucleic acid sequence generated in vitro in an amplification reaction are called “amplicons” or “amplification products.”
  • amplicons Copies of a particular nucleic acid sequence generated in vitro in an amplification reaction are called “amplicons” or “amplification products.”
  • cancer or “tumor” are used interchangeably and refer to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, immortality, metastatic potential, rapid growth and proliferation rate, and certain characteristic morphological features. Cancer cells are often in the form of a tumor, but such cells can exist alone within an animal, or can be a non-tumorigenic cancer cell.
  • cancer includes premalignant, as well as malignant cancers.
  • complementarity refers to the base-pairing rules.
  • nucleic acid sequence refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5' end of one sequence is paired with the 3’ end of the other, is in “antiparallel association.”
  • sequence “5'-A-G-T-3”’ is complementary to the sequence “3’-T-C-A-5.”
  • Certain bases not commonly found in naturally-occurring nucleic acids may be included in the nucleic acids described herein. These include, for example, inosine, 7-deazaguanine, Locked Nucleic Acids (LNA), and Peptide Nucleic Acids (PNA).
  • Complementarity need not be perfect; stable duplexes may contain mismatched base pairs, degenerative, or unmatched bases.
  • Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs.
  • a complement sequence can also be an RNA sequence complementary to the DNA sequence or its complement sequence, and can also be a cDNA.
  • control is an alternative sample used in an experiment for comparison purpose.
  • a control can be "positive” or “negative.”
  • a positive control a compound or composition known to exhibit the desired therapeutic effect
  • a negative control a subject or a sample that does not receive the therapy or receives a placebo
  • the reference or control nucleic acid sample is a wild type or a non-mutated DNA or RNA sequence.
  • the reference nucleic acid sample is purified or isolated ( e.g ., it is removed from its natural state).
  • the reference nucleic acid sample is from a non-tumor sample, e.g., a blood control, a normal adjacent tumor (NAT), or any other non- cancerous sample from the same or a different subject.
  • NAT normal adjacent tumor
  • Detecting refers to determining the presence of a mutation or alteration in a nucleic acid of interest in a sample. Detection does not require the method to provide 100% sensitivity. Analysis of nucleic acid markers can be performed using techniques known in the art including, but not limited to, sequence analysis, and electrophoretic analysis. Non-limiting examples of sequence analysis include Maxam-Gilbert sequencing, Sanger sequencing, capillary array DNA sequencing, thermal cycle sequencing (Sears et al. , Biotechniques, 13:626-633 (1992)), solid-phase sequencing (Zimmerman et al. , Methods Mol.
  • sequencing with mass spectrometry such as matrix-assisted laser desorption/ionization time-of- flight mass spectrometry (MALDI-TOF/MS; Fu etal. , Nat. Biotechnol, 16:381-384 (1998)), and sequencing by hybridization.
  • MALDI-TOF/MS matrix-assisted laser desorption/ionization time-of- flight mass spectrometry
  • Non-limiting examples of electrophoretic analysis include slab gel electrophoresis such as agarose or polyacrylamide gel electrophoresis, capillary electrophoresis, and denaturing gradient gel electrophoresis. Additionally, next generation sequencing methods can be performed using commercially available kits and instruments from companies such as the Life Technologies/Ion Torrent PGM or Proton, the Illumina HiSEQ or MiSEQ, and the Roche/454 next generation sequencing system.
  • Detectable label refers to a molecule or a compound or a group of molecules or a group of compounds used to identify a nucleic acid or protein of interest.
  • the detectable label may be detected directly.
  • the detectable label may be a part of a binding pair, which can then be subsequently detected.
  • Signals from the detectable label may be detected by various means and will depend on the nature of the detectable label.
  • Detectable labels may be isotopes, fluorescent moieties, colored substances, and the like.
  • means to detect detectable labels include but are not limited to spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical, or chemical means, such as fluorescence, chemifluorescence, or chemiluminescence, or any other appropriate means.
  • the term “effective amount” refers to a quantity sufficient to achieve a desired therapeutic and/or prophylactic effect, e.g., an amount which results in the prevention of, or a decrease in a disease or condition described herein or one or more signs or symptoms associated with a disease or condition described herein.
  • the amount of a composition administered to the subject will vary depending on the composition, the degree, type, and severity of the disease and on the characteristics of the individual, such as general health, age, sex, body weight and tolerance to drugs. The skilled artisan will be able to determine appropriate dosages depending on these and other factors.
  • the compositions can also be administered in combination with one or more additional therapeutic compounds.
  • the therapeutic compositions may be administered to a subject having one or more signs or symptoms of a disease or condition described herein.
  • a "therapeutically effective amount" of a composition refers to composition levels in which the physiological effects of a disease or condition are ameliorated or eliminated.
  • a therapeutically effective amount can be given in one or more administrations.
  • Gene refers to a DNA sequence that comprises regulatory and coding sequences necessary for the production of an RNA, which may have a non-coding function (e.g., a ribosomal or transfer RNA) or which may include a polypeptide or a polypeptide precursor.
  • the RNA or polypeptide may be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or function is retained.
  • a sequence of the nucleic acids may be shown in the form of DNA, a person of ordinary skill in the art recognizes that the corresponding RNA sequence will have a similar sequence with the thymine being replaced by uracil, i.e., "T" is replaced with "U.”
  • hybridize refers to a process where two substantially complementary nucleic acid strands (at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, at least about 75%, or at least about 90% complementary) anneal to each other under appropriately stringent conditions to form a duplex or heteroduplex through formation of hydrogen bonds between complementary base pairs.
  • Hybridizations are typically and preferably conducted with probe-length nucleic acid molecules, preferably 15-100 nucleotides in length, more preferably 18-50 nucleotides in length. Nucleic acid hybridization techniques are well known in the art.
  • Hybridization and the strength of hybridization is influenced by such factors as the degree of complementarity between the nucleic acids, stringency of the conditions involved, and the thermal melting point (T m ) of the formed hybrid.
  • T m thermal melting point
  • hybridization conditions and parameters see, e.g., Sambrook, etal., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y. ; Ausubel, F. M. etal. 1994, Current Protocols in Molecular Biology, John Wiley & Sons, Secaucus, N J.
  • specific hybridization occurs under stringent hybridization conditions.
  • An oligonucleotide or polynucleotide e.g., a probe or a primer
  • a probe or a primer that is specific for a target nucleic acid will “hybridize” to the target nucleic acid under suitable conditions.
  • the term “library” refers to a collection of nucleic acid sequences, e.g., a collection of nucleic acids derived from whole genomic, subgenomic fragments, cDNA, cDNA fragments, RNA, RNA fragments, ctDNA, cfDNA, or a combination thereof.
  • a portion or all of the library nucleic acid sequences comprises an adapter sequence.
  • the adapter sequence can be located at one or both ends.
  • the adapter sequence can be useful, e.g ., for a sequencing method (e.g., an NGS method), for amplification, for reverse transcription, or for cloning into a vector.
  • the library can comprise a collection of nucleic acid sequences, e.g., a target nucleic acid sequence (e.g., a tumor nucleic acid sequence), a reference nucleic acid sequence, or a combination thereof.
  • the nucleic acid sequences of the library can be derived from a single subject.
  • a library can comprise nucleic acid sequences from more than one subject (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30 or more subjects).
  • two or more libraries from different subjects can be combined to form a library having nucleic acid sequences from more than one subject.
  • a “library nucleic acid sequence” refers to a nucleic acid molecule, e.g., a DNA, RNA, or a combination thereof, that is a member of a library.
  • a library nucleic acid sequence is a DNA molecule, e.g., genomic DNA or cDNA.
  • a library nucleic acid sequence is fragmented, e.g., sheared or enzymatically prepared, genomic DNA.
  • the library nucleic acid sequences comprise sequence from a subject and sequence not derived from the subject, e.g., adapter sequence, a primer sequence, or other sequences that allow for identification, e.g., “barcode” sequences.
  • multiplex PCR refers to amplification of two or more PCR products or amplicons which are each primed using a distinct primer pair.
  • next-generation sequencing or NGS refers to any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules (e.g., in single molecule sequencing) or clonally expanded proxies for individual nucleic acid molecules in a high throughput parallel fashion (e.g., greater than 10 3 , 10 4 , 10 5 or more molecules are sequenced simultaneously).
  • the relative abundance of the nucleic acid species in the library can be estimated by counting the relative number of occurrences of their cognate sequences in the data generated by the sequencing experiment.
  • Next generation sequencing methods are known in the art, and are described, e.g., in Metzker, M. Nature Biotechnology Reviews 11:31 -46 (2010).
  • oligonucleotide refers to a molecule that has a sequence of nucleic acid bases on a backbone comprised mainly of identical monomer units at defined intervals. The bases are arranged on the backbone in such a way that they can bind with a nucleic acid having a sequence of bases that are complementary to the bases of the oligonucleotide.
  • the most common oligonucleotides have a backbone of sugar phosphate units. A distinction may be made between oligodeoxyribonucleotides that do not have a hydroxyl group at the 2' position and oligoribonucleotides that have a hydroxyl group at the 2' position.
  • Oligonucleotides may also include derivatives, in which the hydrogen of the hydroxyl group is replaced with organic groups, e.g., an allyl group.
  • Oligonucleotides of the method which function as primers or probes are generally at least about 10-15 nucleotides long and more preferably at least about 15 to 25 nucleotides long, although shorter or longer oligonucleotides may be used in the method. The exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide.
  • the oligonucleotide may be generated in any manner, including, for example, chemical synthesis, DNA replication, restriction endonuclease digestion of plasmids or phage DNA, reverse transcription, PCR, or a combination thereof.
  • the oligonucleotide may be modified e.g., by addition of a methyl group, a biotin or digoxigenin moiety, a fluorescent tag or by using radioactive nucleotides.
  • the term “overall survival” or “OS” means the observed length of life from the start of treatment to death or the date of last contact.
  • OS all survival
  • peripheral refers to the time period of a patient's surgical procedure. It commonly includes ward admission, anesthesia, surgery, and recovery.
  • the perioperative period is characterized by a sequence including the time preceding an operation when a patient is being prepared for surgery (“the preoperative period”), followed by the time spent in surgery (“the intraoperative period”), and by the time following an operation when the patient is closely monitored for complications while recovering from the effects of anesthesia (“the postoperative period”).
  • the term “primer” refers to an oligonucleotide, which is capable of acting as a point of initiation of nucleic acid sequence synthesis when placed under conditions in which synthesis of a primer extension product which is complementary to a target nucleic acid strand is induced, i.e., in the presence of different nucleotide triphosphates and a polymerase in an appropriate buffer (“buffer” includes pH, ionic strength, cofactors etc) and at a suitable temperature.
  • buffer includes pH, ionic strength, cofactors etc
  • One or more of the nucleotides of the primer can be modified for instance by addition of a methyl group, a biotin or digoxigenin moiety, a fluorescent tag or by using radioactive nucleotides.
  • a primer sequence need not reflect the exact sequence of the template.
  • a non-complementary nucleotide fragment may be attached to the 5' end of the primer, with the remainder of the primer sequence being substantially complementary to the strand.
  • primer as used herein includes all forms of primers that may be synthesized including peptide nucleic acid primers, locked nucleic acid primers, phosphorothioate modified primers, labeled primers, and the like.
  • the term “forward primer” as used herein means a primer that anneals to the anti-sense strand of dsDNA.
  • a “reverse primer” anneals to the sense-strand ofdsDNA.
  • primer pair refers to a forward and reverse primer pair (i.e., a left and right primer pair) that can be used together to amplify a given region of a nucleic acid of interest.
  • Probe refers to nucleic acid that interacts with a target nucleic acid via hybridization.
  • a probe may be fully complementary to a target nucleic acid sequence or partially complementary. The level of complementarity will depend on many factors based, in general, on the function of the probe.
  • a probe or probes can be used, for example to detect the presence or absence of a mutation in a nucleic acid sequence by virtue of the sequence characteristics of the target. Probes can be labeled or unlabeled, or modified in any of a number of ways well known in the art.
  • a probe may specifically hybridize to a target nucleic acid. Probes may be DNA, RNA or a RNA/DNA hybrid.
  • Probes may be oligonucleotides, artificial chromosomes, fragmented artificial chromosome, genomic nucleic acid, fragmented genomic nucleic acid, RNA, recombinant nucleic acid, fragmented recombinant nucleic acid, peptide nucleic acid (PNA), locked nucleic acid, oligomer of cyclic heterocycles, or conjugates of nucleic acid.
  • PNA peptide nucleic acid
  • Probes may comprise modified nucleobases, modified sugar moieties, and modified internucleotide linkages.
  • a probe may be used to detect the presence or absence of a target nucleic acid. Probes are typically at least about 10, 15, 20, 25, 30, 35, 40, 50, 60, 75, 100 nucleotides or more in length.
  • recurrence-specific survival means the observed length of life from the time of surgical resection to the time of first recurrence of the cancer, otherwise censored at the time of last follow-up. In RSS, deaths not involving recurrence of cancer are excluded.
  • a “sample” refers to a substance that is being assayed for the presence of a mutation in a nucleic acid of interest. Processing methods to release or otherwise make available a nucleic acid for detection are well known in the art and may include steps of nucleic acid manipulation.
  • a biological sample may be a body fluid or a tissue sample.
  • a biological sample may consist of or comprise blood, plasma, sera, urine, feces, epidermal sample, vaginal sample, skin sample, cheek swab, sperm, amniotic fluid, cultured cells, bone marrow sample, tumor biopsies, aspirate and/or chorionic villi, cultured cells, and the like.
  • Fresh, fixed or frozen tissues may also be used.
  • the sample is preserved as a frozen sample or as formaldehyde- or paraformaldehyde-fixed paraffin-embedded (FFPE) tissue preparation.
  • FFPE paraffin-embedded
  • the sample can be embedded in a matrix, e.g., an FFPE block or a frozen sample.
  • Whole blood samples of about 0.5 to 5 ml collected with EDTA, ACD or heparin as anti-coagulant are suitable.
  • sensitivity is a measure of the ability of a method to detect a preselected sequence variant in a heterogeneous population of sequences.
  • a method has a sensitivity of S % for variants of F % if, given a sample in which the preselected sequence variant is present as at least F % of the sequences in the sample, the method can detect the preselected sequence at a preselected confidence of C %, S % of the time.
  • the term “separate” therapeutic use refers to an administration of at least two active ingredients at the same time or at substantially the same time by different routes.
  • the term “sequential” therapeutic use refers to administration of at least two active ingredients at different times, the administration route being identical or different. More particularly, sequential use refers to the whole administration of one of the active ingredients before administration of the other or others commences. It is thus possible to administer one of the active ingredients over several minutes, hours, or days before administering the other active ingredient or ingredients. There is no simultaneous treatment in this case.
  • the term “simultaneous” therapeutic use refers to the administration of at least two active ingredients by the same route and at the same time or at substantially the same time.
  • oligonucleotide primer specifically used herein in reference to an oligonucleotide primer means that the nucleotide sequence of the primer has at least 12 bases of sequence identity with a portion of the nucleic acid to be amplified when the oligonucleotide and the nucleic acid are aligned.
  • An oligonucleotide primer that is specific for a nucleic acid is one that, under the stringent hybridization or washing conditions, is capable of hybridizing to the target of interest and not substantially hybridizing to nucleic acids which are not of interest. Higher levels of sequence identity are preferred and include at least 75%, at least 80%, at least 85%, at least 90%, at least 95% and more preferably at least 98% sequence identity.
  • “Specificity,” as used herein, is a measure of the ability of a method to distinguish a truly occurring preselected sequence variant from sequencing artifacts or other closely related sequences. It is the ability to avoid false positive detections. False positive detections can arise from errors introduced into the sequence of interest during sample preparation, sequencing error, or inadvertent sequencing of closely related sequences like pseudo-genes or members of a gene family.
  • a method has a specificity of X % if, when applied to a sample set of N Total sequences, in which X-True sequences are truly variant and XNot true ayre not truly variant, the method selects at least X % of the not truly variant as not variant.
  • a method has a specificity of 90% if, when applied to a sample set of 1,000 sequences, in which 500 sequences are truly variant and 500 are not truly variant, the method selects 90% of the 500 not truly variant sequences as not variant.
  • Exemplary specificities include 90, 95, 98, and 99%.
  • stringent hybridization conditions refers to hybridization conditions at least as stringent as the following: hybridization in 50% formamide, 5xSSC, 50 mM NaH2PO4, pH 6.8, 0.5% SDS, 0.1 mg/mL sonicated salmon sperm DNA, and 5x Denharf s solution at 42° C. overnight; washing with 2x SSC, 0.1% SDS at 45° C; and washing with 0.2x SSC, 0.1% SDS at 45° C.
  • stringent hybridization conditions should not allow for hybridization of two nucleic acids which differ over a stretch of 20 contiguous nucleotides by more than two bases.
  • the terms “subject”, “patient”, or “individual” can be an individual organism, a vertebrate, a mammal, or a human. In some embodiments, the subject, patient or individual is a human.
  • target sequence and “target nucleic acid sequence” refer to a specific nucleic acid sequence to be detected and/or quantified in the sample to be analyzed.
  • the term “therapeutic agent” is intended to mean a compound that, when present in an effective amount, produces a desired therapeutic effect on a subject in need thereof.
  • Treating” or “treatment” as used herein covers the treatment of a disease or disorder described herein, in a subject, such as a human, and includes: (i) inhibiting a disease or disorder, i.e., arresting its development; (ii) relieving a disease or disorder, i.e., causing regression of the disorder; (iii) slowing progression of the disorder; and/or (iv) inhibiting, relieving, or slowing progression of one or more symptoms of the disease or disorder.
  • treatment means that the symptoms associated with the disease are, e.g., alleviated, reduced, cured, or placed in a state of remission.
  • the various modes of treatment of disorders as described herein are intended to mean “substantial,” which includes total but also less than total treatment, and wherein some biologically or medically relevant result is achieved.
  • the treatment may be a continuous prolonged treatment for a chronic disease or a single, or few time administrations for the treatment of an acute condition.
  • Polynucleotides associated with responsiveness to carboxylic acid derivative NSAIDs may be detected by a variety of methods known in the art. Non-limiting examples of detection methods are described below.
  • the detection assays in the methods of the present technology may include purified or isolated DNA (genomic or cDNA), RNA or protein or the detection step may be performed directly from a biological sample without the need for further DNA, RNA or protein purification/isolation.
  • Polynucleotides associated with responsiveness to carboxylic acid derivative NSAIDs can be detected by the use of nucleic acid amplification techniques that are well known in the art.
  • the starting material may be genomic DNA, cDNA, RNA, ctDNA, cfDNA, or mRNA.
  • Nucleic acid amplification can be linear or exponential.
  • Specific variants or mutations may be detected by the use of amplification methods with the aid of oligonucleotide primers or probes designed to interact with or hybridize to a particular target sequence in a specific manner, thus amplifying only the target variant.
  • Non-limiting examples of nucleic acid amplification techniques include polymerase chain reaction (PCR), real-time quantitative PCR (qPCR), digital PCR (dPCR), reverse transcriptase polymerase chain reaction (RT-PCR), nested PCR, ligase chain reaction (see Abravaya, K. etal., Nucleic Acids Res. (1995), 23:675-682), branched DNA signal amplification (see Urdea, M. S.
  • RNA reporters etal., AIDS (1993), 7(suppl 2) : S 11 - S14
  • amplifiable RNA reporters Q-beta replication, transcription-based amplification, boomerang DNA amplification, strand displacement activation, cycling probe technology, isothermal nucleic acid sequence based amplification (NASBA) (see Kievits, T. et al., J Virological Methods (1991), 35:273-286), Invader Technology, next-generation sequencing technology or other sequence replication assays or signal amplification assays.
  • Oligonucleotide primers for use in amplification methods can be designed according to general guidance well known in the art as described herein, as well as with specific requirements as described herein for each step of the particular methods described.
  • oligonucleotide primers for cDNA synthesis and PCR are 10 to 100 nucleotides in length, preferably between about 15 and about 60 nucleotides in length, more preferably 25 and about 50 nucleotides in length, and most preferably between about 25 and about 40 nucleotides in length.
  • Tm of a polynucleotide affects its hybridization to another polynucleotide (e.g ., the annealing of an oligonucleotide primer to a template polynucleotide).
  • the oligonucleotide primer used in various steps selectively hybridizes to a target template or polynucleotides derived from the target template (i.e., first and second strand cDNAs and amplified products).
  • selective hybridization occurs when two polynucleotide sequences are substantially complementary (at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, preferably at least about 75%, more preferably at least about 90% complementary).
  • Kanehisa, M Polynucleotides Res. (1984), 12:203, incorporated herein by reference.
  • mismatch may be small, such as a mono-, di- or tri-nucleotide. In certain embodiments, 100% complementarity exists.
  • Probes are capable of hybridizing to at least a portion of the nucleic acid of interest or a reference nucleic acid (i.e., wild-type sequence). Probes may be an oligonucleotide, artificial chromosome, fragmented artificial chromosome, genomic nucleic acid, fragmented genomic nucleic acid, RNA, recombinant nucleic acid, fragmented recombinant nucleic acid, peptide nucleic acid (PNA), locked nucleic acid, oligomer of cyclic heterocycles, or conjugates of nucleic acid. Probes may be used for detecting and/or capturing/purifying a nucleic acid of interest.
  • probes can be about 10 nucleotides, about 20 nucleotides, about 25 nucleotides, about 30 nucleotides, about 35 nucleotides, about 40 nucleotides, about 50 nucleotides, about 60 nucleotides, about 75 nucleotides, or about 100 nucleotides long. However, longer probes are possible.
  • Longer probes can be about 200 nucleotides, about 300 nucleotides, about 400 nucleotides, about 500 nucleotides, about 750 nucleotides, about 1,000 nucleotides, about 1,500 nucleotides, about 2,000 nucleotides, about 2,500 nucleotides, about 3,000 nucleotides, about 3,500 nucleotides, about 4,000 nucleotides, about 5,000 nucleotides, about 7,500 nucleotides, or about 10,000 nucleotides long.
  • Probes may also include a detectable label or a plurality of detectable labels.
  • the detectable label associated with the probe can generate a detectable signal directly. Additionally, the detectable label associated with the probe can be detected indirectly using a reagent, wherein the reagent includes a detectable label, and binds to the label associated with the probe.
  • detectably labeled probes can be used in hybridization assays including, but not limited to Northern blots, Southern blots, microarray, dot or slot blots, and in situ hybridization assays such as fluorescent in situ hybridization (FISH) to detect a target nucleic acid sequence within a biological sample.
  • FISH fluorescent in situ hybridization
  • Certain embodiments may employ hybridization methods for measuring expression of a polynucleotide gene product, such as mRNA. Methods for conducting polynucleotide hybridization assays have been well developed in the art. Hybridization assay procedures and conditions will vary depending on the application and are selected in accordance with the general binding methods known including those referred to in: Maniatis el al.
  • Detectably labeled probes can also be used to monitor the amplification of a target nucleic acid sequence.
  • detectably labeled probes present in an amplification reaction are suitable for monitoring the amount of amplicon(s) produced as a function of time.
  • probes include, but are not limited to, the 5'- exonuclease assay (TAQMAN® probes described herein (see also U.S. Pat. No. 5,538,848) various stem-loop molecular beacons (see for example, U.S. Pat. Nos.
  • the detectable label is a fluorophore.
  • Suitable fluorescent moieties include but are not limited to the following fluorophores working individually or in combination: 4-acetamido-4'-isothiocyanatostilbene- 2,2'disulfonic acid; acridine and derivatives: acridine, acridine isothiocyanate; Alexa Fluors: Alexa Fluor® 350, Alexa Fluor® 488, Alexa Fluor® 546, Alexa Fluor® 555, Alexa Fluor® 568, Alexa Fluor® 594, Alexa Fluor® 647 (Molecular Probes); 5-(2- aminoethyl)aminonaphthalene-l -sulfonic acid (EDANS); 4- amino-N-[3- vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (Lucifer Yellow VS); N-(4- anilino-1- naphthyl)male
  • Detector probes can also comprise sulfonate derivatives of fluorescenin dyes with S03 instead of the carboxylate group, phosphoramidite forms of fluorescein, phosphoramidite forms of CY 5 (commercially available for example from Amersham).
  • Detectably labeled probes can also include quenchers, including without limitation black hole quenchers (Biosearch), Iowa Black (IDT), QSY quencher (Molecular Probes), and Dabsyl and Dabcel sulfonate/carboxylate Quenchers (Epoch).
  • quenchers including without limitation black hole quenchers (Biosearch), Iowa Black (IDT), QSY quencher (Molecular Probes), and Dabsyl and Dabcel sulfonate/carboxylate Quenchers (Epoch).
  • Detectably labeled probes can also include two probes, wherein for example a fluorophore is on one probe, and a quencher is on the other probe, wherein hybridization of the two probes together on a target quenches the signal, or wherein hybridization on the target alters the signal signature via a change in fluorescence.
  • interchelating labels such as ethidium bromide, SYBR®
  • real-time visualization may involve the use of both an intercalating detector probe and a sequence-based detector probe.
  • the detector probe is at least partially quenched when not hybridized to a complementary sequence in the amplification reaction, and is at least partially unquenched when hybridized to a complementary sequence in the amplification reaction.
  • the amount of probe that gives a fluorescent signal in response to an excited light typically relates to the amount of nucleic acid produced in the amplification reaction.
  • the amount of fluorescent signal is related to the amount of product created in the amplification reaction. In such embodiments, one can therefore measure the amount of amplification product by measuring the intensity of the fluorescent signal from the fluorescent indicator.
  • Primers or probes may be designed to selectively hybridize to any portion of a nucleic acid sequence encoding a polypeptide selected from among MDM2, KEAP1 and NFE2L2. Exemplary nucleic acid sequences of the human orthologs of these genes are provided below: [0092] NM_002392.6 Homo sapiens MDM2 proto-oncogene (MDM2), transcript variant 1, mRNA (SEQ ID NO: 1)
  • Primers or probes can be designed so that they hybridize under stringent conditions to mutant nucleotide sequences of KEAP1, but not to the respective wild-type nucleotide sequences. Primers or probes can also be prepared that are complementary and specific for the wild-type nucleotide sequence of KEAP1, but not to any of the corresponding mutant nucleotide sequences.
  • the mutant nucleotide sequences of KEAP1 may be a frameshift mutation, a missense mutation, a deletion, an insertion, a nonsense mutation, an inversion, or a translocation, that results in the loss of expression and/or activity of KEAP1 (i.e., loss of function mutations).
  • primers or probes can be designed so that they selectively hybridize to mutant nucleotide sequences of MDM2 or NFE2L2.
  • the mutant nucleotide sequences of MDM2 or NFE2L2 are gain of function mutations.
  • detection can occur through any of a variety of mobility dependent analytical techniques based on the differential rates of migration between different nucleic acid sequences.
  • mobility-dependent analysis techniques include electrophoresis, chromatography, mass spectroscopy, sedimentation, gradient centrifugation, field-flow fractionation, multi-stage extraction techniques, and the like.
  • mobility probes can be hybridized to amplification products, and the identity of the target nucleic acid sequence determined via a mobility dependent analysis technique of the eluted mobility probes, as described in Published PCT Applications WO04/46344 and WOO 1/92579.
  • detection can be achieved by various microarrays and related software such as the Applied Biosystems Array System with the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer and other commercially available array systems available from Affymetrix, Agilent, Illumina, and Amersham Biosciences, among others (see also Gerry etal, J. Mol. Biol. 292:251-62, 1999; De Beilis et al, Minerva Biotec 14:247-52, 2002; and Stears etal, Nat. Med. 9:14045, including supplements, 2003).
  • Applied Biosystems Array System with the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer and other commercially available array systems available from Affymetrix, Agilent, Illumina, and Amersham Biosciences, among others (see also Gerry etal, J. Mol. Biol. 292:251-62, 1999; De Beilis et al, Minerva Biotec 14:247-52, 2002;
  • detection can comprise reporter groups that are incorporated into the reaction products, either as part of labeled primers or due to the incorporation of labeled dNTPs during an amplification, or attached to reaction products, for example but not limited to, via hybridization tag complements comprising reporter groups or via linker arms that are integral or attached to reaction products.
  • unlabeled reaction products may be detected using mass spectrometry.
  • high throughput, massively parallel sequencing employs sequencing-by-synthesis with reversible dye terminators.
  • sequencing is performed via sequencing-by-ligation.
  • sequencing is single molecule sequencing. Examples of Next Generation Sequencing techniques include, but are not limited to pyrosequencing, Reversible dye-terminator sequencing, SOLiD sequencing, Ion semiconductor sequencing, Helioscope single molecule sequencing etc.
  • the Ion TorrentTM (Life Technologies, Carlsbad, CA) amplicon sequencing system employs a flow-based approach that detects pH changes caused by the release of hydrogen ions during incorporation of unmodified nucleotides in DNA replication.
  • a sequencing library is initially produced by generating DNA fragments flanked by sequencing adapters. In some embodiments, these fragments can be clonally amplified on particles by emulsion PCR. The particles with the amplified template are then placed in a silicon semiconductor sequencing chip. During replication, the chip is flooded with one nucleotide after another, and if a nucleotide complements the DNA molecule in a particular microwell of the chip, then it will be incorporated.
  • a proton is naturally released when a nucleotide is incorporated by the polymerase in the DNA molecule, resulting in a detectable local change of pH.
  • the pH of the solution then changes in that well and is detected by the ion sensor. If homopolymer repeats are present in the template sequence, multiple nucleotides will be incorporated in a single cycle. This leads to a corresponding number of released hydrogens and a proportionally higher electronic signal.
  • the 454TM GS FLX TM sequencing system employs a light-based detection methodology in a large-scale parallel pyrosequencing system. Pyrosequencing uses DNA polymerization, adding one nucleotide species at a time and detecting and quantifying the number of nucleotides added to a given location through the light emitted by the release of attached pyrophosphates.
  • adapter-ligated DNA fragments are fixed to small DNA-capture beads in a water-in-oil emulsion and amplified by PCR (emulsion PCR).
  • Each DNA-bound bead is placed into a well on a picotiter plate and sequencing reagents are delivered across the wells of the plate.
  • the four DNA nucleotides are added sequentially in a fixed order across the picotiter plate device during a sequencing run. During the nucleotide flow, millions of copies of DNA bound to each of the beads are sequenced in parallel.
  • the nucleotide complementary to the template strand is added to a well, the nucleotide is incorporated onto the existing DNA strand, generating a light signal that is recorded by a CCD camera in the instrument.
  • Sequencing technology based on reversible dye-terminators: DNA molecules are first attached to primers on a slide and amplified so that local clonal colonies are formed. Four types of reversible terminator bases (RT -bases) are added, and non-incorporated nucleotides are washed away. Unlike pyrosequencing, the DNA can only be extended one nucleotide at a time. A camera takes images of the fluorescently labeled nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle.
  • RT -bases reversible terminator bases
  • Helicos's single-molecule sequencing uses DNA fragments with added polyA tail adapters, which are attached to the flow cell surface. At each cycle, DNA polymerase and a single species of fluorescently labeled nucleotide are added, resulting in template-dependent extension of the surface-immobilized primer-template duplexes. The reads are performed by the Helioscope sequencer. After acquisition of images tiling the full array, chemical cleavage and release of the fluorescent label permits the subsequent cycle of extension and imaging.
  • Sequencing by synthesis like the "old style" dye-termination electrophoretic sequencing, relies on incorporation of nucleotides by a DNA polymerase to determine the base sequence.
  • a DNA library with affixed adapters is denatured into single strands and grafted to a flow cell, followed by bridge amplification to form a high-density array of spots onto a glass chip.
  • Reversible terminator methods use reversible versions of dye-terminators, adding one nucleotide at a time, detecting fluorescence at each position by repeated removal of the blocking group to allow polymerization of another nucleotide.
  • the signal of nucleotide incorporation can vary with fluorescently labeled nucleotides, phosphate-driven light reactions and hydrogen ion sensing having all been used.
  • SBS platforms include Illumina GA and HiSeq 2000.
  • the MiSeq® personal sequencing system (Illumina, Inc.) also employs sequencing by synthesis with reversible terminator chemistry.
  • the sequencing by ligation method uses a DNA ligase to determine the target sequence.
  • This sequencing method relies on enzymatic ligation of oligonucleotides that are adjacent through local complementarity on a template DNA strand.
  • This technology employs a partition of all possible oligonucleotides of a fixed length, labeled according to the sequenced position.
  • Oligonucleotides are annealed and ligated and the preferential ligation by DNA ligase for matching sequences results in a dinucleotide encoded color space signal at that position (through the release of a fluorescently labeled probe that corresponds to a known nucleotide at a known position along the oligo).
  • This method is primarily used by Life Technologies’ SOLiDTM sequencers.
  • the DNA is amplified by emulsion PCR.
  • the resulting beads, each containing only copies of the same DNA molecule, are deposited on a solid planar substrate.
  • SMRTTM sequencing is based on the sequencing by synthesis approach.
  • the DNA is synthesized in zero-mode wave-guides (ZMWs)-small well-like containers with the capturing tools located at the bottom of the well.
  • the sequencing is performed with use of unmodified polymerase (attached to the ZMW bottom) and fluorescently labeled nucleotides flowing freely in the solution.
  • the wells are constructed in a way that only the fluorescence occurring at the bottom of the well is detected.
  • the fluorescent label is detached from the nucleotide at its incorporation into the DNA strand, leaving an unmodified DNA strand.
  • the present disclosure provides a method for selecting a cancer patient undergoing tumor resection surgery for lung cancer for treatment with a carboxylic acid derivative nonsteroidal anti-inflammatory drug (NSAID) comprising (a) determining (i) the absence of mutations in MDM2 or (ii) the absence of mutations in the Nrf2 pathway in a biological sample obtained from the cancer patient; and (b) administering to the cancer patient an effective amount of a carboxylic acid derivative NSAID during the tumor resection surgery.
  • NSAID carboxylic acid derivative nonsteroidal anti-inflammatory drug
  • the biological sample is assayed via next-generation sequencing, PCR, real-time quantitative PCR (qPCR), digital PCR (dPCR), Southern blotting, Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • the biological sample comprises genomic DNA, cDNA, ctDNA, cfDNA, RNA, and/or mRNA.
  • the present disclosure provides a method for prolonging survival of a cancer patient undergoing tumor resection surgery for lung cancer comprising administering to the cancer patient an effective amount of a carboxylic acid derivative NSAID during the tumor resection surgery.
  • mRNA or polypeptide expression and/or activity levels of MDM2, KEAPl and NFE2L2 in a biological sample obtained from the cancer patient are comparable to that observed in a control sample obtained from a healthy subject or a predetermined threshold.
  • mRNA expression levels are detected via real-time quantitative PCR (qPCR), digital PCR (dPCR), Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • polypeptide expression levels are detected via Western blotting, enzyme-linked immunosorbent assays (ELISA), dot blotting, immunohistochemistry, immunofluorescence, immunoprecipitation, Immunoelectrophoresis, or mass-spectrometry.
  • the carboxylic acid derivative NSAID is an acetic acid NSAID or a propionic acid NSAID.
  • carboxylic acid derivative NSAID examples include, but are not limited to, ibuprofen, dexibuprofen, naproxen, fenoprofen, ketoprofen, dexketoprofen, flurbiprofen, oxaprozin, loxoprofen, pelubiprofen, zaltoprofen, indomethacin, tolmetin, sulindac, etodolac, ketorolac, diclofenac, aceclofenac, bromfenac, or nabumeton.
  • the carboxylic acid derivative NSAID is administered orally, intravenously, or intramuscularly. Additionally or alternatively, in some embodiments, the effective amount of the carboxylic acid derivative NSAID is administered intraoperatively and/or postoperatively. The effective amount of the carboxylic acid derivative NSAID may be administered to the cancer patient during closing of an incision.
  • the effective amount of the carboxylic acid derivative NSAID is about 10 mg- 1500 mg. In some embodiments of the methods disclosed herein, the effective amount of the carboxylic acid derivative NSAID is about 10 mg, about 15 mg, about 20 mg, about 25 mg, about 30 mg, about 35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 mg, about 60 mg, about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about 90 mg, about 95 mg, about 100 mg, about 150 mg, about 200 mg, about 250 mg, about 300 mg, about 350 mg, about 400 mg, about 450 mg, about 500 mg, about 550 mg, about 600 mg, about 650 mg, about 700 mg, about 750 mg, about 800 mg, about 850 mg, about 900 mg, about 950 mg, about 1000 mg, about 1050 mg, about 1100 mg, about 1150 mg, about 1200 mg, about 1250 mg, about 1300 mg, about 1350 mg
  • the effective amount of the carboxylic acid derivative NSAID is administered as a bolus dose during the tumor resection surgery.
  • the carboxylic acid derivative NSAID is administered as a bolus of 0.25 mg/kg-10 mg/kg.
  • the carboxylic acid derivative NSAID is administered as a bolus of about 0.25 mg/kg, about 0.5 mg/kg, about 0.75 mg/kg, about 1 mg/kg, about 1.5 mg/kg, about 2 mg/kg, about 2.5 mg/kg, about 3 mg/kg, about 3.5 mg/kg, about 4 mg/kg, about 4.5 mg/kg, about 5 mg/kg, about 5.5 mg/kg, about 6 mg/kg, about 6.5 mg/kg, about 7 mg/kg, about 7.5 mg/kg, about 8 mg/kg, about 8.5 mg/kg, about 9 mg/kg, about 9.5 mg/kg, or about 10 mg/kg.
  • the methods of the present technology further comprises administering to the cancer patient an effective amount of an intraoperative opioid analgesic.
  • intraoperative opioid analgesic include, but are not limited to fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, and sufentanil.
  • the effective amount of the intraoperative opioid analgesic may range from about 1 MME to about 200 MMEs. In certain embodiments, the effective amount of the intraoperative opioid analgesic is about 1 MME to about 20 MMEs, about 20 MMEs to about 45 MMEs, or about 45 MMEs to about 200 MMEs.
  • the effective amount of the intraoperative opioid analgesic is about 1 MME, about 2 MMEs, about 3 MMEs, about 4 MMEs, about 5 MMEs, about 6 MMEs, about 7 MMEs, about 8 MMEs, about 9 MMEs, about 10 MMEs, about 11 MMEs, about 12 MMEs, about 13 MMEs, about 14 MMEs, about 15 MMEs, about 16 MMEs, about 17 MMEs, about 18 MMEs, about 19 MMEs, about 20 MMEs, about 21 MMEs, about 22 MMEs, about 23 MMEs, about 24 MMEs, about 25 MMEs, about 26 MMEs, about 27 MMEs, about 28 MMEs, about 29 MMEs, about 30 MMEs, about 31 MMEs, about 32 MMEs, about 33 MMEs, about 34 MMEs, about 35 MMEs, about 36 MMEs, about 37 MMEs, about 38 MMEs, about 39 MMEs, about 40-45
  • the effective amount of the intraoperative opioid analgesic is administered as a series of bolus doses or as a continuous infusion during the tumor resection surgery. In certain embodiments, the effective amount of the intraoperative opioid analgesic is administered to the cancer patient prior to incision. Additionally or alternatively, in some embodiments, the effective amount of the intraoperative opioid analgesic is administered intravenously.
  • the method further comprises administering to the cancer patient an effective amount of a local anesthetic solution that comprises one or more of lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, or benzocaine, and optionally an opioid.
  • the methods of the present technology further comprise administering to the cancer patient an effective amount of a local anesthetic solution via an epidural catheter before, during and/or after the tumor resection surgery.
  • the effective amount of the local anesthetic solution may range from about 0.05%-4% local anesthetic solution in a volume of 1-10 ml per hour when administered via an epidural catheter.
  • the effective amount of the local anesthetic solution is about 0.05 %, about 0.06 %, about 0.07 %, about 0.08 %, about 0.09 %, about 0.1 %, about 0.15 %, about 0.2 %, about 0.25 %, about 0.3 %, about 0.35 %, about 0.4 %, about 0.45 %, about 0.5 %, about 0.55 %, about 0.6 %, about 0.65 %, about 0.7 %, about 0.75 %, about 0.8 %, about 0.85 %, about 0.9 %, about 0.95 %, about 1.0 %, about 1.1 %, about 1.2 %, about 1.3 %, about 1.4 %, about 1.5 %, about 1.6 %, about 1.7 %, about 1.8 %,
  • the effective amount of the local anesthetic solution is administered as a series of bolus doses or as a continuous infusion during the tumor resection surgery.
  • suitable local anesthetics include, but are not limited to, lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, and benzocaine.
  • the effective amount of the local anesthetic solution may be administered before, during and/or after the tumor resection surgery using any regional anesthesia technique directed at nerves innervating the thorax and chest wall (e.g ., via serratus plane nerve block, intercostal nerve block, or paravertebral block).
  • the effective amount of the local anesthetic solution may range from about 0.05%-4% local anesthetic solution in a volume of 10-40 ml when administered using any regional anesthesia technique directed at nerves innervating the thorax and chest wall (e.g., via serratus plane nerve block, intercostal nerve block, or paravertebral block).
  • the effective amount of the local anesthetic solution is about 0.05 %, about 0.06 %, about 0.07 %, about 0.08 %, about 0.09 %, about 0.1 %, about 0.15 %, about 0.2 %, about 0.25 %, about 0.3 %, about 0.35 %, about 0.4 %, about 0.45 %, about 0.5 %, about 0.55 %, about 0.6 %, about 0.65 %, about 0.7 %, about 0.75 %, about 0.8 %, about 0.85 %, about 0.9 %, about 0.95 %, about 1.0 %, about 1.1 %, about 1.2 %, about 1.3 %, about 1.4 %, about 1.5 %, about 1.6 %, about 1.7 %, about 1.8 %, about 1.9 %, about 2.0 %, about 2.1 %, about 2.2 %, about 2.3 %, about 2.4 %, about 2.5 %, about 2.6 %, about
  • Suitable local anesthetics include, but are not limited to, lidocaine, mepivacaine, prilocaine, bupivacaine, etidocaine, ropivacaine, levobupivacaine, cocaine, procaine, tetracaine, chloroprocaine, and benzocaine.
  • the local anesthetic solution may further comprise an opioid (e.g., fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil).
  • an opioid e.g., fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the local anesthetic solution may comprise 0.5 mcg/ml-50 mcg/ml opioid.
  • the local anesthetic solution may comprise about 0.5 mcg/ml, about 0.6 mcg/ml, about 0.7 mcg/ml, about 0.8 mcg/ml, about 0.9 mcg/ml, about 1.0 mcg/ml, about 1.5 mcg/ml, about 2.0 mcg/ml, about 2.5 mcg/ml, about 3.0 mcg/ml, about 3.5 mcg/ml, about 4.0 mcg/ml, about 4.5 mcg/ml, about 5.0 mcg/ml, about 5.5 mcg/ml, about 6.0 mcg/ml, about 6.5 mcg/ml, about 7.0 mcg/ml, about 7.5 mcg/ml, about 8.0 mcg/ml, about 8.5 mcg/ml, about 9.0 mcg/ml, about 10
  • the methods of the present technology further comprise administering to the cancer patient an effective amount of a postoperative opioid analgesic after the tumor resection surgery.
  • post-operative opioid analgesics include, but are not limited to, fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the postoperative opioid analgesic and the intraoperative opioid analgesic are the same opioid analgesic or different opioid analgesics.
  • the effective amount of the post-operative opioid analgesic and the effective amount of the intraoperative opioid analgesic are the same or different.
  • the effective amount of the postoperative opioid analgesic is administered to the cancer patient as a bolus of about 0.005 mg to about 100 mg.
  • the effective amount of the post-operative opioid analgesic is administered to the cancer patient as a bolus of about 0.005 mg, about 0.006 mg, about 0.007 mg, about 0.008 mg, about 0.009 mg, about 0.01 mg, about 0.02 mg, about 0.03 mg, about 0.04 mg, about 0.05 mg, about 0.06 mg, about 0.07 mg, about 0.08 mg, about 0.09 mg, about 0.1 mg, about 0.2 mg, about 0.3 mg, about 0.4 mg, about 0.5 mg, about 0.6 mg, about 0.7 mg, about 0.8 mg, about 0.9 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 1-5 mg, about 5-10 mg, about 10-15 mg, about 15-20 mg, about 20-25 mg, about 25-30 mg, about
  • the effective amount of the post-operative opioid analgesic may be continuously delivered to the cancer patient at a per hour rate of about 0.01 mg/hr to about 10 mg/hr. In certain embodiments, the effective amount of the post-operative opioid analgesic is continuously delivered to the cancer patient at a per hour rate of about 0.01 mg/hr, about 0.02 mg/hr, about 0.03 mg/hr, about 0.04 mg/hr, about 0.05 mg/hr, about 0.06 mg/hr, about 0.07 mg/hr, about 0.08 mg/hr, about 0.09 mg/hr, about 0.1 mg/hr, about 0.2 mg/hr, about 0.3 mg/hr, about 0.4 mg/hr, about 0.5 mg/hr, about 0.6 mg/hr, about 0.7 mg/hr, about 0.8 mg/hr, about 0.9 mg/hr, about 1 mg/hr, about 1.5 mg/hr, about 2 mg/hr, about 2.5 mg/hr, about 3 mg
  • the method further comprises administering to the cancer patient an effective amount of ketamine, precedex, or acetaminophen during the tumor resection surgery.
  • the present disclosure provides a method for selecting a cancer patient undergoing tumor resection surgery for lung cancer for treatment with a NSAID-free intraoperative analgesic comprising (a) (i) detecting the presence of at least one gain of function mutation in MDM2 in a biological sample obtained from the cancer patient, and/or (ii) detecting the presence of one or more mutations that result in elevated activity of Nrf2 pathway in a biological sample obtained from the cancer patient; and (b) administering to the cancer patient an effective amount of a NSAID-free intraoperative analgesic during the tumor resection surgery.
  • the mutations in MDM2 and/or the Nrf2 pathway may be detected via next-generation sequencing, PCR, real-time quantitative PCR (qPCR), digital PCR (dPCR), Southern blotting, Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH).
  • the biological sample comprises genomic DNA, cDNA, ctDNA, cfDNA, RNA, and/or mRNA.
  • the present disclosure provides a method for prolonging survival of a cancer patient undergoing tumor resection surgery for lung cancer comprising administering to the cancer patient an effective amount of a NSAID-free intraoperative analgesic during the tumor resection surgery, wherein mRNA or polypeptide expression and/or activity levels of MDM2 or Nrf2 pathway in a biological sample obtained from the cancer patient are elevated compared to that observed in a control sample obtained from a healthy subject or a predetermined threshold.
  • mRNA expression levels are detected via real-time quantitative PCR (qPCR), digital PCR (dPCR), Reverse transcriptase-PCR (RT-PCR), Northern blotting, microarray, dot or slot blots, in situ hybridization, or fluorescent in situ hybridization (FISH). Additionally or alternatively, in certain embodiments, polypeptide expression levels are detected via Western blotting, enzyme- linked immunosorbent assays (ELISA), dot blotting, immunohistochemistry, immunofluorescence, immunoprecipitation, Immunoelectrophoresis, or mass-spectrometry.
  • qPCR real-time quantitative PCR
  • dPCR digital PCR
  • RT-PCR Reverse transcriptase-PCR
  • Northern blotting microarray
  • dot or slot blots in situ hybridization
  • FISH fluorescent in situ hybridization
  • polypeptide expression levels are detected via Western blotting, enzyme- linked immunosorbent assays (ELISA), dot blotting, immunohistochemistry, immunofluorescence, immuno
  • the NSAID-free intraoperative analgesic is an opioid, or acetaminophen.
  • opioids include, but are not limited to, fentanyl, hydromorphone, morphine, oxycodone, hydrocodone, codeine, meperidine, remifentanil, or sufentanil.
  • the effective amount of the NSAID-free intraoperative analgesic may be administered as a series of bolus doses, or as a continuous infusion during the tumor resection surgery.
  • the effective amount of the opioid may range from about 1 MME to about 200 MMEs. In certain embodiments, the effective amount of the opioid is about 1 MME to about 20 MMEs, about 20 MMEs to about 45 MMEs, or about 45 MMEs to about 200 MMEs.
  • the effective amount of the opioid is about 1 MME, about 2 MMEs, about 3 MMEs, about 4 MMEs, about 5 MMEs, about 6 MMEs, about 7 MMEs, about 8 MMEs, about 9 MMEs, about 10 MMEs, about 11 MMEs, about 12 MMEs, about 13 MMEs, about 14 MMEs, about 15 MMEs, about 16 MMEs, about 17 MMEs, about 18 MMEs, about 19 MMEs, about 20 MMEs, about 21 MMEs, about 22 MMEs, about 23 MMEs, about 24 MMEs, about 25 MMEs, about 26 MMEs, about 27 MMEs, about 28 MMEs, about 29 MMEs, about 30 MMEs, about 31 MMEs, about 32 MMEs, about 33 MMEs, about 34 MMEs, about 35 MMEs, about 36 MMEs, about 37 MMEs, about 38 MMEs, about 39 MMEs, about 40-45 MMEs, about 45
  • the effective amount of the acetaminophen may range from about 80 mg to about 1000 mg. In some embodiments, the effective amount of the acetaminophen is about 80 mg, about 90 mg, about 100 mg, about 110 mg, about 120 mg, about 130 mg, about 140 mg, about 150 mg, about 160 mg, about 170 mg, about 180 mg, about 190 mg, about 200 mg, about 210 mg, about 220 mg, about 230 mg, about 240 mg, about 250 mg, about 260 mg, about 270 mg, about 280 mg, about 290 mg, about 300 mg, about 310 mg, about 320 mg, about 330 mg, about 340 mg, about 350 mg, about 360 mg, about 370 mg, about 380 mg, about 390 mg, about 400 mg, about 410 mg, about 420 mg, about 430 mg, about 440 mg, about 450 mg, about 460 mg, about 470 mg, about 480 mg, about 490 mg, about 500 mg, about 510 mg, about 520 mg, about
  • the cancer patient exhibits stage I, stage II or stage III lung cancer. Additionally or alternatively, in some embodiments, the cancer patient has been diagnosed with lung adenocarcinoma (LUAD).
  • the histologic subtype of the lung adenocarcinoma may be lepidic, acinar, papillary, micropapillary, solid or unknown.
  • the cancer patient has received an adjuvant therapy.
  • the adjuvant therapy may be chemotherapy, radiation therapy or chemoradiation therapy. Additionally or alternatively, in some embodiments of the methods disclosed herein, the patient is human.
  • the biological sample obtained from the cancer patient comprises biopsied tumor tissue, whole blood, plasma, or serum.
  • Administration of any of the intraoperative or postoperative analgesics disclosed herein can be carried out by any suitable route, including but not limited to, orally, intranasally, parenterally (intravenously, intramuscularly, intraperitoneally, or subcutaneously), rectally, intrathecally, intratumorally or topically.
  • EvW Elixhauser-van Walraven
  • NGS next generation sequencing
  • MSK-IMPACT next generation sequencing
  • the CONSORT diagram shows exclusion criteria for the patient cohort (FIG. 3). Metachronous and synchronous tumors were excluded with metachronous tumors differentiated from recurrent tumors in accordance with the Martini and Melamed criteria, as previously described in Martini N, Melamed MR. J Thorac Cardiovasc Surg. 70(4):606-612 (1975).
  • TMB Tumor mutation burden
  • Fraction genome altered was defined as the number of bases in sequenced genomic segments with log2 copy number fold change >0.2 or ⁇ -0.2 over the total number of bases in all sequenced segments.
  • Known mutations and copy number alterations which have been described to activate oncogenes or inactivate tumor suppressor genes were identified using the proprietary OncoKB Knowledge Base. This system was necessary to distinguish between those mutations and alterations with known or presumed functional implications against benign variants or those with unknown clinical significance (Chakravarty D et al, JCO Precision Oncology. 1:1-84 6 (2017)).
  • Immunohistochemistry on LUAD Samples was performed on ten patient samples using a hydrogen peroxidase method. Frozen tissue samples were chosen based on tissue availability from a subset of available tissue in this patient cohort.
  • the LUAD samples were run in duplicate against matched adjacent non-tumor lung tissue samples to detect expression levels of the MOR.
  • Tissue samples were homogenized in PBS (lOmg in lOOpl PBS) and samples were centrifuged at 3000rpm for 15 minutes at which point, the supernatant was removed and run on quantitative sandwich enzyme linked immunosorbent assay (ELISA) kits for the mu opioid receptor (MOR) purchased from MyBioSource, Inc. (San Diego, CA).
  • ELISA sandwich enzyme linked immunosorbent assay
  • ELISA sensitivities were ⁇ 7.81pg/ml with intra-assay coefficient of variability (CV) ⁇ 8% and inter-assay CV ⁇ 10% precision.
  • Median optical density (OD) levels for all tumor samples were obtained and compared against non-tumor matched controls. Standard OD levels were analyzed on a logistic regression and median sample concentrations were estimated for both the tumor and non-tumor specimens. Standard error of the mean was estimated for tumor and non-tumor MOR sample composite concentrations.
  • the primary objective of the study was to quantify the association between intraoperative opioid dose and oncologic outcomes.
  • the primary outcome was recurrence- specific survival (RSS).
  • Time to event was determined from the time of surgical resection to the time of first recurrence, otherwise censored at the time of last follow-up.
  • RSS was chosen in place of the alternative recurrence-free survival (RFS), time to recurrence or death from any cause, in order to determine whether opioids and the adjuncts were associated with disease progression in stage I-III LUAD.
  • the secondary outcome was cancer specific survival (OS), which was defined as time to death from any cause.
  • the predicted 5-year recurrence-specific survival (RSS) estimate curves was generated based on the most frequently observed characteristics or median value for each continuous variable in the MVA (papillary/acinar histologic subtype, median Exlihauser-van Walraven score, lobectomy procedure, median age, and pathologic stage I).
  • the predicted RSS estimates by MME curve were generated for the MV As without genomic factors.
  • ketorolac Five hundred eighteen of the 740 patients in the cohort received ketorolac intraoperatively, and this exposure was associated with improved RSS on univariable analysis (hazard ratio [HR], 0.48 [95% confidence interval (FIG. 1A). Consequently, the original multivariable analysis was repeated, this time including ketorolac.
  • the method inputs a patient cohort with both outcome and RNA sequencing data, such as TCGA, as well as a priori knowledge of a drug’s effects on gene expression, generally from the cancer-derived Connectivity Map database as described in Subramanian A, et al., Cell 171(6): 1437-1452 (2017).
  • the method then calculates gene coexpression networks associated with patient survival in a data-driven manner and projects a drug’s effects on gene expression onto these networks.
  • the result is a prediction of the drug’s regulation of the survival-associated networks and, by extension, the survival outcome itself. For example, a drug that upregulates a network associated with improved survival would be expected to itself improve survival.
  • ketorolac for the TCGA-LUAD cohort of 392 surgical patients predicts a net antitumour effect of ketorolac on lung adenocarcinoma (ketorolac regulates five of six survival-associated gene networks in an antitumour direction; FIG. ID).
  • Survival curves for one of the strongest-regulated networks are shown in FIG. IE, where it is seen that downregulation is associated with improved survival (note that, because of greater reliability and validity of this endpoint in TCGA, overall survival is used in the TCGA analysis; see Supplement).
  • the predicted antitumour regulation of this highlighted network by ketorolac is shown in FIG.
  • ketorolac is seen to be in the >90th percentile, compared with all 8558 other drugs in the Connectivity Map database, in terms of strength of network regulation with specific drugs commonly used for the treatment of lung adenocarcinoma, which are highlighted as well for comparison.
  • this method provides external validation of the antitumour effect of ketorolac seen in the overall cohort, it is more limited in addressing the specific tumour genomic alterations found in our clinical cohort (i.e., NRF2 and TP53 pathways), as gene coexpression networks are fundamentally different from mutational signatures and transcend individual functional genomic pathways. That said, the method predicts that ketorolac does regulate one of the six survival- associated coexpression networks in a protumour direction, which is consistent with the existence of smaller genomic subgroups in which ketorolac results in worse patient survival.
  • a range includes each individual member.
  • a group having 1-3 cells refers to groups having 1, 2, or 3 cells.
  • a group having 1-5 cells refers to groups having 1, 2, 3, 4, or 5 cells, and so forth.

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Epidemiology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Public Health (AREA)
  • Veterinary Medicine (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Oncology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Acyclic And Carbocyclic Compounds In Medicinal Compositions (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)

Abstract

Sont divulguées ici des méthodes permettant de déterminer si un patient chez qui a été diagnostiqué un cancer du poumon et subissant une intervention chirurgicale de résection tumorale bénéficiera ou non d'un traitement par une classe de médicaments anti-inflammatoires non stéroïdiens (AINS) (par exemple, des AINS du type dérivé d'acide carboxylique). Ces méthodes sont basées sur la recherche, chez un patient cancéreux, de mutations de MDM2 et/ou de mutations au niveau des voies de signalisation de NRF2. Sont également divulguées ici des méthodes permettant d'améliorer la survie de patients atteints d'un cancer du poumon subissant une intervention chirurgicale de résection tumorale, consistant à administrer au sujet une quantité efficace d'AINS du type dérivé d'acide carboxylique.
PCT/US2022/035921 2021-07-02 2022-07-01 Méthodes de sélection de patients atteints d'un cancer du poumon pour un traitement avec des médicaments anti-inflammatoires non stéroïdiens Ceased WO2023278826A2 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202163217784P 2021-07-02 2021-07-02
US63/217,784 2021-07-02

Publications (2)

Publication Number Publication Date
WO2023278826A2 true WO2023278826A2 (fr) 2023-01-05
WO2023278826A3 WO2023278826A3 (fr) 2023-05-11

Family

ID=84690637

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2022/035921 Ceased WO2023278826A2 (fr) 2021-07-02 2022-07-01 Méthodes de sélection de patients atteints d'un cancer du poumon pour un traitement avec des médicaments anti-inflammatoires non stéroïdiens

Country Status (1)

Country Link
WO (1) WO2023278826A2 (fr)

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030100540A1 (en) * 2001-07-27 2003-05-29 Vanderbilt University Identification of NSAID-regulated genes

Also Published As

Publication number Publication date
WO2023278826A3 (fr) 2023-05-11

Similar Documents

Publication Publication Date Title
US20230348992A1 (en) Methylation markers for diagnosing hepatocellular carcinoma and lung cancer
US12351876B2 (en) Colon cancer methylation markers and uses thereof
JP2021003108A (ja) 癌の状態を判定する方法とシステム
US12359257B2 (en) Liver cancer methylation markers and uses thereof
US12404556B2 (en) Compositions and methods for detecting circulating tumor DNA
WO2017008117A1 (fr) Procédé de diagnostic, de pronostic et de suivi d'un cancer du sein et réactifs correspondants
EP3976822A1 (fr) Procédés et systèmes pour améliorer une surveillance de patient après une intervention chirurgicale
WO2021253138A1 (fr) Analyse multimodale de molécules d'acide nucléique tumorales circulantes
EP3500686B1 (fr) Méthodes de détection de craniopharyngiomes et procédés pour la selection d'une médication et des patients.
WO2022197770A1 (fr) Méthodes pour personnaliser un schéma posologique d'analgésique chez des patients atteints d'un cancer du poumon ou du côlon sur la base de la génomique tumorale
US20250354218A1 (en) Methods for detecting acute myeloid leukemia
WO2023278826A2 (fr) Méthodes de sélection de patients atteints d'un cancer du poumon pour un traitement avec des médicaments anti-inflammatoires non stéroïdiens
WO2022125871A1 (fr) Procédés de personnalisation d'un régime analgésique chez les patients atteints de cancer en fonction de la transcriptomique des tumeurs
BR112017015413B1 (pt) Plataforma de computação para utilização de dados de metilação de cpg de câncer, método para a geração de um banco de dados de perfil de metilação de cpg de câncer, método de determinação da presença de câncer em um indivíduo necessitado e método de seleção de uma terapia para um indivíduo que possui um câncer
HK1248285B (zh) 判定癌症状态之系统

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 22834297

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 22834297

Country of ref document: EP

Kind code of ref document: A2