Compositions and Methods for Identification, Assessment, Prevention, and Treatment of Cancer Using PD-L1 Isoforms

Abstract

The present invention relates to methods for identifying, assessing, preventing, and treating cancer (e.g., head, neck, and/or lung cancers in humans). A variety of PD-L1 isoforni biomarkers are provided, wherein alterations in the copy number of one or more of the biomarkers and/or alterations in the amount, structure, and/or activity of one or more of the biomarkers is associated with cancer status and indicates amenability to treatment or prevention by modulating PD-1 and/or PD-L! levels.

What is claimed: 
     
         1 . A method of determining whether a subject is afflicted with a head, neck, or lung cancer or at risk for developing a head, neck, or lung cancer, the method comprising:
 a) obtaining a biological sample from the subject;   b) determining the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof in the subject sample;   c) determining the copy number, level of expression, or level of activity of the one or more biomarkers in a control; and   d) comparing the copy number, level of expression, or level of activity of said one or more biomarkers detected in steps b) and c);   wherein a significant increase in the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample relative to the control copy number, level of expression, or level of activity of the one or more biomarkers indicates that the subject is afflicted with the head, neck, or lung cancer or is at risk for developing the head, neck, or lung cancer.   
     
     
         2 . A method of determining whether a subject afflicted with a head, neck, or lung cancer or at risk for developing a head, neck, or lung cancer would benefit from modulating PD-1 and/or PD-L1 levels, the method comprising:
 a) obtaining a biological sample from the subject;   b) determining the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof in the subject sample;   c) determining the copy number, level of expression, or level of activity of the one or more biomarkers in a control; and   d) comparing the copy number, level of expression, or level of activity of said one or more biomarkers detected in steps b) and c);   wherein a significant increase in the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample relative to the control copy number, level of expression, or level of activity of the one or more biomarkers indicates that the subject afflicted with the head, neck, or lung cancer or at risk for developing the head, neck, or lung cancer would benefit from modulating PD-L1 and/or PD-L1 levels.   
     
     
         3 . A method for monitoring the progression of a head, neck, or lung cancer in a subject, the method comprising:
 a) detecting in a subject sample at a first point in time the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof;   b) repeating step a) at a subsequent point in time; and   c) comparing the copy number, level of expression, or level of activity of said one or more biomarkers detected in steps a) and b) to monitor the progression of the head, neck, or lung cancer.   
     
     
         4 . The method of any one of  claims 1 - 3 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15. 
     
     
         5 . The method of  claim 3 , wherein an at least twenty percent increase or an at least twenty percent decrease between the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample at a first point in time relative to the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample at a subsequent point in time indicates progression of the head, neck, or lung cancer; or wherein less than a twenty percent increase or less than a twenty percent decrease between the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample at a first point in time relative to the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample at a subsequent point in time indicates a lack of significant progression of the head, neck, or lung cancer. 
     
     
         6 . The method of  claim 3 , wherein between the first point in time and the subsequent point in time, the subject has undergone treatment to modulate PD-1 and/or PD-L1 levels. 
     
     
         7 . A method for stratifying subjects afflicted with a head, neck, or lung cancer according to predicted clinical outcome of treatment with one or more modulators of PD-1 and/or PD-L1 levels, the method comprising:
 a) determining the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof in a subject sample;   b) determining the copy number, level of expression, or level of activity of the one or more biomarkers in a control sample; and   c) comparing the copy number, level of expression, or level of activity of said one or more biomarkers detected in steps a) and b);   wherein a significant modulation in the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample relative to the normal copy number, level of expression, or level of activity of the one or more biomarkers in the control sample predicts the clinical outcome of the patient to treatment with one or more modulators of PD-1 and/or PD-L1 levels.   
     
     
         8 . The method of  claim 7 , wherein the predicted clinical outcome is (a) cellular growth, (b) cellular proliferation, or (c) survival time resulting from treatment with one or more modulators of PD-1 and/or PD-L1 levels. 
     
     
         9 . The method of  claim 7 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         10 . The method of  claim 7 , wherein an at least twenty percent increase or an at least twenty percent decrease between the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample compared to the control sample predicts that the subject has a poor clinical outcome; or wherein less than a twenty percent increase or less than a twenty percent decrease between the copy number, level of expression, or level of activity of the one or more biomarkers in the subject sample compared to the control sample predicts that the subject has a favorable clinical outcome. 
     
     
         11 . The method of  claim 7 , further comprising treating the subject with a therapeutic agent that specifically modulates the copy number, level of expression, or level of activity of the one or more biomarkers. 
     
     
         12 . The method of  claim 7 , further comprising treating the subject with one or more modulators of PD-1 and/or PD-L1 levels. 
     
     
         13 . A method of determining the efficacy of a test compound for inhibiting a head, neck, or lung cancer in a subject, the method comprising:
 a) determining the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof in a first sample obtained from the subject and exposed to the test compound;   b) determining the copy number, level of expression, or level of activity of the one or more biomarkers in a second sample obtained from the subject, wherein the second sample is not exposed to the test compound, and   c) comparing the copy number, level of expression, or level of activity of the one or more biomarkers in the first and second samples,   wherein a significantly modulated copy number, level of expression, or level of activity of the biomarker, relative to the second sample, is an indication that the test compound is efficacious for inhibiting the head, neck, or lung cancer in the subject.   
     
     
         14 . The method of  claim 13 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO:13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         15 . The method of  claim 13 , wherein the first and second samples are portions of a single sample obtained from the subject or portions of pooled samples obtained from the subject. 
     
     
         16 . A method of determining the efficacy of a therapy for inhibiting a head, neck, or lung cancer in a subject, the method comprising:
 a) determining the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof in a first sample obtained from the subject prior to providing at least a portion of the therapy to the subject;   b) determining the copy number, level of expression, or level of activity of the one or more biomarkers in a second sample obtained from the subject following provision of the portion of the therapy; and   c) comparing the copy number, level of expression, or level of activity of the one or more biomarkers in the first and second samples,   wherein a significantly decreased copy number, level of expression, or level of activity of the one or more biomarkers in the second sample, relative to the first sample, is an indication that the therapy is efficacious for inhibiting the head, neck, or lung cancer in the subject.   
     
     
         17 . The method of  claim 16 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO:13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         18 . A method for identifying a compound which inhibits a head, neck, or lung cancer, the method comprising:
 a) contacting one or more biomarkers listed in Table 1 or a fragment thereof with a test compound; and   b) determining the effect of the test compound on the copy number, level of expression, or level of activity of the one or more biomarkers to thereby identify a compound which inhibits the head, neck, or lung cancer.   
     
     
         19 . The method of  claim 18 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         20 . The method of  claim 18 , wherein the one or more biomarkers is expressed on or in a cell. 
     
     
         21 . The method of  claim 20 , wherein said cells are isolated from an animal model of a head, neck, or lung cancer. 
     
     
         22 . The method of  claim 20 , wherein said cells are from a subject afflicted with a head, neck, or lung cancer. 
     
     
         23 . A method for inhibiting a head, neck, or lung cancer, the method comprising contacting a cell with an agent that modulates the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof to thereby inhibit the cancer. 
     
     
         24 . The method of  claim 23 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         25 . The method of  claim 23 , wherein the copy number, level of expression, or level of activity of the one or more biomarkers is downmodulated. 
     
     
         26 . The method of  claim 23 , wherein the step of contacting occurs in vivo, ex vivo, or in vitro. 
     
     
         27 . The method of  claim 23 , further comprising contacting the cell with an additional agent that inhibits the head, neck, or lung cancer. 
     
     
         28 . A method for treating a subject afflicted with a head, neck, or lung cancer, the method comprising administering an agent that downregulates the copy number, level of expression, or level of activity of one or more biomarkers listed in Table 1 or a fragment thereof such that the head, neck, or lung cancer is treated. 
     
     
         29 . The method of  claim 28 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         30 . The method of  claim 28 , further comprising administering one or more additional agents that treats the cancer. 
     
     
         31 . The method of  claim 28 , wherein the agent is one or more modulators of PD-1 levels. 
     
     
         32 . The method of  claim 28 , wherein the agent is one or more modulators of PD-L1 levels. 
     
     
         33 . A pharmaceutical composition comprising an antisense polynucleotide that specifically binds to a polynucleotide of one or more biomarkers listed in Table 1 or a fragment thereof useful for treating a head, neck, or lung cancer in a pharmaceutically acceptable carrier. 
     
     
         34 . The pharmaceutical composition of  claim 33 , wherein the antisense polynucleotide further comprises an expression vector. 
     
     
         35 . A method of using the pharmaceutical composition of  claims 33  or  34  for treating a head, neck, or lung cancer in a subject. 
     
     
         36 . A kit comprising an agent which selectively binds to one or more biomarkers listed in Table 1 or a fragment thereof and instructions for use. 
     
     
         37 . The kid of  claim 36 , wherein the agent is selected from the group consisting of polynucleotides and antibodies. 
     
     
         38 . A biochip comprising a solid substrate, said substrate comprising one or more probes capable of detecting one or more biomarkers listed in Table 1 or a fragment thereof wherein each probe is attached to the substrate at a spatially defined address. 
     
     
         39 . The biochip of  claim 51 , wherein the probes are complementary to a genomic or transcribed polynucleotide associated with the one or more biomarkers. 
     
     
         40 . The pharmaceutical composition of  claim 33 , the kit of  claim 36 , or the biochip of  claim 38 , wherein the one or more biomarkers comprises soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO:13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         41 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the control is determined from a non-cancerous sample from the subject or member of the same species to which the subject belongs. 
     
     
         42 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the sample consists of or comprises body fluid, cells, cell lines, histological slides, paraffin embedded tissue, fresh frozen tissue, fresh tissue, biopsies, blood, plasma, serum, buccal scrape, saliva, cerebrospinal fluid, urine, stool, mucus, or bone marrow, obtained from the subject. 
     
     
         43 . The method of  claim 42 , wherein the body fluid is selected from group consisting of amniotic fluid, aqueous humor, bile, blood and blood plasma, cerebrospinal fluid, cerumen and earwax, cowper's fluid or pre-ejaculatory fluid, chyle, chyme, stool, female ejaculate, interstitial fluid, intracellular fluid, lymph, menses, breast milk, mucus, pleural fluid, peritoneal fluid, pus, saliva, sebum, semen, serum, sweat, synovial fluid, tears, urine, vaginal lubrication, vitreous humor, and vomit. 
     
     
         44 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the copy number is assessed by microarray, quantitative PCR (qPCR), high-throughput sequencing, comparative genomic hybridization (CGH), or fluorescent in situ hybridization (FISH). 
     
     
         45 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the expression level of the one or more biomarkers is assessed by detecting the presence in the samples of a polynucleotide molecule encoding the biomarker or a portion of said polynucleotide molecule. 
     
     
         46 . The method of  claim 44 , wherein the polynucleotide molecule is a mRNA, cDNA, or functional variants or fragments thereof and, optionally, wherein the step of detecting further comprises amplifying the polynucleotide molecule. 
     
     
         47 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the expression level of the one or more biomarkers is assessed by annealing a nucleic acid probe with the sample of the polynucleotide encoding the one or more biomarkers or a portion of said polynucleotide molecule under stringent hybridization conditions. 
     
     
         48 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the expression level of the biomarker is assessed by detecting the presence in the samples of a protein of the biomarker, a polypeptide, or protein fragment thereof comprising said protein. 
     
     
         49 . The method of  claim 48 , wherein the presence of said protein, polypeptide or protein fragment thereof is detected using a reagent which specifically binds with said protein, polypeptide or protein fragment thereof. 
     
     
         50 . The method of  claim 49 , wherein the reagent is selected from the group consisting of an antibody, an antibody derivative, and an antibody fragment. 
     
     
         51 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the activity level of the biomarker is assessed by determining the magnitude of modulation of the activity or expression level of downstream targets of the one or more biomarkers. 
     
     
         52 . The method of any one of  claims 1 ,  6 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the agent or test compound modulates PD-1, PD-L1, and or soluble PD-L1 levels. 
     
     
         53 . The method of  claim 52 , wherein the agent or test compound inhibits the expression and/or activity of soluble PD-L1, optionally wherein the soluble PD-L1 a) comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15; or b) comprises a nucleic acid molecule comprising a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 1. 
     
     
         54 . The method of  claim 53 , wherein the agent or test compound is an antibody against soluble PD-L1, optionally wherein the soluble PD-L1 comprises an amino acid sequence of SEQ ID NO: 13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO:13 or 15. 
     
     
         55 . The method of  claim 52 , wherein the agent or test compound is a small molecule inhibitor of soluble PD-L1, optionally wherein the soluble PD-L1 comprises an amino acid sequence of SEQ ID NO:13 or 15 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13 or 15. 
     
     
         56 . The method of  claim 52 , wherein the agent or test compound is an anti-PD-L1 inhibitor selected from the group consisting of a small molecule, antisense nucleic acid, interfering RNA, shRNA, siRNA, aptamer, ribozyme, and dominant-negative protein binding partner. 
     
     
         57 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 ,  28 , and  35 , wherein the head or neck cancer is squamous cell carcinomas of the head and neck (SCCHN) or associated with human papillomavirus infection. 
     
     
         58 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 ,  28 , and  35 , wherein the lung cancer is small-cell lung carcinoma (SCLC) or non-small-cell lung carcinoma (NSCLC). 
     
     
         59 . The method of any one of  claims 1 ,  2 ,  3 ,  7 ,  13 ,  16 ,  18 ,  23 , and  28 , wherein the subject is a mammal. 
     
     
         60 . The method of  claim 59 , wherein the mammal is a human.