WO2023235415A1

WO2023235415A1 - Method to identify a patient with an increased likelihood of chemotherapy-induced peripheral neuropathy

Info

Publication number: WO2023235415A1
Application number: PCT/US2023/024040
Authority: WO
Inventors: Tushar Ramesh BHANGALE; Zia Khan
Original assignee: Genentech, Inc.
Priority date: 2022-06-01
Filing date: 2023-05-31
Publication date: 2023-12-07

Abstract

Provided herein are methods of treating a cancer in a subject, comprising selecting a subject having one or more single neucleotide variants in one more genes selected from GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68 and administering to the subject an anti-cancer treatment. In some embodiments, the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced peripheral neuropathy (PN). In some embodiments, the methods provided herein allow for selection of subjects for treatment with a chemotherapy regimen.

Description

METHOD TO IDENTIFY A PATIENT WITH AN INCREASED LIKELIHOOD OF CHEMOTHERAPY-INDUCED PERIPHERAL NEUROPATHY

BACKGROUND

[0001] Cancer is one of the most deadly threats to human health. In the U.S. alone, cancer affects nearly 1.3 million new patients each year, and is the second leading cause of death after cardiovascular disease, accounting for approximately 1 in 4 deaths. Solid tumors are responsible for most of those deaths. Although there have been significant advances in the medical treatment of certain cancers, the overall 5-year survival rate for all cancers has improved only by about 10% in the past 20 years. Cancers, or malignant tumors, metastasize and grow rapidly in an uncontrolled manner, making timely detection and treatment extremely difficult.

[0002] Depending on the cancer ty pe, patients typically have several treatment options available to them including chemotherapy, radiation and antibody -based drugs. Diagnostic methods useful for predicting clinical outcome from the different treatment regimens would greatly benefit clinical management of these patients. During cancer treatment, patients endure toxicities of chemotherapies to achieve remission. Substantial consideration is placed into drug dosing to limit these toxicities without sacrificing efficiency (Tyson et al. Front Pharmacol 11 :420 (2020)). Yet, it still remains unclear why a subset of patients develop toxicities at recommended doses. This raises the possibility that this inter-individual variability may have a genetic component (Roden et al. Lancet 394(10197):521-32 (2019)). Whole genome sequencing in patients receiving drugs can uncover the genetic architecture of toxicity risk and enable identification of both rare and common genetic variants that contribute to this risk. As drug targets that have human genetic support are more likely to lead to approved drugs, rare coding variants have provided translatable insights for novel drug targets for disease treatment (King et al. Pios Genet 15(12):el008489 (2019); Akbari et al. Science 373(6550) (2021)). However, an untapped potential exists to use human genetics to identify novel targets for drugs that can mitigate dose limiting toxicities - potentially enabling more optimal dosing of existing drugs to achieve better patient outcomes.

[0003] Peripheral Neuropathy (PN) is a dose limiting neurological toxicity of chemotherapy. PN in cancer patients often begins with sensory deficits and paresthesia - predominantly in the hands and feet (Starobova Front Mol Neurosci 10: 174 (2017)). In severe cases, PN can persist after the completion of cancer therapy - significantly impacting patient quality of life. Despite several decades of study, the prevention or treatment of Chemotherapy -induced PN (CIPN) remains challenging (Hu et al. Curr Neuropharmacol 17(2): 184-96 (2019)). Identifying genetic variation that acts to increase or decrease risk of CIPN promises mechanistic insights that are difficult to obtain from animal models and physiological or pathological risk factors. To this end, several small-scale genome-wide association studies have been conducted to identify common genetic variants associated with risk of PN (Sucheston-Campbell et al. Pharmacogenet Genom 28(2):49-55 (2018); Abraham et al. Clin Cancer Res 20(9):2466-75 (2014); Adjei et al. Cancers 3(5): 1084 (2021); Dolan et al. Clin Cancer Res 23(19)5757-68 (2017); Chua et al. Clin Pharmacol Ther 108(3):625-34 (2020)). While variants found in these studies did not reach genome-wide significance, genes near variants with the smallest p-values have implicated neurogenesis, neurodegeneration, and pharmacokinetics. Prior meta-analyses have been limited to a small number of cohorts and cancer indications mainly due to the challenges in uniformly grading the PN events and compiling harmonized clinical or phenotype data at scale. Moreover, the impact of rare genetic variation on PN has not been examined.

[0004] The present disclosure addresses this need.

SUMMARY

[0005] A meta-analysis of genome-wide association studies (GW AS) of time to first PN event was conducted, which included European ancestry patients across 14 randomized controlled trials across the development path of the PD-L1 inhibitor atezolizumab where germline whole genome sequencing data were available. The trials used similar protocols and uniform strategies to identify' and grade PN events, overcoming the challenges with previously published meta-analyses and enabling sensitive detection of genetic associations. The present meta-analysis spanned a range of cancers and treatments including chemotherapies, immunotherapies, and their treatment combinations. Two loci reaching genome-wide significance in an intron of GRID2 and downstream of SCG2 were identified. An exome-wide significant rare coding variation association in the pH sensing G-protein coupled receptor GPR68 was also identified. These findings provide insights into mechanisms that contribute to risk of CIPN with potential implications for therapeutic intervention.

[0006] In one aspect, provided herein is a method of treating a cancer in a subject, comprising (ajselecting a subject having one or more single nucleotide variants in one more genes selected from GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68; and (b) administering to the subject an anti-cancer treatment.

[0007] In some embodiments, the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy -induced peripheral neuropathy (PN).

[0008] In some embodiments, the one or more single nucleotide variants is located at one or more loci selected from rs 17020773, rsl 15575220, rsl 17987557, rsl 13371772, rsl2943567, rs371157151, rs550771753, rs61745750, or rs61745752.

[0009] In some embodiments, the locus of the single nucleotide variant is rsl7020773. In some embodiments, the variant comprises a T to C nucleotide change. In some embodiments, the locus of the single nucleotide variant is rsl 15575220. In some embodiments, the variant comprises a G to T nucleotide change. In some embodiments, the locus of the single nucleotide variant comprises rs61745750 and rs61745752.

[0010] In some embodiments, the treatment does not include a taxane. In embodiments, the cancer treatment regimen does not include a taxane other than nab-paclitaxel.

[0011] In some embodiments, the cancer is a neoplasm or malignant tumor found in mammals (e.g., humans), including leukemia, lymphoma, carcinomas and sarcomas. Exemplary cancers that may be treated with a compound or methods provided herein include cancer of the thyroid, endocrine system, bram, breast, cervix, colon, head and neck, liver, kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus medulloblastoma, colorectal cancer, or pancreatic cancer. Additional examples include Hodgkin's Disease, Non-Hodgkin’s Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primary' macroglobulinemia, primary brain tumors, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms of the endocrine or exocrine pancreas, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer. [0012] In some embodiments, the treatment comprises one or more of a chemotherapeutic drug, an immunotherapy, or an alkylating agent.

[0013] In some embodiments, the method further comprises administering a chemotherapeutic drug, a monoclonal antibody, or an alkylating agent to the subject.

[0014] In some embodiments, the chemotherapeutic drug is etoposide.

[0015] In some embodiments, the immunotherapy is a checkpoint inhibitor. In some embodiments, the checkpoint inhibitor is a PD-L1 inhibitor. In some embodiments, the PD- L1 inhibitor is atezohzumab, durvalumab, or avelumab.

[0016] In some embodiments, the alkylating agent is carboplatin.

[0017] In some embodiments, the subject is not administered paclitaxel, docetaxel, or cabazitaxel if the subject has a single nucleotide variant in the one or more genes.

[0018] In some embodiments, the subject is administered nab-paclitaxel if the subject has a single nucleotide vanant in one or more genes.

[0019] In another aspect, the present disclosure provides a method of minimizing the incidence of chemotherapy-induced PN in a cancer subject, comprising (a) selecting a subject having a single nucleotide variant in one or more genes selected from GRID2, SCG2, OXGRI, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68; and (b) administering to the subj ect a cancer treatment regimen, wherein the cancer treatment regimen does not include taxanes. In embodiments, the cancer treatment regimen does not include taxanes other than nab-paclitaxel.

[0020] In some embodiments, selecting the subject comprises (i) providing a biological sample from the subject, and (ii) identifying the sequence of the one or more genes from the sample, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced peripheral neuropathy (PN).

[0021] In yet another aspect, the present disclosure provides a method for selecting a subject at nsk of developing chemotherapy-mduced peripheral neuropathy (PN), the method comprising providing a biological sample from the subject and identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, 0XGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced PN.

[0022] In some embodiments, identifying the sequence comprises amplifying the one or more genes in the sample and detecting the presence of one or more single nucleotide variants in the one or more genes; or wherein identifying the sequence comprises sequencing the one of more genes in the sample.

[0023] In some embodiments, the cancer treatment regimen comprises a monoclonal antibody, an alkylating agent, or a combination thereof

[0024] In some embodiments, the monoclonal antibody is a PD-L1 inhibitor.

[0025] In some embodiments, the alkylating agent is carboplatin.

[0026] In some embodiments, the risk of developing chemotherapy-induced PN is higher for a subject having the one or more single nucleotide variants than for a subject lacking the one or more single nucleotide variants.

[0027] In yet another aspect, the present disclosure provides a method of preventing chemotherapy-induced NP in a subject in need of cancer treatment, comprising administering to the subject an inhibitor that targets GPR68. In embodiments, the inhibitor is a small molecule inhibitor.

[0028] In some embodiments, the method further comprises administering a chemotherapeutic drug, a monoclonal antibody, or an alkylating agent to the subject.

[0029] In some embodiments, the method further comprises determining whether the subject has one or more single nucleotide variants in GPR68 prior to administering the inhibitor. In some embodiments, the subject has two single nucleotide variants in GPR68. In some embodiments, the two single nucleotide variants comprise rs61745750 and rs61745752.

[0030] In yet another aspect, the present disclosure provides a method for selecting a subject for treatment with a chemotherapy regimen, comprising (a) providing a biological sample from the subject, (b) identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, 0XGR1, D0K5, ASIC2, SBSPON, SLAIN2, and/or GPR68, and (c) selecting the subject for treatment with the chemotherapy regimen when the subject lacks one or more single nucleotide variants in the one or more genes.

[0031] In some embodiments, the chemotherapy regimen comprises a taxane.

[0032] In some embodiments, the taxane comprises paclitaxel, docetaxel, or cabazitaxel.

[0033] In some embodiments, the chemotherapy regimen comprises a checkpoint inhibitor. In some embodiments, the checkpoint inhibitor comprises an anti-PD-Ll antibody. In some embodiments, the anti-PD-Ll antibody comprises atezolizumab, durvalumab, or avelumab.

[0034] In some embodiments, the one or more single nucleotide variants is located at one or more loci selected from rs 17020773, rsl 15575220, rsl 17987557, rsl 13371772, rs!2943567, rs371157151, rs550771753, rs61745750, or rs61745752.

[0035] In some embodiments, the locus of the single nucleotide variant is rsl7020773.

[0036] In some embodiments, the variant comprises a T to C nucleotide change.

[0037] In some embodiments, the locus of the single nucleotide variant is rs l 15575220.

[0038] In some embodiments, the variant comprises a G to T nucleotide change.

[0039] In some embodiments, the locus of the single nucleotide variant comprises rs61745750 and rs61745752.

[0040] In some embodiments, the cancer is renal cell carcinoma, non-small cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, melanoma, squamous cell cancer, lung cancer, cancer of the peritoneum, hepatocellular cancer, stomach cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer, B-cell lymphoma, low grade/follicular non-Hodgkin's lymphoma (NHL), small lymphocytic (SL) NHL, intermediate grade/follicular NHL, intermediate grade diffuse NHL, high grade immunoblastic NHL, high grade lymphoblastic NHL, high grade small non-cleaved cell NHL, bulky disease NHL, mantle cell lymphoma, AIDS-related lymphoma, Waldenstrom's Macroglobuhnerma, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), Hairy cell leukemia, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), or Meigs' syndrome.

BRIEF DESCRIPTION OF THE DRAWINGS

[0041] Embodiments will now be described, by way of example only, with reference to the accompanying drawings, in which:

[0042] FIGs. 1A-1E show results from a meta-analysis of time to first peripheral neuropathy (PN) event across clinical trials in whole genome sequencing data from European ancestry cancer patients, which identifies two genome-wide significant loci. (1 A) Manhattan plot showing -logl 0 p-values testing for association between common (MAF > 0.01) genetic variants and time to first PN event using a Cox proportional hazards model. SNPs reaching genome-wide significance are highlighted in red. Horizontal dashed line shows the genomewide significance cutoff (p < 5 ■ 10'⁸). The nearest gene to the index SNP is indicated above the relevant association peak. (IB) Regional plot around the GRID2 intron locus. The colors indicate the strength of linkage disequilibrium (r2) relative to the index SNP (rsl7020773) shown as a purple diamond. (1C) Locus zoom plot showing the SNP (rsl 15575220) illustrated as a purple diamond downstream of SCG2. The blue line designates recombination peaks. (ID) Forest plot illustrating the 95% confidence intervals around the log hazard ratio (log-HR) associating the alternate allele of rsl7020773 to time to first PN event. The non- taxane trial arms have been grouped. Trial arm and treatment abbreviations are provided in Table 1. The inverse variance weighted log-HR is provided as a diamond with the corresponding fixed effects p-value. * p < 0.05, ** p < 0.01 , *** p < 0.001, **** p < 0.0001. (IE) Cumulative incidence plot showing the association between dosage of the alternate allele of rsl7020773 and time to PN event. Shaded regions designate the 95% confidence intervals around the cumulative incidence curves.

[0043] FIGs. 2A-2D show that a rare coding variation in GPR68 is associated with risk of chemotherapy-induced peripheral neuropathy. (2A) Cumulative incidence plot showing the association between the burden of rare coding variants in GPR68 and time to PN event. Shaded regions designate the 95% confidence interval around the cumulative incidence curves. (2B) Lollipop plot of rare coding variants in GPR68 that were used for burden testing with time to PN event in the entire clinical trial cohort. The y-axis of the plot provides the number of patients that earned the rare coding vanant as designated by rsID and coding sequence consequence along the top of the plot. Rare coding haplotype consisting of rs61745750 (330K>330N) and truncating variant rs61745752 (336E>336*) is highlighted by the gray square. (2C) Protein plot illustrating the trans-membrane domains of GPR68 as well as the position of rs61745750 (330K>330N) highlighted in blue and rs61745752 (336E>336*) highlighted in red on the C-terminus of the protein. (2D) Gray squares illustrate amino acids starting at position 290 in GPR68 interspersed with purple squares that designate predicted phosphorylation sites. Complete arrestin binding motif matches shown in the first row of blue squares (“complete motifs”). Partial motif matches are shown in peach color below (“partial motifs”) where darker squares correspond to amino acids involved in more binding motifs. The position of rs61745750 (330K>330N) highlighted in blue and rs61745752 (336E>336*) truncation is highlighted in red. Positions and sequence of the motif matches are provided in the table where PL = partial long, PS=partial short, L=complete long. The lysine substituted by asparagine is shown across motif matches in purple. Motifs removed by rs61745752 (336E>336*) are highlighted in red.

[0044] FIGs. 3A-3C show that in human dorsal root ganglia (DRG), SCG2 and GPR68 are primarily expressed in PEP1 sensory neurons whereas GRID2 is primarily expressed in satellite glia. Bar plots for (3A) GRID2, (3B) SCG2, and (3C) GPR68 provide the pseudobulk counts from single cell RNA-seq. Labeled cell types are across the x-axis of the bar plots. DRG neurons are designated in green whereas non-neuronal cells are shown in orange (first four bars).

[0045] FIG. 4 shows a QQ-plot of p-values from a common variant GW AS of time to first peripheral neuropathy. Each point represents a single common variant. A._gc=1.004

[0046] FIG. 5 shows effect size (HR) comparison across trials for rsl 15575220 (SCG2 locus) along with meta-analysis results.

[0047] FIG. 6 top two panels show p-value, posterior causal probability respectively. Bottom four panels include data from and include ATAC-seq data in neurons, inferred locations of neuronal enhancers and chromatin interactions in neuronal, microglia, and oligodendrocyte PLAC-seq data, respectively (Nott et al. Science 366: 1134-1139 (2019)). The index SNP (rsl 15575220) falls in a region enriched with neuron specific enhancers that show chromatin interaction with the promoter of SCG2.

[0048] FIG. 7 shows a Kaplan Meier plot for PN events stratified by genotype dosage at rsl 15575220 (SCG2 locus).

[0049] FIG. 8 shows a QQ-plot of p-values from a rare variant burden test of time to first peripheral neuropathy. Each point represents a gene. X_gc=l .009.

[0050] FIG. 9 shows a cumulative incidence plot for PN events stratified by rare coding variant burden in GPR68.

[0051] FIG. 10 shows that expression patterns GPR68 in different DRG cell types in macaque (top from Kupari et al. Nat Commun 12:1510 (2021)) and in mouse (bottom from Renthal et al. Neuron 108: 128-144. e9 (2020)) indicates a similar expression pattern to GPR68 in human DRG. PEP1 neurons show relatively high expression of GRP68 in both organisms.

[0052] FIG. 11 top shows expression of SCG2 in macaque DRG obtained from Kupari et al. (Nat Commun 12: 1510 (2021)) and bottom in mouse (Renthal et al. Neuron 108: 128- 144.e9 (2020)).

[0053] FIG. 12 shows expression of GRID2 in satellite glial cells as compared to expression in whole DRG in mouse (Liang et al. Pain 161 :2089-2106 (2020)).

DETAILED DESCRIPTION

DEFINITIONS

[0054] It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.

[0055] In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “ includes,” “including,” and the like. “Consisting essentially of or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments. “Consisting of’ shall mean excluding more than trace elements of other ingredients and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this disclosure.

[0056] The term “consists essentially of’ as used herein means that only the element(s) explicitly indicated are present in the composition, but that said composition may also contain a further constituent, such as a pharmaceutically appropriate carrier, diluent, excipient, antibiotic (e.g., chemical antibiotic), etc., or combinations thereof.

[0057] As used herein, the term “about” when used before a numerical designation, e.g., temperature, time, amount, concentration, and such other, including a range, indicates approximations which may vary by (+) or (-) 10%, 5%, or 1%. All values in this disclosure are preceded by the term “about,” even if not explicitly recited.

[0058] When a range (e.g., dosage range) is listed herein, it is to be understood that the value may include any individual value or range within the recited range(s), including endpoints.

[0059] As used herein, the terms “treating” or “treatment” (and as well understood in the art) are used in accordance with their plain and ordinary meaning and broadly includes any approach for obtaining beneficial or desired results in a subject’s condition, including clinical results. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of the extent of a disease, stabilizing (i.e., not worsening) the state of disease, prevention of a disease’s transmission or spread, delay or slowing of disease progression, amelioration or palliation of the disease state, diminishment of the reoccurrence of disease, and remission, whether partial or total and whether detectable or undetectable. In other words, “treatment” as used herein includes any cure, amelioration, or prevention of a disease. Treatment may prevent the disease from occurring; inhibit the disease’s spread; relieve the disease’s symptoms, fully or partially remove the disease’s underlying cause, shorten a disease’s duration, or do a combination of these things. As used herein, the term “treat” or “treating” is intended to encompass prophylactic treatment as well as corrective treatment (treatment of a subject already suffering from a disease).

[0060] As used herein, the term “administering” means oral, intravenous, parenteral, intraperitoneal, intramuscular, intrathecal, intranasal, pulmonary, or subcutaneous administration for example, or the implantation of a slow-release device, e.g, a mini-osmotic pump, to a subject. Administration is by any route, including parenteral and transmucosal (e.g., buccal, sublingual, palatal, gingival, nasal, vaginal, rectal, or transdermal). Parenteral administration includes, e.g., intravenous, intramuscular, intra-arteriole, intradermal, subcutaneous, intraperitoneal, intraventricular, and intracranial. Other modes of delivery include, but are not limited to, the use of liposomal formulations, intravenous infusion, transdermal patches, and the like. In embodiments, the administering does not include administration of any active agent other than the recited active agent. In embodiments, administration of compositions described herein is by intravenous administration. In embodiments, administration of compositions described herein is by intranasal administration such as inhalation or nebulization. In embodiments, administration may be pulmonary delivery via nasal or oral administration e.g. by aerosolization or nebulization). The administering step may consist of a single administration or may include a series of administrations. The length of the treatment period depends on a variety of factors, such as the severity of the risk or condition, the age of the patient, the concentration of active agent, the activity of the compositions used in the treatment, or a combination thereof. It will also be appreciated that the effective dosage of an agent used for the treatment or prophylaxis may increase or decrease over the course of a particular treatment or prophylaxis regime. Changes in dosage may result and become apparent by standard diagnostic assays known in the art. In some instances, chronic administration may be required. For example, the compositions are administered to the subject in an amount and for a duration sufficient to treat the patient.

[0061] “Co-administer” it is meant that a composition described herein is administered at the same time, just prior to, or just after the administration of one or more additional therapies. The compounds provided herein can be administered alone or can be coadministered to the patient. Co-administration is meant to include simultaneous or sequential administration of the compounds individually or in combination (more than one compound). Thus, the preparations can also be combined, when desired, with other active substances (e.g. antibiotic).

[0062] As used herein, the term “subject” or “patient” refers to a human or non-human animal. Preferably, the subject is a human. Preferably, the subject or patient is in need of treatment with the composition as described herein, e.g., has a cancer susceptible to treatment with the composition. [0063] As used herein, the term “obtainable” as used herein also encompasses the term “obtained.” In one embodiment, the term “obtainable” means obtained.

[0064] A “disorder” or “disease” is any condition that would benefit from treatment with a substance/molecule or method of the invention. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein include cancer (e.g., malignant and benign tumors; non-leukemias and lymphoid malignancies); neuronal, glial, astrocytal, hypothalamic and other glandular, macrophagal, epithelial, stromal and blastocoelic disorders; and inflammatory, immunologic and other angiogenesis-related disorders.

[0065] The terms “cell proliferative disorder” and “proliferative disorder” refer to disorders that are associated with some degree of abnormal cell proliferation. In one embodiment, the cell proliferative disorder is cancer. In one embodiment, the cell proliferative disorder is angiogenesis.

[0066] "Tumor", as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms “cancer”, “cancerous”, “cell proliferative disorder”, “proliferative disorder” and “tumor” are not mutually exclusive as referred to herein.

[0067] A “disorder” or “disease” is any condition that would benefit from treatment with a substance/molecule or method of the invention. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non-limiting examples of disorders to be treated herein include cancer (e.g., malignant and benign tumors; non-leukemias and lymphoid malignancies); neuronal, glial, astrocytal, hypothalamic and other glandular, macrophagal, epithelial, stromal and blastocoelic disorders; and inflammatory, immunologic and other angiogenesis-related disorders.

[0068] The terms "cancer" and "cancerous" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell proliferation in a part of the body. The cancer may be locally advanced or metastatic. In some instances, the cancer is locally advanced. In some instances, the cancer is metastatic. In some instances, the cancer may be unresectable (e.g., unresectable locally advanced or metastatic cancer). Examples of cancer include but are not limited to, a neoplasm or malignant tumor found in mammals (e.g., humans), including leukemia, lymphoma, carcinomas and sarcomas. Exemplary cancers that may be treated with a compound or method provided herein include cancer of the thyroid, endocrine system, brain, breast, cervix, colon, head and neck, liver, kidney, lung, non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach, uterus medulloblastoma, colorectal cancer, or pancreatic cancer. Additional examples include Hodgkin's Disease, Non-Hodgkin’s Lymphoma, multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme, ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia, primary brain tumors, malignant pancreatic insulanoma, malignant carcinoid, urinary bladder cancer, premalignant skin lesions, testicular cancer, lymphomas, thyroid cancer, esophageal cancer, genitourinary tract cancer, malignant hypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms of the endocrine or exocrine pancreas, medullary thyroid cancer, medullary thyroid carcinoma, melanoma, colorectal cancer, papillary thyroid cancer, hepatocellular carcinoma, or prostate cancer..

[0069] The term "leukemia" refers broadly to progressive, malignant diseases of the blood-forming organs and is generally characterized by a distorted proliferation and development of leukocytes and their precursors in the blood and bone marrow. Leukemia is generally clinically classified on the basis of (1) the duration and character of the diseaseacute or chronic; (2) the type of cell involved; myeloid (myelogenous), ly mphoid (lymphogenous), or monocytic; and (3) the increase or non-increase in the number abnormal cells in the blood-leukemic or aleukemic (subleukemic). Exemplary' leukemias that may be treated with a compound or method provided herein include, for example, acute nonlymphocytic leukemia, chronic lymphocytic leukemia, acute granulocytic leukemia, chronic granulocytic leukemia, acute promyelocytic leukemia, adult T-cell leukemia, aleukemic leukemia, a leukocythemic leukemia, basophylic leukemia, blast cell leukemia, bovine leukemia, chronic myelocytic leukemia, leukemia cutis, embryonal leukemia, eosinophilic leukemia, Gross' leukemia, hairy-cell leukemia, hemoblastic leukemia, hemocytoblastic leukemia, histiocytic leukemia, stem cell leukemia, acute monocytic leukemia, leukopenic leukemia, lymphatic leukemia, lymphoblastic leukemia, lymphocytic leukemia, lymphogenous leukemia, lymphoid leukemia, lymphosarcoma cell leukemia, mast cell leukemia, megakaryocytic leukemia, micromyeloblastic leukemia, monocytic leukemia, myeloblastic leukemia, myelocytic leukemia, myeloid granulocytic leukemia, myelomonocytic leukemia, Naegeli leukemia, plasma cell leukemia, multiple myeloma, plasmacytic leukemia, promyelocytic leukemia, Rieder cell leukemia, Schilling's leukemia, stem cell leukemia, subleukemic leukemia, or undifferentiated cell leukemia.

[0070] As used herein, the term “lymphoma” refers to a group of cancers affecting hematopoietic and lymphoid tissues. It begins in lymphocytes, the blood cells that are found primarily in lymph nodes, spleen, thymus, and bone marrow. Two main types of lymphoma are non-Hodgkin lymphoma and Hodgkin’s disease. Hodgkin’s disease represents approximately 15% of all diagnosed lymphomas. This is a cancer associated with Reed- Sternberg malignant B lymphocytes. Non-Hodgkin’s lymphomas (NHL) can be classified based on the rate at which cancer grows and the type of cells involved. There are aggressive (high grade) and indolent (low grade) types of NHL. Based on the type of cells involved, there are B-cell and T-cell NHLs. Exemplary B-cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, small lymphocytic lymphoma, Mantle cell lymphoma, follicular lymphoma, marginal zone lymphoma, extranodal (MALT) lymphoma, nodal (monocytoid B-cell) lymphoma, splenic lymphoma, diffuse large cell B-lymphoma, Burkitt’s lymphoma, lymphoblastic lymphoma, immunoblastic large cell lymphoma, or precursor B-lymphoblastic lymphoma. Exemplary T- cell lymphomas that may be treated with a compound or method provided herein include, but are not limited to, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, anaplastic large cell lymphoma, mycosis fungoides, and precursor T-lymphoblastic lymphoma.

[0071] The term "sarcoma" generally refers to a tumor which is made up of a substance like the embryonic connective tissue and is generally composed of closely packed cells embedded in a fibrillar or homogeneous substance. Sarcomas that may be treated with a compound or method provided herein include a chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abernethy's sarcoma, adipose sarcoma, liposarcoma, alveolar soft part sarcoma, ameloblastic sarcoma, botryoid sarcoma, chloroma sarcoma, chorio carcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometnal sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhagic sarcoma, immunoblastic sarcoma of B cells, lymphoma, immunoblastic sarcoma of T-cells, Jensen's sarcoma, Kaposi's sarcoma, Kupffer cell sarcoma, angiosarcoma, leukosarcoma, malignant mesenchymoma sarcoma, parosteal sarcoma, reticulocytic sarcoma, Rous sarcoma, serocystic sarcoma, synovial sarcoma, or telangiectaltic sarcoma.

[0072] The term "melanoma" is taken to mean a tumor arising from the melanocytic system of the skin and other organs. Melanomas that may be treated with a compound or method provided herein include, for example, acral-lentiginous melanoma, amelanotic melanoma, benign juvenile melanoma, Cloudman's melanoma, S91 melanoma, Harding- Passey melanoma, juvenile melanoma, lentigo maligna melanoma, malignant melanoma, nodular melanoma, subungal melanoma, or superficial spreading melanoma.

[0073] The term "carcinoma" refers to a malignant new growth made up of epithelial cells tending to infiltrate the surrounding tissues and give rise to metastases. Exemplary carcinomas that may be treated with a compound or method provided herein include, for example, medullary thyroid carcinoma, familial medullary thyroid carcinoma, acinar carcinoma, acinous carcinoma, adenocystic carcinoma, adenoid cystic carcinoma, carcinoma adenomatosum, carcinoma of adrenal cortex, alveolar carcinoma, alveolar cell carcinoma, basal cell carcinoma, carcinoma basocellulare, basaloid carcinoma, basosquamous cell carcinoma, bronchioalveolar carcinoma, bronchiolar carcinoma, bronchogenic carcinoma, cerebriform carcinoma, cholangiocellular carcinoma, chorionic carcinoma, colloid carcinoma, comedo carcinoma, corpus carcinoma, cribriform carcinoma, carcinoma en cuirasse, carcinoma cutaneum, cylindrical carcinoma, cylindrical cell carcinoma, duct carcinoma, carcinoma durum, embryonal carcinoma, encephaloid carcinoma, epiermoid carcinoma, carcinoma epitheliale adenoides, exophytic carcinoma, carcinoma ex ulcere, carcinoma fibrosum, gelatinifomi carcinoma, gelatinous carcinoma, giant cell carcinoma, carcinoma gigantocellulare, glandular carcinoma, granulosa cell carcinoma, hair-matrix carcinoma, hematoid carcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, hyaline carcinoma, hypemephroid carcinoma, infantile embryonal carcinoma, carcinoma in situ, intraepidermal carcinoma, intraepithelial carcinoma, Krompecher's carcinoma, Kulchitzky- cell carcinoma, large-cell carcinoma, lenticular carcinoma, carcinoma lenticulare, lipomatous carcinoma, lymphoepithelial carcinoma, carcinoma medullare, medullary carcinoma, melanotic carcinoma, carcinoma molle, mucinous carcinoma, carcinoma muciparum, carcinoma mucocellulare, mucoepidermoid carcinoma, carcinoma mucosum, mucous carcinoma, carcinoma myxomatodes, nasopharyngeal carcinoma, oat cell carcinoma, carcinoma ossificans, osteoid carcinoma, papillary carcinoma, periportal carcinoma, preinvasive carcinoma, prickle cell carcinoma, pultaceous carcinoma, renal cell carcinoma of kidney, reserve cell carcinoma, carcinoma sarcomatodes, Schneiderian carcinoma, scirrhous carcinoma, carcinoma scroti, signet-nng cell carcinoma, carcinoma simplex, small-cell carcinoma, solanoid carcinoma, spheroidal cell carcinoma, spindle cell carcinoma, carcinoma spongiosum, squamous carcinoma, squamous cell carcinoma, string carcinoma, carcinoma telangiectaticum, carcinoma telangiectodes, transitional cell carcinoma, carcinoma tuberosum, tuberous carcinoma, verrucous carcinoma, or carcinoma villosum.

[0074] As used herein, the terms "metastasis," "metastatic," and "metastatic cancer" can be used interchangeably and refer to the spread of a proliferative disease or disorder, e.g., cancer, from one organ or another non-adjacent organ or body part. “Metastatic cancer” is also called “Stage IV cancer.” Cancer occurs at an originating site, e.g., breast, which site is referred to as a primary tumor, e.g., primary breast cancer. Some cancer cells in the primary tumor or originating site acquire the ability to penetrate and infiltrate surrounding normal tissue in the local area and/or the ability to penetrate the walls of the lymphatic system or vascular system circulating through the system to other sites and tissues in the body. A second clinically detectable tumor formed from cancer cells of a primary tumor is referred to as a metastatic or secondary tumor. When cancer cells metastasize, the metastatic tumor and its cells are presumed to be similar to those of the original tumor. Thus, if lung cancer metastasizes to the breast, the secondary tumor at the site of the breast consists of abnormal lung cells and not abnormal breast cells. The secondary tumor in the breast is referred to a metastatic lung cancer. Thus, the phrase metastatic cancer refers to a disease in which a subject has or had a primary tumor and has one or more secondary tumors. The phrases non- metastatic cancer or subjects with cancer that is not metastatic refers to diseases in which subjects have a primary tumor but not one or more secondary tumors. For example, metastatic lung cancer refers to a disease in a subject with or with a history of a primary lung tumor and with one or more secondary tumors at a second location or multiple locations, e.g., in the breast.

[0075] The terms “cutaneous metastasis” or “skin metastasis” refer to secondary malignant cell growths in the skin, wherein the malignant cells originate from a primary cancer site (e.g., breast). In cutaneous metastasis, cancerous cells from a primary cancer site may migrate to the skin where they divide and cause lesions. Cutaneous metastasis may result from the migration of cancer cells from breast cancer tumors to the skin. [0076] The term “visceral metastasis” refer to secondary malignant cell growths in the interal organs (e.g., heart, lungs, liver, pancreas, intestines) or body cavities (e.g., pleura, peritoneum), wherein the malignant cells originate from a primary cancer site (e.g., head and neck, liver, breast). In visceral metastasis, cancerous cells from a primary cancer site may migrate to the internal organs where they divide and cause lesions. Visceral metastasis may result from the migration of cancer cells from liver cancer tumors or head and neck tumors to internal organs.

[0077] The terms “cell proliferative disorder” and “proliferative disorder” refer to disorders that are associated with some degree of abnormal cell proliferation. In one embodiment, the cell proliferative disorder is cancer. In one embodiment, the cell proliferative disorder is angiogenesis.

[0078] "Tumor", as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms “cancer”, “cancerous”, “cell proliferative disorder”, “proliferative disorder” and “tumor” are not mutually exclusive as referred to herein.

[0079] As used herein, the term “diagnosis” refers to an identification or likelihood of the presence of a certain condition, disease, or outcome in a subject. As also used herein, the term “prognosis” refers to the likelihood or risk of a subject developing a particular outcome or particular event.

[0080] The term “prevent” refers to a decrease in the occurrence of disease symptoms in a patient. The prevention may be complete (no detectable symptoms) or partial, such that fewer symptoms are observed than would likely occur absent treatment.

[0081] As used herein, an “effective amount” refers to the amount of a therapeutic agent or a combination of therapeutic agents that achieves a therapeutic result. In some examples, the effective amount of a therapeutic agent or a combination of therapeutic agents is the amount of the agent or of the combination of agents that achieves a clinical endpoint of improved overall response rate (ORR), a complete response (CR), a pathological complete response (pCR), a partial response (PR), improved survival (e.g., disease-free survival (DFS), progression-free survival (PFS) and/or overall survival (OS)), and/or improved duration of response (DOR). Improvement (e.g., in terms of response rate (e.g., ORR, CR, and/or PR), survival (e.g., PFS and/or OS), or DOR) may be relative to a suitable reference treatment, for example, treatment that does not include the PD-1 axis binding antagonist and/or treatment that does not include the chemotherapeutic drug.

[0082] As used herein, the term “detection” includes any means of detecting, including direct and indirect detection.

[0083] As used herein, the term “biomarker” refers to an indicator, e.g., predictive, diagnostic, and/or prognostic, which can be detected in a sample, for example, a single nucleotide variant or single nucleotide polymorphism. The biomarker may serve as an indicator of a particular subtype of a disease or disorder (e.g., cancer) characterized by certain, molecular, pathological, histological, and/or clinical features. In some embodiments, a biomarker is a gene. Biomarkers include, but are not limited to, polynucleotides (e g , DNA and/or RNA), polynucleotide copy number alterations (e.g., DNA copy numbers), polypeptides, polypeptide and polynucleotide modifications (e.g., post-translational modifications), carbohydrates, and/or glycolipid-based molecular markers.

[0084] The “amount” or “level” of a biomarker associated with an increased clinical benefit to an individual is a detectable level in a biological sample. These can be measured by methods known to one skilled in the art and also disclosed herein. The expression level or amount of biomarker assessed can be used to determine the response to the treatment.

[0085] “Control” or “control experiment” is used in accordance with its plain and ordinary meaning and refers to an experiment in which the subjects or reagents of the experiment are treated as in a parallel experiment except for omission of a procedure, reagent, or variable of the experiment. In some instances, the control is used as a standard of comparison in evaluating experimental effects. In some embodiments, a control is the measurement of the activity of a protein in the absence of a compound as described herein (including embodiments and examples). In some instances, the control is a quantification standard used as a reference for assay measurements. The quantification standard may be a synthetic protein marker, a recombinantly expressed purified protein marker, a purified protein marker isolated from its natural environment, a protein fragment, a synthesized polypeptide, or the like.

[0086] As used herein, a “biological sample” encompasses essentially any sample type that can be used in a diagnostic or prognostic method described herein. The biological sample may be any bodily fluid, tissue or any other sample from which clinically relevant protein marker levels may be determined. The definition encompasses blood and other liquid samples of biological origin, solid tissue samples such as a biopsy specimen or tissue cultures or cells derived therefrom and the progeny thereof. The definition also includes samples that have been manipulated in any way after their procurement, such as by treatment with reagents, solubilization, or enrichment for certain components, such as polypeptides or proteins. The term "biological sample" encompasses a clinical sample, but also, in some instances, includes cells in culture, cell supernatants, cell lysates, whole blood, serum, plasma, urine, cerebral spinal fluid, biological fluid, and tissue samples. The sample may be pretreated as necessary by dilution in an appropriate buffer solution or concentrated, if desired. Any of a number of standard aqueous buffer solutions, employing one of a variety of buffers, such as phosphate, Tris, or the like, preferably at physiological pH can be used.

[0087] As used herein, the terms “identifying the sequence” or “sequencing” or “sequence determination” or “determining a nucleotide sequence”, are used in accordance with their ordinary meaning in the art, and refer to determination of partial as well as full sequence information of the nucleic acid being sequenced, and particular physical processes for generating such sequence information. That is, the term includes sequence comparisons, fingerprinting, and like levels of information about a target nucleic acid, as well as the express identification and ordering of nucleotides in a target nucleic acid. The term also includes the determination of the identification, ordering, and locations of one, two, or three of the four types of nucleotides within a target nucleic acid.

[0088] The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible mutations, e.g, naturally occurring mutations, that may be present in minor amounts. Thus, the modifier “monoclonal” indicates the character of the antibody as not being a mixture of discrete antibodies. In certain embodiments, such a monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones, or recombinant DNA clones. It should be understood that a selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target-binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this invention. In contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal-antibody preparation is directed against a single determinant on an antigen. In addition to their specificity, monoclonal-antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins.

[0089] The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by a variety of techniques, including, for example, the hybridoma method (e.g., Kohler and Milstein., Nature, 256:495-97 (1975); Hongo etaL, Hybridoma, 14 (3): 253-260 (1995), Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2^nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g, U.S. Patent No. 4,816,567), phage-display technologies (see, e.g., Clackson etal., Nature, 352: 624-628 (1991); Marks et al., J. Mol. Biol. 222: 581-597 (1992); Sidhu et al., J. Mol. Biol. 338(2): 299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004); Fellouse, PNAS USA 101(34): 12467-12472 (2004); and Lee et al., J. Immunol. Methods 284(1-2): 119-132(2004), and technologies for producing human or human-like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences (see, e.g., WO 1998/24893; WO 1996/34096; WO 1996/33735; WO 1991/10741; Jakobovits et al., PNAS USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993); Bruggemann et al.. Year in Immunol. 7:33 (1993); U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; and 5,661,016; Marks et al., Bio/Technology 10: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild et al., Nature Biotechnol. 14: 845-851 (1996); Neuberger, Nature Biotechnol. 14: 826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol. 13: 65-93 (1995).

[0090] The monoclonal antibodies herein specifically include “chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (e.g., U.S. Pat. No. 4,816,567 and Morrison et al., PNAS USA 81:6851-6855 (1984)). Chimeric antibodies include PRIMATIZED® antibodies wherein the antigen-binding region of the antibody is derived from an antibody produced by, e.g. , immunizing macaque monkeys with the antigen of interest.

[0091] “Humanized” forms of non-human (e.g., murine) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin. In one embodiment, a humanized antibody is a human immunoglobulin (recipient antibody) in which residues from a HVR of the recipient are replaced by residues from a HVR of a non- human species (donor antibody) such as mouse, rat, rabbit, or nonhuman primate having the desired specificity, affinity, and/or capacity. In some instances, FR residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications may be made to further refine antibody performance. In general, a humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin, and all, or substantially all, of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see, e.g., Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also, for example, Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1: 105-115 (1998); Harris, Biochem. Soc. Transactions 23: 1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech. 5:428-433 (1994); and U.S. Pat. Nos. 6,982,321 and 7,087,409.

[0092] A “human antibody” is one which possesses an amino-acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues. Human antibodies can be produced using various techniques known in the art, including phage-display libraries. Hoogenboom and Winter, J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991). Also available for the preparation of human monoclonal antibodies are methods described in Cole et al. , Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985); Boerner et al., J. Immunol., 147(l):86-95 (1991). See also van Dijk and van de Winkel, Curr. Opin. Pharmacol., 5: 368-74 (2001). Human antibodies can be prepared by administering the antigen to a transgenic animal that has been modified to produce such antibodies in response to antigenic challenge, but whose endogenous loci have been disabled, e.g., immunized xenomice (see, e.g, U.S. Pat. Nos. 6,075,181 and 6,150,584 regarding XENOMOUSE™ technology). See also, for example, Li et al., PNAS USA, 103:3557-3562 (2006) regarding human antibodies generated via a human B-cell hybridoma technology.

[0093] The term “hypervariable region,” “HVR,” or “HV,” when used herein refers to the regions of an antibody-vanable domain which are hypervariable in sequence and/or form structurally defined loops. Generally, antibodies comprise six HVRs; three in the VH (Hl, H2, H3), and three in the VL (LI, L2, L3). In native antibodies, H3 and L3 display the most diversity of the six HVRs, and H3 in particular is believed to play a unique role in conferring fine specificity to antibodies. See, e.g., Xu et al. Immunity 13:37-45 (2000); Johnson and Wu inMethods in Molecular Biology 248:1-25 (Lo, ed., Human Press, Totowa, NJ, 2003).

Indeed, naturally occurring camelid antibodies consisting of a heavy chain only are functional and stable in the absence of light chain. See, e.g, Hamers-Casterman et al., Nature 363:446- 448 (1993) and Sheriff et al., Nature Struct. Biol. 3:733-736 (1996).

[0094] Immunotherapy of cancer represents an option of specific targeting of cancer cells while minimizing side effects. Immunotherapies designed to elicit or amplify an immune response are classified as activation immunotherapies, while immunotherapies that reduce or suppress are classified as suppression immunotherapies. Cancer immunotherapy makes use of the existence of tumor associated antigens. Cell-based immunotherapies are effective for some cancers. Immune effector cells such as lymphocytes, macrophages, dendritic cells, natural killer cells (NK Cell), cytotoxic T lymphocytes (CTL), etc., work together to defend the body against cancer by targeting abnormal antigens expressed on the surface of tumor cells. [0095] Therapies such as granulocyte colony-stimulating factor (G-CSF), interferons, imiquimod and cellular membrane fractions from bacteria are licensed for medical use. Others including IL-2, IL-7, IL- 12, various chemokmes, synthetic cytosine phosphateguanosine (CpG) oligodeoxynucleotides and glucans are involved in clinical and preclinical studies.

[0096] Active cellular therapies aim to destroy cancer cells by recognition of distinct markers known as antigens. In cancer vaccines, the goal is to generate an immune response to these antigens through a vaccine. Currently, only one vaccine (sipuleucel-T for prostate cancer) has been approved. In cell-mediated therapies like CAR-T cell therapy, immune cells are extracted from the patient, genetically engineered to recognize tumor specific antigens, and returned to the patient. Cell types that can be used in this way are natural killer (NK) cells, lymphokine-activated killer cells, cytotoxic T cells and dendritic cells. Finally, specific antibodies can be developed that recognize cancer cells and target them for destruction by the immune system. Examples of such antibodies include rituximab (targeting CD- 20), trastuzumab (targeting HER-2), and cetuximab (targeting EGFR).

[0097] Passive antibody therapies aim to increase the activity of the immune system without specifically targeting cancer cells. For example, cytokines directly stimulate the immune system and increase immune activity. Checkpoint inhibitors target proteins (immune checkpoints) that normally dampen the immune response. This enhances the ability of the immune system to attack cancer cells. Current research is identifying new potential targets to enhance immune function. Approved checkpoint inhibitors include antibodies such as ipilimumab, nivolumab, and pembrolizumab.

[0098] The term “PD-L1 binding antagonist” or “PD-L1 inhibitor” refers to a molecule that decreases, blocks, inhibits, abrogates, or interferes with signal transduction resulting from the interaction of PD-L1 with either one or more of its binding partners, such as PD-1 and/or B7-1. In some instances, a PD-L1 binding antagonist is a molecule that inhibits the binding of PD-L1 to its binding partners. In a specific aspect, the PD-L1 binding antagonist inhibits binding of PD-L1 to PD-1 and/or B7-1. In some instances, the PD-L1 binding antagonists include anti-PD-Ll antibodies, antigen-binding fragments thereof, immunoadhesms, fusion proteins, oligopeptides and other molecules that decrease, block, inhibit, abrogate or interfere with signal transduction resulting from the interaction of PD-L1 with one or more of its binding partners, such as PD-1 and/or B7-1. In one instance, a PD-L1 binding antagonist reduces the negative co-stimulatory signal mediated by or through cell surface proteins expressed on T lymphocytes mediated signaling through PD-L1 so as to render a dysfunctional T-cell less dysfunctional (e.g., enhancing effector responses to antigen recognition). In some instances, the PD-L1 binding antagonist binds to PD-L1. In some instances, a PD-L1 binding antagonist is an anti-PD-Ll antibody (e.g., an anti-PD-Ll antagonist antibody). Exemplary anti-PD-Ll antagonist antibodies include atezolizumab, MDX-1105, MEDI4736 (durvalumab), MSB0010718C (avelumab), SHR-1316, CS1001, envafolimab, TQB2450, ZKAB001, LP-002, CX-072, IMC-001, KL-A167, APL-502, cosibelimab, lodapolimab, FAZ053, TG-1501, BGB-A333, BCD-135, AK-106, LDP, GR1405, HLX20, MSB2311, RC98, PDL-GEX, KD036, KY1003, YBL-007, and HS-636. In some aspects, the anti-PD-Ll antibody is atezolizumab, MDX-1105, MEDI4736 (durvalumab), or MSB0010718C (avelumab). In one specific aspect, the PD-L1 binding antagonist is MDX-1105. In another specific aspect, the PD-L1 binding antagonist is MEDI4736 (durvalumab). In another specific aspect, the PD-L1 binding antagonist is MSB0010718C (avelumab). In other aspects, the PD-L1 binding antagonist may be a small molecule, e.g., GS-4224, INCB086550, MAX-10181, INCB090244, CA-170, or ABSK041, which in some instances may be administered orally. Other exemplary PD-L1 binding antagonists include AVA-004, MT-6035, VXM10, LYN192, GB7003, and JS-003. In a preferred aspect, the PD-L1 binding antagonist is atezolizumab.

[0099] The terms “programmed death ligand 1” and “PD-L1” refer herein to native sequence human PD-L1 polypeptide. Native sequence PD-L1 polypeptides are provided under Uniprot Accession No. Q9NZQ7. For example, the native sequence PD-L1 may have the amino acid sequence as set forth in Uniprot Accession No. Q9NZQ7-1 (isoform 1). In another example, the native sequence PD-L1 may have the amino acid sequence as set forth in Uniprot Accession No. Q9NZQ7-2 (isoform 2). In yet another example, the native sequence PD-L1 may have the amino acid sequence as set forth in Uniprot Accession No. Q9NZQ7-3 (isoform 3). PD-L1 is also referred to in the art as “programmed cell death 1 ligand 1,” “PDCD1LG1,” “CD274,” “B7-H,” and “PDLI.”

[0100] As used herein, the terms “increase,” high,” “higher,” “maximal,” “elevate,” or “elevation” refer to increases above basal levels, e.g., as compared to a control. The terms “reduce,” “decrease,” “reduction,” “minimal,” “low,” or “lower” refer to decreases below basal levels, e.g., as compared to a control. Likewise, the term “increased risk” refers to a higher or elevated risk compared to a control subject, of developing a certain condition. Increases, elevations, decreases, or reductions can be 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%,

41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%,

57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%,

73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,

89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% compared to a control or standard level. Each of the values or ranges recited herein may include any value or subrange therebetween, including endpoints.

[0101] “Subject in need of treatment” or “subject in need of cancer treatment” refers to a living organism suffering from or prone to a disease or condition that can be treated by administration of a pharmaceutical composition. In specific embodiments, the disease or condition is cancer. Non-limiting examples include humans, other mammals, bovines, rats, nuce, dogs, monkeys, goat, sheep, cows, deer, and other non-mammalian animals. In some embodiments, the subject is human.

[0102] Additional terms and phrases are defined below.

METHODS OF TREATING CANCER OR PREVENTING CHEMOTHERAPY- INDUCED PERIPHERAL NEUROPATHY

[0103] In some embodiments, the present disclosure relates to methods of treating cancer in a subject, comprising (a) selecting a subject having one or more single nucleotide variants in one more genes selected from GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, GPR68, or any combination thereof; and (b) administering to the subject an anticancer treatment.

[0104] In some aspects, the present disclosure provides a method of minimizing the incidence of chemotherapy-induced PN in a cancer subject, comprising (a) selecting a subject having a single nucleotide variant in one or more genes selected from GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, GPR68, or any combination thereof; and (b) administering to the subject a cancer treatment regimen, wherein the cancer treatment regimen does not include taxanes. [0105] In some embodiments, selecting the subject comprises (i) providing a biological sample from the subject, and (ii) identifying the sequence of the one or more genes from the sample, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced peripheral neuropathy (PN).

[0106] In some embodiments, the subject has a single nucleotide variant in GR1D2. In some embodiments, the subject has a single nucleotide variant in SCG2. In some embodiments, the subject has a single nucleotide variant in OXGR1. In some embodiments, the subject has a single nucleotide variant in DOK5. In some embodiments, the subject has a single nucleotide variant in ASIC2. In some embodiments, the subject has a single nucleotide variant in SBSPON. In some embodiments, the subject has a single nucleotide variant in SLAIN2. In some embodiments, the subject has a single nucleotide variant in GPR68.

[0107] In some embodiments, the cancer is renal cell carcinoma, non-small cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, melanoma, squamous cell cancer, lung cancer, cancer of the peritoneum, hepatocellular cancer, stomach cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer, B-cell lymphoma, low grade/follicular non-Hodgkin's lymphoma (NHL), small lymphocytic (SL) NHL, intermediate grade/follicular NHL, intermediate grade diffuse NHL, high grade immunoblastic NHL, high grade lymphoblastic NHL, high grade small non-cleaved cell NHL, bulky disease NHL, mantle cell lymphoma, AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), Hairy cell leukemia, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), or Meigs' syndrome.

[0108] In some embodiments, the taxane may be paclitaxel, docetaxel, cabazitaxel, or nab-paclitaxel (ABRAXANE®). In some embodiments, the taxane may be paclitaxel. In some embodiments, the taxane may be docetaxel. In some embodiments, the taxane may be cabazitaxel. In some embodiments, the taxane may be nab-pachtaxel. [0109] In some embodiments, the treatment does not include a taxane. In some embodiments, the treatment does not include a taxane other than nab-paclitaxel.

[0110] In some embodiments, the chemotherapeutic drug includes, but is not necessarily limited to, cyclophosphamide, methotrexate, 5 -fluorouracil, vinorelbine, doxorubicin, docetaxel, bleomycin, vinblastine, dacarbazine, mustine, vincristine, procarbazine, prednisolone, etoposide, cisplatin, epirubicin, capecitabme, fohmc acid, oxaliplatin, gemcitabine, and/or ifosfamide. In some embodiments, the chemotherapeutic drug includes cyclophosphamide. In some embodiments, the chemotherapeutic drug includes methotrexate. In some embodiments, the chemotherapeutic drug includes 5 -fluorouracil. In some embodiments, the chemotherapeutic drug includes vinorelbine. In some embodiments, the chemotherapeutic drug includes doxorubicin. In some embodiments, the chemotherapeutic drug includes docetaxel. In some embodiments, the chemotherapeutic drug includes bleomycin. In some embodiments, the chemotherapeutic drug includes vinblastine. In some embodiments, the chemotherapeutic drug includes dacarbazine. In some embodiments, the chemotherapeutic drug includes mustine. In some embodiments, the chemotherapeutic drug includes vincristine. In some embodiments, the chemotherapeutic drug includes procarbazine. In some embodiments, the chemotherapeutic drug includes prednisolone. In some embodiments, the chemotherapeutic drug includes cisplatin. In some embodiments, the chemotherapeutic drug includes epirubicin. In some embodiments, the chemotherapeutic drug includes capecitabine. In some embodiments, the chemotherapeutic drug includes folinic acid. In some embodiments, the chemotherapeutic drug includes oxaliplatin. In some embodiments, the chemotherapeutic drug includes gemcitabine. In some embodiments, the chemotherapeutic drug includes ifosfamide.

[OHl] In some embodiments, the chemotherapeutic drug is etoposide.

[0112] In some embodiments, the immunotherapy is a checkpoint inhibitor.

[0113] In some embodiments, the checkpoint inhibitor is a PD-L1 inhibitor.

[0114] In some embodiments, the PD-L1 inhibitor is atezolizumab, durvalumab, or avelumab. In some embodiments, the PD-L1 inhibitor is atezolizumab. In some embodiments, the PD-L1 inhibitor is durvalumab. In some embodiments, the PD-L1 inhibitor is avelumab. [0115] Durvalumab, also known as MEDI4736, is an Fc-optimized human monoclonal IgGl kappa anti -PD-L1 antibody (Medlmmune, AstraZeneca) described in WO 2011/066389 and US 2013/034559. Avelumab, also known as MSB0010718C, is a human monoclonal IgGl anti-PD-Ll antibody (Merck KGaA, Pfizer).

[0116] An alkylating agent is any highly reactive drug that binds to certain chemical groups (phosphate, ammo, sullhydryl, hydroxyl, and imidazole groups) commonly found in nucleic acids and other macromolecules, bringing about changes in the DNA and RNA of cells. Since cancer cells, in general, proliferate faster and with less error-correcting than healthy cells, cancer cells are more sensitive to DNA damage — such as being alkylated. Alkylating agents are used to treat several cancers. However, they are also toxic to normal cells (cytotoxic), particularly cells that divide frequently, such as those in the gastrointestinal tract, bone marrow, testicles and ovaries, which can cause loss of fertility. Exemplary alkylating agents include, but are not necessarily limited to, altretamine, bendamustine, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, and cyclophosphamide.

[0117] In some embodiments, the alkylating agent is carboplatin.

[0118] In some embodiments, the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy -induced peripheral neuropathy (PN).

[0119] Single nucleotide variants, or single nucleotide polymorphisms (SNPs) are the most abundant of variations in the human genome, accounting for >90% of sequence polymorphisms. They occur on average once every 1000 nucleotides so that, as a rule of thumb, there is a 0.1% chance of any base position being heterozygous in a particular individual. Nucleotide diversity is not constant over the entire genome, with areas of extremely low diversity, for example, the X chromosome, and areas of extremely high diversity, for example, up to 10% in the human leukocyte antigen (HLA) loci (Twyman and Primrose, Pharmacogenomics 4: 1-13 (2002)). Highly polymorphic SNP target sequences are also known in other species, e.g., plants (Ching A, Caldwell K S, Jung M, Dolan M, Smith O S, Tingey S, Morgante M, Rafalski A J. BMC Genet. 3: 19 (2002)) and viruses (Miller V, Larder B A. Antivir Ther. 6 Suppl 3:25-44 (2001)).

[0120] In some embodiments, the one or more single nucleotide variants may be located at, but are not necessarily limited to, one or more loci selected from rsl7020773, rsl 15575220, rsl 17987557, rsl 13371772, rsl2943567, rs371157151, rs550771753, rs61745750, rs61745752, or any combination thereof. In some embodiments, the SNP is located at rsl7020773. In some embodiments, the SNP is located at rsl 15575220. In some embodiments, the SNP is located at rsl 17987557. In some embodiments, the SNP is located at rsll3371772. In some embodiments, the SNP is located at rs!2943567. In some embodiments, the SNP is located at rs371157151. In some embodiments, the SNP is located at rs550771753. In some embodiments, the SNP is located at rs61745750. In some embodiments, the SNP is located at rs61745752.

[0121] In some embodiments, the locus of the single nucleotide variant is rs!7020773. In some embodiments, the locus of the single nucleotide variant is rsl 15575220.

[0122] In some embodiments, the variant comprises a T to C nucleotide change. In some embodiments, the variant comprises a G to T nucleotide change.

[0123] In some embodiments, the locus of the single nucleotide variant comprises rs61745750 and rs61745752.

[0124] In some embodiments, the subject is not administered paclitaxel, docetaxel, or cabazitaxel if the subject has a single nucleotide variant in the one or more genes. In some embodiments, the subject is not administered paclitaxel, docetaxel, or cabazitaxel in combination with a checkpoint inhibitor (e.g., anti-PD-Ll antibody) if the subject has a single nucleotide variant in the one or more genes.

[0125] In some embodiments, the subject is administered nab-paclitaxel if the subject has a single nucleotide variant in one or more genes. In some embodiments, the subject is administered nab-paclitaxel in combination with a checkpoint inhibitor (e.g., anti-PD-Ll antibody) if the subject has a single nucleotide variant in one or more genes.

[0126] In other aspects, the present disclosure also provides methods of preventing chemotherapy -induced NP in a subject in need of cancer treatment, comprising administering to the subject an inhibitor that targets GPR68. In embodiments, the inhibitor is a small molecule inhibitor.

[0127] As used herein, the term “small molecule inhibitor” is an organic compound of low molecular weight (< 1000 daltons) that may regulate a biological process. Many drugs are small molecules. Small molecules may be used as research tools to probe biological functions as well as leads in the development of new therapeutic agents. Some can inhibit a specific function of a protein or disrupt protein-protein interactions. Pharmacology usually restricts the term "small molecule" to molecules that bind specific biological macromolecules and act as an effector, altering the activity or function of the target.

[0128] Small molecules can have a variety of biological functions or applications, serving as cell signaling molecules, drugs in medicine, pesticides in farming, and in many other roles. These compounds can be natural (such as secondary metabolites) or artificial (such as antiviral drugs); they may have a beneficial effect against a disease (such as drugs) or may be detrimental (such as teratogens and carcinogens). Small molecule cancer drugs, because of their small size, have been successfully used to target the extracellular, cell surface ligandbinding receptors as well as the intracellular proteins, including anti-apoptotic proteins that play a key role in transducing downstream signaling for cell grow th and metastasis promotion. Research on molecularly targeted cancer drug discovery over the last few decades has resulted in a number of small molecule drugs being successfully introduced in the clinic for cancer treatment. Most of these drugs inhibit critical cancer targets such as serine/threonine/tyrosine kinases, matrix metalloproteinases (MMPs), heat shock proteins (HSPs), proteosome and other proteins playing a role in signal transduction pathways.

[0129] In some embodiments, the method further comprises administering a chemotherapeutic drug, a monoclonal antibody, or an alkylating agent to the subject as described in detail elsewhere herein.

[0130] In some embodiments, the method may further comprise determining whether the subject has one or more single nucleotide variants in GPR68 prior to administering the inhibitor (e.g., small molecule inhibitor).

[0131] In some embodiments, the subject has two single nucleotide variants in GPR68.

[0132] In some embodiments, the two single nucleotide variants comprise rs61745750 and rs61745752. METHODS FOR SELECTING PATIENTS FOR TREATMENT

[0133] In some embodiments, the present disclosure relates to a method for selecting a subject at risk of developing chemotherapy-induced PN, the method comprising providing a biological sample from the subject and identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLA1N2, and/or GPR68, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy- induced PN. In some embodiments, the subject has a single nucleotide variant in GRID2. In some embodiments, the subject has a single nucleotide variant in SCG2. In some embodiments, the subject has a single nucleotide variant in OXGR1. In some embodiments, the subject has a single nucleotide variant in DOK5. In some embodiments, the subject has a single nucleotide variant in ASIC2. In some embodiments, the subject has a single nucleotide variant in SBSPON. In some embodiments, the subject has a single nucleotide variant in SLAIN2. In some embodiments, the subject has a single nucleotide variant in GPR68.

[0134] In some embodiments, identifying the sequence comprises amplifying the one or more genes in the sample and detecting the presence of one or more single nucleotide variants in the one or more genes; or wherein identifying the sequence comprises sequencing the one of more genes in the sample, as described in detail above.

[0135] A gene or nucleic acid can be amplified by any suitable method known in the art. The term “amplified” as used herein refers to subjecting a target nucleic acid in a sample to a process that linearly or exponentially generates amplicon nucleic acids having the same or substantially the same (e g. , substantially identical) nucleotide sequence as the target nucleic acid, or segment thereof, and/or a complement thereof. In some embodiments an amplification reaction comprises a suitable thermal stable polymerase. Thermal stable polymerases are known in the art and are stable for prolonged periods of time, at temperature greater than 80° C. when compared to common polymerases found in most mammals. In certain embodiments the term “amplified” refers to a method that comprises a polymerase chain reaction (PCR). Conditions conducive to amplification (i.e., amplification conditions) often comprise at least a suitable polymerase, a suitable template, a suitable primer or set of primers, suitable nucleotides (e.g., dNTPs), a suitable buffer, and application of suitable annealing, hybridization and/or extension times and temperatures. In certain embodiments an amplified product (e.g., an amplicon) can contain one or more additional and/or different nucleotides than the template sequence, or portion thereof, from which the amplicon was generated (e.g., a primer can contain “extra” nucleotides (such as a 5' portion that does not hybridize to the template), or one or more mismatched bases within a hybridizing portion of the primer).

[0136] In some embodiments, the cancer treatment regimen comprises a monoclonal antibody, an alkylating agent, or a combination thereof, as descnbed in detail elsewhere herein.

[0137] In some embodiments, the monoclonal antibody is a PD-L1 inhibitor.

[0138] In some embodiments, the alkylating agent is carboplatin.

[0139] In some embodiments, the risk of developing chemotherapy-induced PN is higher than for a subject lacking the one or more single nucleotide variants.

[0140] In other aspects, the present disclosure provides a method for selecting a subject for treatment with a chemotherapy regimen, comprising (a) providing a biological sample from the subject, (b) identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68, and (c) selecting the subject for treatment with the chemotherapy regimen when the subject lacks one or more single nucleotide variants in the one or more genes. In some embodiments, the subject has a single nucleotide variant in GRID2. In some embodiments, the subject has a single nucleotide variant in SCG2. In some embodiments, the subject has a single nucleotide variant in OXGR1. In some embodiments, the subject has a single nucleotide variant in DOK5. In some embodiments, the subject has a single nucleotide variant in ASIC2. In some embodiments, the subject has a single nucleotide variant in SBSPON. In some embodiments, the subject has a single nucleotide variant in SLAIN2. In some embodiments, the subject has a single nucleotide variant in GPR68.

[0141] In some embodiments, the chemotherapy regimen comprises a taxane.

[0142] In some embodiments, the taxane comprises paclitaxel, docetaxel, or cabazitaxel. In some embodiments, the taxane may be paclitaxel. In some embodiments, the taxane may be docetaxel. In some embodiments, the taxane may be cabazitaxel. In some embodiments, the taxane may be nab-paclitaxel. [0143] In some embodiments, the chemotherapy regimen comprises a checkpoint inhibitor.

[0144] In some embodiments, the checkpoint inhibitor comprises an anti-PD-Ll antibody.

[0145] In some embodiments, the anti-PD-Ll antibody comprises atezolizumab, durvalumab, or avelumab. In some embodiments, the PD-L1 inhibitor is atezolizumab. In some embodiments, the PD-L1 inhibitor is durvalumab. In some embodiments, the PD-L1 inhibitor is avelumab.

[0146] In some embodiments, the one or more single nucleotide variants is located at one or more loci selected from rs 17020773, rsl 15575220, rsl 17987557, rsl 13371772, rs!2943567, rs371157151, rs550771753, rs61745750, rs61745752, or any combination thereof. In some embodiments, the SNP is located at rsl 7020773. In some embodiments, the SNP is located at rsl 15575220. In some embodiments, the SNP is located at rsl 17987557. In some embodiments, the SNP is located at rsl 13371772. In some embodiments, the SNP is located at rsl2943567. In some embodiments, the SNP is located at rs371157151. In some embodiments, the SNP is located at rs550771753. In some embodiments, the SNP is located at rs61745750. In some embodiments, the SNP is located at rs61745752.

[0147] In some embodiments, the locus of the single nucleotide variant is rsl7020773.

[0148] In some embodiments, the variant comprises a T to C nucleotide change.

[0149] In some embodiments, the locus of the single nucleotide variant is rsl 15575220.

[0150] In some embodiments, the variant comprises a G to T nucleotide change.

[0151] In some embodiments, the locus of the single nucleotide variant comprises rs61745750 and rs61745752.

[0152] In some embodiments, the cancer is renal cell carcinoma, non-small cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, melanoma, squamous cell cancer, lung cancer, cancer of the peritoneum, hepatocellular cancer, stomach cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer, B-cell lymphoma, low grade/follicular non-Hodgkin's lymphoma (NHL), small lymphocytic (SL) NHL, intermediate grade/follicular NHL, intermediate grade diffuse NHL, high grade immunoblastic NHL, high grade lymphoblastic NHL, high grade small non-cleaved cell NHL, bulky disease NHL, mantle cell lymphoma, AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), Hairy cell leukemia, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), or Meigs' syndrome.

EXAMPLES

EXAMPLE 1: RISK OF PN IS ELEVATED IN TAXANE-TREATED PATIENTS

[0153] PN event data from 14 randomized clinical trials spanning a portion of the development path of the PD-L1 inhibitor atezolizumab where whole genome germline sequencing was also available were combined. The trials spanned a number of cancers including renal cell carcinoma (IMmotionl51¹²), triple negative breast cancer (IMpassionl30¹³), non-small cell lung cancer (IMpowerl l0¹⁴/130¹⁵/131¹⁶/132¹⁷/150¹⁸), small cell lung cancer (IMpowerl33¹⁹), bladder cancer (IMvigor010²°/130²¹/211²²), ovarian cancer (IMagyn050²³), melanoma (IMspirel70²⁴), and a Phase 1 trial in several solid cancers (Jung et al. Clin Cancer Res 25(1 l):clincanres.2740.2018 (2019)). The clinical trials tested several agents with atezolizumab and considered combinations with both platinum chemotherapy and taxanes (Table 1). In total, the cohort spanned 30 different clinical trial arms including immunotherapy combination arms and control chemotherapy arms. The study focused on 4,900 patients that provided informed consent for genetic data collection. They were of European ancestry (EUR > 0.7), and met strict population and genotype data quality control filters (see Methods).

Table 1. Frequency and grade of PN events in cancer patients of European ancestry across 14 randomized controlled trials testing immunotherapy and chemotherapy combinations.

Trial abbreviations are as follows: impXXX = IMpowerXXX, imml51=IMmotionl51, imvXX = IMvigorXXX; imsl70=IMspirel70; imvXXX=IMvigorXXX. Treatments in the trial arms are abbreviated as follows: A = atezolizumab, ido = ido inhibitor; Atezo = atezolizumab montheerapy; B = bevacizumab; cobi=cobimetinib; Pembro=pembrolizumab; C = carboplatin or cisplatin; P = paclitaxel; NabP = nab-pachtaxel; Pem=Pemetrexed; G=Gemcitabine; Observ = designates observation after surgery; Chemo = physicians choice chemotherapy vinflunine, docetaxel, or paclitaxel in IMvigor211; and carboplatin or cisplatin plus pemetrexed or gemcitabine in IMpowerl 10; E = eptoiside; SUN = sunitinib. Grayed rows designate trial arms where a taxane was used.

[0154] In the randomized clinical trial cohort, 1,117 patients experienced PN events. The majority, 1,038 events, were of CTCAE grade 1 or 2. PN events were not associated with sex (meta-analysis p=0.85, HR=0.98, 95% CI 0.83-1.16), but only modestly associated with patient age (meta-analysis p = 0.0004, HR=1.01, 95% CI 1.005-1.017 per year of age). The cohort could be subdivided into patients that received taxanes (N=2,534) and anon-taxane treated group (N=2,362). 89.7% (1,002/1,117) of all PN events occurred in trial arms where a taxane was used, reflecting significantly elevated risk (p=10 ²², HR=10.17, 95% CI=8 38- 12.34) of PN when these agents are used as compared to immunotherapies and platinumbased chemotherapies. Among taxane-treated patients, nab-paclitaxel led to a lower risk of PN (p=10^-21, HR=0.50, 95% CI=0.43-0.58), consistent with its improved safety profile relative to solvent-based paclitaxel. The majority, 1,038 events, were of Common Terminology Criteria for Adverse Events (CTCAE) grade 1 or 2. PN events were not associated with sex (meta-analysis p=0.85, HR=0.98, 95% CI 0.83-1.16), but only modestly associated with patient age (meta-analysis p = 0.0004, HR=1.01, 95% CI 1.005-1.017 per year of age). Risk of PN was associated with body surface area (BSA) (meta-analysis p = 7.31 ■ 10'⁸, HR=2.13 per m², 95% CI 1.61-2.81) which is used to dose chemotherapies and is consistent with PN’s status as a dose limiting toxicity.

EXAMPLE 2: COMMON VARIANTS NEAR GRID2 AND SCG2 ARE ASSOCIATED WITH PN RISK

[0155] Across these clinical trials, a GWAS was conducted for time-to-first PN event using 8,448,402 common variants (MAF > 0.01) across 4,900 individuals with European ancestry (Fig. 1 A). The Cox model used in this GWAS was stratified by trial arm to account for the differing baseline hazard for PN in each of the trial arms (see Methods). As the likelihood is well specified, this approach accounted for both rare events and small trial arms (Burke et al. Stat Med 36(5): 855— 75 (2017)). Consistent with these observations, the test statistics of this GWAS were well calibrated (X_gc=1.004, Fig. 4).

[0156] Two loci reaching genome-wide significance (p < 5 ■ 10‘⁸) were identified (Fig. 1A, Table 2). The first locus was located on chromosome 4 in the intron of the GRID2 gene. The index SNP for the locus was rsl7020773 (T/C, with C being the allele associated with higher PN risk, meta-analysis p = 2.03 ■ W⁸, HR=1.85, 95% CI=1.50-2.31, EAF = 0.032) (Fig. IB). It was additionally confirmed that the coefficient corresponding to genotype status in the Cox model did not violate the proportional hazards assumption (zph test p=0.55). The second locus was a single variant rsl 15575220 (G/T with T being the risk allele, meta- analysis p = 4.15 ■ 10'⁸, HR=2.44, 95% CI=1.77-3.35, EAF = 0.011) downstream of the SCG2 gene (Fig. 1C). Here, as well, the genotype status did not violate the proportional hazards assumption (zph test p = 0.40). The data set was stratified and the hazard ratio was considered within each trial arm, separately illustrating that no one trial drove the association observed (Fig. ID, 5). The variant was flanked by proximity ligation-assisted H3K4me3 ChlP-seq interactions with SCG2 in neurons, but not oligodendrocytes or microglia (Fig. 6). Although this approach does not account for the differing baseline hazard in each trial arm, the effect of the variants was evident in the cumulative incidence plots after combining all of the data (Fig. ID, Fig. 7).

Table 2. Common variants associated with risk of PN across N=4,900 cancer patients from randomized controlled trials at meta-analysis p < 10‘⁶.

EXAMPLE 3: RARE CODING VARIANT BURDEN IDENTIFIES GPR68 AS PN

SUSCEPTIBILITY GENE

[0157] Given the availability of whole genome sequencing data in the cohort, it was possible to interrogate rare coding variants for their association with PN risk. Protein altering variants were aggregated with MAF < 0.01 in the gene to compute a burden score and they were tested for their association with PN risk, limiting burden tests to genes where there were at least 30 carriers (see Methods). Burden tests were performed on 13,264 genes. As the Cox model was stratified by trial arm, it was confirmed that the burden test statistics were well calibrated (k_gc=1.009, Fig. 8). One gene that reached exome-wide significance cutoff was identified (p < 3.77 ■ 10'⁶, 0.05/13,264 genes). GPR68 had 51 rare variant carriers, and rare variant burden was significantly associated with PN risk (meta-analysis p=1.59 ■ IO^-6, HR=2.44, 95% CI=1.52-2.72). It was additionally confirmed that the variable corresponding to the rare variant burden in the Cox model did not violate proportional hazards assumption (zph test p = 0.88). Given that the majority of PN events were in taxane treated patients, a burden test using only patients treated with taxanes was conducted. In this subset of patients, there were 38 GPR68 rare variant carriers, and the effect of these rare variants on PN risk was even more clear (meta-analysis p=3.47 ■ 10'⁸, HR=2.25, 95% CI=1.69-3.01, zph test p=0.88) (Fig. 9).

[0158] The cumulative incidence plot showing the burden of rare variants in GPR68 and association with PN risk was next examined. It turned out that 15/51 patients in all treatment arms and 1 1/33 patients in the taxane arms carried 2 rare variants in GPR68 that were strongly associated with risk of PN (Fig. 2A). All of these patents carried two variants in the C-terminal end of GPR68: rs61745750 (330K>330N) and truncating variant rs61745752 (336E>336*) (Fig. 2B-2C). Therefore, these two variants could be considered a rare haplotype where rs61745750 and rs61745752 were in perfect linkage disequilibrium (LD). These two variants were also in perfect LD within the Haplotype Reference Consortium imputation panel with the haplotype frequency of 0.0010727. It is estimated that carriers of the rs61745750 and rs61745752 haplotype are 5.62 times more likely to develop PN as compared to taxane-treated patients who have no rare coding variants in GPR68 (HR=4.48, 95% CI 2.25-8.91, all patients, and HR=5.62 95% CI 2.87-11.00 taxane treated). In addition, rs61745750 (330K>330N) and rs61745752 (3360336*) were excluded and it was found that the remaining variants were nominally associated with time to PN across all patients (p=0.015, HR=1.89, 95% CI=1. 12-3. 16) and within taxane treated patients (p=0.009, HR=2.02, 95% CI=1. 19-3.45), indicating that additional rare coding variants may impact GPR68 to increase risk of PN.

[0159] The C-terminus is important for GPCR function. It is phosphorylated by GPCR kinases, preparing the GPCR for arrestin binding and blocking GPCR signaling through internalization of the receptor and in some cases initiation of alternative pathways independent of the G-protein signaling. Px(x)PxxP amino acid motifs in the C-termini of GPCRs are thought to encode phosphorylation sites that are required for arrestin binding (Zhou et al. Cell 170(3):457-469.el3 (2017)) (P in the motif corresponds to serine or threonine and x any amino acid and the parentheses denote an optional match). Using PhosCoFinder, 3 partial motif matches were identified that were removed by the truncating rs61745752 (336E>336*) variant, 3 additional partial motif matches that were altered by the rs61745750 (330K>330N) substitution, and loss of several predicted phosphorylation sites in the C-terminus of GPR68 (Fig. 2D). Disruption of these motifs and predicted phosphorylation sites may impact arrestin mediated deactivation of GPR68 signaling to contribute to PN risk.

EXAMPLE 4: GRID2, SCG2, AND GPR68 HAVE DISTINCT EXPRESSION PATTERNS IN DRG

[0160] The pathophysiology of CIPN implicates the peripheral nervous system and sensory neurons in dorsal root ganglia (DRG) (Eldridge et al. Toxicol Pathol 48(1): 190-201 (2020)). Data from a recent publication that collected single-nucleus RNA-seq data from human DRG were re-analyzed (see Methods) (Nguyen et al. Elife 10: e71 752 (2021)). Even though the authors of the publication enriched for neuronal nuclei using NeuN, many nonneuronal nuclei still remained in the data. Using these data, it was possible to discern several neuron cell types as well as a small number of non-neuronal cell types including satellite glia. The expression patterns of GRID2, SCG2, and GPR68 were examined in labeled cell types (Figs. 3A-3C). Consistent with previous reports by antisense probe labeling and Western blot that GPR68 is expressed in nociceptor neurons in DRG, it was found that GPR68 was preferentially expressed in PEP1 sensory neurons in single cell data (Huang et al. Mol Cell Neurosci 36(2): 195-210 (2007)). It was also found that SCG2 had a similar pattern of higher expression in PEP1 sensory neurons Tn addition, the higher expression in PEP1 sensory neurons of GPR68 and SCG2 was conserved across macaque and mouse (Fig. 10-11). In contrast, GRID2 was highly expressed in satellite glia which wrap the soma of sensory neurons. This pattern was conserved in mice in a data set that compared expression in satellite glial cells to overall expression in DRG (Fig. 12) (Jager et al. Glia 68(7): 1375-95 (2020)). Taken together, the distinct and detectable expression pattern of these genes in DRG supports their role in the peripheral nervous system.

Discussion

[0161] A rare coding haplotype consisting of two variants in the C-terminus of a pH- sensing GPCR that contributes substantially to risk of PN was identified. This haplotype was identified due to its large effect size in taxane-treated patients (>5x increased risk relative to patients without any GPR68 coding variants). Using single cell RNA-seq data, it was found that GPR68 was expressed preferentially in PEP1 sensory neurons and this pattern was conserved across species. These neurons are nociceptors that respond to intense mechanical or thermal stimuli and sensitivity of these neurons to chemotherapy may underlie the paresthesia experienced during CIPN. The variants in the small coding haplotype lead to loss and alteration of predicted phosphorylation sites and arrestin-binding motifs in the C- terminus of GPR68. Loss of these sites and motifs may block receptor internalization prolonging activation of GPR68 signaling to sensitize PEP1 sensory neurons to chemotherapies. Consistent with this model, a recent study has provided evidence that the C- terminal truncating variant rs61745752(336E>336*) alone prevents receptor internalization in acidic conditions in transfected HEK293T cells (Williams et al. Biorxiv 612549 (2021)). GPCRs are highly druggable, and several inhibitors and allosteric ligands of GPR68 are known (Williams et al. Biorxiv 612549 (2021); Huang et al. Nature 527 (7579):477-83 (2015)). These human genetic findings suggest that these small molecules may be therapeutically useful to prevent CIPN by inhibition of GPR68 signaling.

[0162] Further insight was also gamed into the genetic architecture of PN. Two common non-coding variant genome-wide significant signals near GRID2 and SCG2 were found. GRID2 is a member of the glutamate receptor family. Although glutamate plays an important role in pain perception, GRID2 is not known to bind glutamate and is considered an orphan receptor (Lemoine et al. Elife 9:e59026 (2020)). Within DRG, GRID2 is preferentially expressed in satellite glial cells, which are important for neuronal homeostasis and response to neuronal stress through bidirectional communication with neurons through ion channels and receptors (Hanani et al. Nat Rev Neurosci 21(9):485-98 (2020)). Furthermore, satellite glial cells have been implicated in CIPN models in mice. SCG2, like GPR68, is preferentially expressed in PEP1 sensory neurons. SCG2 encodes for a neuroendocrine peptide that aggregates in acidic conditions, a process that might be important for its sorting into secretory granules and further implicates pH dependent processes in CIPN risk (Gerdes et al. J Biol Chem 264(20):12009-15 (1989)).

[0163] The study has several limitations. Although the variants identified were genomewide significant in a meta-analysis, additional studies are needed to understand the therapeutic agents where these variants have the largest effects. Constructing a replication cohort for the rare variant association found in GPR68 will be challenging. Obtaining informed patient consent for whole genome sequencing for human genetic studies is significantly more difficult than obtaining consent for studying somatic mutations in the clinic. The study focused on patients of European ancestry as they represented the majority of patients in the clinical trials where WGS data were available. Well-powered studies of CIPN in non-European ancestries will be enabled by ongoing efforts to increase the diversity of patients enrolled in clinical trials.

[0164] In summary', the present study illustrates the potential of whole genome sequencing in patient populations that receive drugs with known dose limiting toxicities. Findings from these studies provide an opportunity for drug development to elucidate the genetic architecture of toxicities and identify rare genetic variants associated with toxicity risk. Insights gained from these human genetic studies may lead to approaches to mitigate toxicities that have higher potential for clinical success. Given that the cost of whole genome sequencing continues to decrease, studies of toxicities can scale across health systems and large drug development programs. This approach opens up space for innovation for discovery of drug combinations that provide a more favorable risk benefit profile for patients.

Methods

Patient Cohorts

[0165] A retrospective meta-analysis of peripheral neuropathy events was conducted using individual participant data from 14 previously completed randomized controlled trials. Detailed clinical trial results have been previously reported. All of the trials were sponsored by F. Hoffmann-La Roche/Genentech. The sponsor provided the study drugs and collaborated with the investigators across countries and study sites on the clinical trial and collection of the data. Each trial was conducted in accordance with the International Conference on Harmonization Good Clinical Practice guidelines and with the principles of the Declaration of Helsinki. An independent data monitoring committee reviewed safety data from these studies.

[0166] All patients provided informed consent for the main study. A subset of patients signed an optional Research Biosample Repository (RBR) Informed Consent Form (ICF) to provide whole blood samples for future research. By signing the optional RBR ICF, patients provided informed consent for study of inherited and non-inherited genetic variation from these whole blood samples. Whole genome sequencing data were collected from whole blood only from patients that signed the optional RBR ICF. Ethics Committees (EC) and Institutional Review Boards (IRB) at each study site for each clinical trial approved the clinical trial protocol, the main study ICF, and the RBR ICF.

Whole Genome Sequencing

[0167] Genomic DNA was extracted from blood samples using the DNA Blood400 kit (Chemagic) and eluted in 50pL Elution Buffer (EB, Qiagen). DNA was sheared (Covaris LE220) and sequencing libraries were prepared using the TruSeq Nano DNA HT kit (Illumina Inc.). Libraries were sequenced at Human Longevity (San Diego, CA, USA) and the Broad Institute (Boston, MA, USA). All sequencing data were checked for concordance with SNP fingerprint data collected before sequencing. 150bp paired-end whole-genome sequencing (WGS) data were generated to an average read depth of 30x using the HiSeq platform (Illumina X10, San Diego, CA, USA).

Sample and Variant Level QC

[0168] Reads were aligned using the functionally equivalent (FEB) BAM pipeline. Samples were jointly genotyped using Sentieon GATK. Only variants flagged as PASS and genotype calls with GQ >20 were used. After application of the GQ filter, variants with genotype call missing rate of >0.01 were removed. Multi-allelic sites were handled by variant splitting. Samples were removed if the proportion of sites with missing genotypes exceeded 0.1. Samples LD pruned and merged with 1000G samples. Then, ADMIXTURE vl.23 was used to estimate ancestry in the 5 major populations using supervised ancestry estimation. Only samples with ancestry EUR > 0.7 were used in subsequent steps. Observed and expected homozygous/heterozygous genotype counts for each sample were tabulated and method-of-moments estimates of the F-coefficient were generated for each sample. Samples with an F-statistic more than 5 standard deviations above the mean were removed. Samples were then analyzed for relatedness using the KING-robust method as implemented in plink2. Sample pairs with a KING kinship coefficient greater than 0. 177 were identified and one of the pair of samples was removed randomly. We then performed PCA using the implementation in the proPC A package. Six rounds of PCA outlier removal iterations were performed. Samples that were >5 standard deviations from the top 5 eigenvectors at each iteration were removed from the analysis. The final PCA was then performed to compute 5 eigenvectors that were subsequently used to account for any remaining population stratification. Variants were also analyzed for violation of Hardy Weinberg Equilibrium (HWE). Sites where the p-value for HWE was below 10-8 were excluded from the analysis. Variants with >0.01 minor allele frequency (MAF) were designated as common variants. In total, 8,448,402 common variants were identified after these QC steps. Missense variants were annotated using bcftools esq. Missense variants associated with canonical coding transcript were used for a gene designated in Ensembl Release-104 of the genome build GRCh38.pl3. In total, there were 605,052 missense variants found in the cohort at all allele frequencies.

Time to Event GW AS Meta- Analysis

[0169] A Cox model was used to conduct a time to event GW AS using time to PN. The GW AS was adjusted for 5 genotype eigenvectors, sex, and age. In addition, the model was stratified by trial arms to allow for an individual participant data meta-analysis. The final Cox model could be specified using the coxph function the R survival package as follows: coxph(Surv(PN.time, PN.occured) ~ dosage + EV.l + EV.2 + EV.3 + EV.4 + EV.5 + AGE + SEX + strata(trial.arm)).

[0170] For each significant variant, it was confirmed that there was no strong violation of the Cox proportional hazards assumption using the cox.zph test.

Time to Event Rare Variant Burden Tests

[0171] A simple burden test using rare coding variants (MAF < 0.01) was used. Rare variant burden tests were limited to genes with at least 30 rare coding variant carriers across the cohort. The association between the number of rare variants carried by an individual the time to a PN event was tested. The Cox model used can be coxph(Surv(PN.time, PN.occured) ~ burden + EV. 1 + EV.2 + EV.3 + EV.4 + EV.5 + AGE + SEX + strata(tnal.arm)).

Single-Nuclei Analysis of Human DRGs

[0172] Human DRG single-nuclei RNA sequencing data from Nguyen et al. 2021 were downloaded from NCBI GEO database (GSE168243) in FASTQ format and processed with a CellRanger analysis pipeline v6.1.2. Nuclei greater than 25% mitochondrial UMIs were discarded. After the filtering step, the gene x cell matrix of raw UM1 counts was log- normalized using ‘NormalizeDataO’ in SeuratV338. Samples were integrated using ‘FindlntegrationAnchorsQ’ and TntegrateData()’ functions in SeuratV3. Then, the integrated data were scaled, a dimensionality reduction was performed by PCA, UMAP coordinates and Louvain clustering were calculated for all nuclei using SeuratV3. DRG neuron and non- neuronal clusters were identified based on the expression of known cell-type specific markers (SNAP25, UCHL1, RBFOX3, APOE, SPARC, PLP1, PMP22, MPZ1, MBP, PECAM1, VWF, PNPLA2, ADIPOQ). Then, DRG neurons were subsetted to perform analysis to obtain high-resolution clusters within the DRG neuron group. First, all non-neuronal nuclei barcodes were removed from the initial clustering and then nuclei that express any satellite glial specific transcripts (PLP1 < 1 & MPZ < 1) were removed. The resulting digital geneexpression matrix (DGE) was carried forward for clustering. Based on previous literature (Nguyen et al. Elife 10:e71752 (2021); Kupari et al. Nat Commun 2(1): 1510 (2021); Renthal et al. Neuron 108(1): 128-144. e9 (2020); Tavares-Ferreira et al. Sei Transl Med 14(632):eabj8186 (2022); Usoskin et al. NatNeurosci 18(1): 145-53 (2015); Li et al. Cell Res 26(l):83-102 (2016)), different subsets of large diameter myelinated A-LTMRs were annotated using NEFH, PVALB, VSNL1, SLC17A7, CALB1, NTRK3, SCN5A, NTRK2, NECAB2, CNTNAP2, and FAM19A1. Non-peptidergic C -fiber nociceptors (NPs) subsets were annotated using GFRA1, GFRA2, TRPC3, LPAR3, CHRNA3, SST, IL31RA, NPPB, TRPV1, TRPA1, RET, SCN10A, SCN11A, P2RX3, and PLXNC1. C-fiber peptidergic nociceptors (PEPs) subsets were annotated using TAC1, ADCYAP1, GAL, KIT, CALC A, NTRK1 , TRPA1 , FAM19A1 , SCNI Oa and SCN11 A. Cold thermoreceptors subsets were annotated using TRPM8, TAC1, FOXP2, CDH8, and PENK.

Claims

WHAT IS CLAIMED IS:

1. A method of treating a cancer in a subject, comprising:

(a) selecting a subject having one or more single nucleotide variants in one more genes selected from GRID2, SCG2, 0XGR1, D0K5, ASIC2, SBSPON, SLAIN2. and/or GPR68; and

(b) administering to the subject an anti-cancer treatment.

2. The method of claim 1, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced peripheral neuropathy (PN).

3. The method of claim 1, wherein the one or more single nucleotide variants is located at one or more loci selected from rsl7020773, rsl 15575220, rsl 17987557, rsl l3371772, rsl2943567, rs371157151, rs550771753, rs61745750, or rs61745752.

4. The method of claim 3, wherein the locus of the single nucleotide variant is rsl 7020773.

5. The method of claim 4, wherein the variant comprises a T to C nucleotide change.

6. The method of claim 3, wherein the locus of the single nucleotide variant is rsl 15575220.

7. The method of claim 6, wherein the variant comprises a G to T nucleotide change.

8. The method of claim 3, wherein the locus of the single nucleotide variant comprises rs61745750 and rs61745752.

9. The method of any one of claims 1-8, wherein the treatment does not include a taxane.

10. The method of any one of claims 1-9, wherein the cancer is renal cell carcinoma, nonsmall cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, melanoma, squamous cell cancer, lung cancer, cancer of the peritoneum, hepatocellular cancer, stomach cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer, B-cell lymphoma, low grade/follicular non-Hodgkin's lymphoma (NHL), small lymphocytic (SL) NHL, intermediate grade/follicular NHL, intermediate grade diffuse NHL, high grade immunoblastic NHL, high grade lymphoblastic NHL, high grade small non-cleaved cell NHL, bulky disease NHL, mantle cell lymphoma, AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), Hairy cell leukemia, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), or Meigs' syndrome. The method of any of claims 1 to 10, wherein the treatment comprises one or more of a chemotherapeutic drug, an immunotherapy, or an alkylating agent. The method of any of claims 1 to 11, further comprising administering a chemotherapeutic drug, an immunotherapy, or an alkylating agent to the subject. The method of claim 11 or 12, wherein the chemotherapeutic drug is etoposide. The method of claim 11 or 12, wherein the immunotherapy is a checkpoint inhibitor. The method of claim 11 or 12, wherein the checkpoint inhibitor is a PD-L1 inhibitor. The method of claim 15, wherein the PD-L1 inhibitor is atezolizumab, durvalumab, or avelumab. The method of claim 11 or 12, wherein the alkylating agent is carboplatin. The method of any of claims 1 to 17, wherein the subject is not administered paclitaxel, docetaxel, or cabazitaxel if the subject has a single nucleotide variant in the one or more genes. The method of any of claims 1 to 18, wherein the subject is administered nab- paclitaxel if the subject has a single nucleotide variant in one or more genes. A method of minimizing the incidence of chemotherapy-induced PN in a cancer subject, comprising (a) selecting a subject having a single nucleotide variant in one or more genes selected from GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68; and (b) administering to the subject a cancer treatment regimen, wherein the cancer treatment regimen does not include taxanes. The method of any one of claims 1 to 20, wherein selecting the subject comprises (i) providing a biological sample from the subject, and (ii) identifying the sequence of the one or more genes from the sample, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced peripheral neuropathy (PN). A method for selecting a subject at risk of developing chemotherapy -induced peripheral neuropathy (PN), the method comprising providing a biological sample from the subject and identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2, and/or GPR68, wherein the presence of one or more single nucleotide variants in the one or more genes indicates an increased risk of developing chemotherapy-induced PN. The method of claim 21 or 22, wherein identifying the sequence comprises amplifying the one or more genes in the sample and detecting the presence of one or more single nucleotide variants in the one or more genes; or wherein identifying the sequence comprises sequencing the one of more genes in the sample. The method of claim 20, 21, or 23, wherein the cancer treatment regimen comprises a monoclonal antibody, an alkylating agent, or a combination thereof. The method of claim 24, wherein the monoclonal antibody is a PD-L1 inhibitor. The method of claim 24, wherein the alkylating agent is carboplatin. The method of any one of claims 22 to 26, wherein the risk of developing chemotherapy-induced PN is higher than for a subject lacking the one or more single nucleotide variants. A method of preventing chemotherapy-induced peripheral neuropathy (PN) in a subject in need of cancer treatment, comprising administering to the subject a small molecule inhibitor that targets GPR68. The method of claim 28, further comprising administering a chemotherapeutic drug, a monoclonal antibody, or an alkylating agent to the subject. The method of claim 28 or 29, further comprising determining whether the subject has one or more single nucleotide variants in GPR68 prior to administering the small molecule inhibitor. The method of claim 30, wherein the subject has two single nucleotide variants in GPR68 The method of claim 31, wherein the two single nucleotide variants are located at rs61745750 and rs61745752. A method for selecting a subject for treatment with a chemotherapy regimen, comprising (a) providing a biological sample from the subject, (b) identifying the sequence of one or more genes from the sample, the one or more genes comprising GRID2, SCG2, OXGR1, DOK5, ASIC2, SBSPON, SLAIN2. and/or GPR68, and (c) selecting the subject for treatment with the chemotherapy regimen when the subject lacks one or more single nucleotide variants in the one or more genes. The method of claim 33, wherein the chemotherapy regimen comprises ataxane. The method of claim 34, wherein the taxane comprises paclitaxel, docetaxel, or cabazitaxel. The method of any one of claim 33 to 35, wherein the chemotherapy regimen comprises a checkpoint inhibitor. The method of claim 36, wherein the checkpoint inhibitor comprises an anti-PD-Ll antibody. The method of claim 37, wherein the anti-PD-Ll antibody comprises atezolizumab, durvalumab, or avelumab. The method of any one of claims 20-27 and 33-38, wherein the one or more single nucleotide variants is located at one or more loci selected from rsl7020773, rsl l5575220, rsll7987557, rsl l3371772, rsl2943567, rs371157151, rs550771753, rs61745750, or rs61745752. The method of claim 39, wherein the locus of the single nucleotide variant is rs 17020773. The method of claim 40, wherein the variant comprises a T to C nucleotide change. The method of claim 39, wherein the locus of the single nucleotide variant is rsl 15575220. The method of claim 42, wherein the variant comprises a G to T nucleotide change. The method of claim 39, wherein the locus of the single nucleotide variant comprises rs61745750 and rs61745752. The method of any one of claims 20-44, wherein the cancer is renal cell carcinoma, non-small cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, melanoma, squamous cell cancer, lung cancer, cancer of the peritoneum, hepatocellular cancer, stomach cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma and various types of head and neck cancer, B-cell lymphoma, low grade/follicular non-Hodgkin's lymphoma (NHL), small lymphocytic (SL) NHL, intermediate grade/follicular NHL, intermediate grade diffuse NHL, high grade immunoblastic NHL, high grade lymphoblastic NHL, high grade small non-cleaved cell NHL, bulky disease NHL, mantle cell lymphoma, AIDS-related lymphoma, Waldenstrom's Macroglobulinemia, chronic lymphocytic leukemia (CLL), acute lymphoblastic leukemia (ALL), Hairy cell leukemia, chronic myeloblastic leukemia, and post-transplant lymphoproliferative disorder (PTLD), or Meigs' syndrome.