Biomarkers for the detection of head and neck tumors

Abstract

A method of detecting the presence of specific human papilloma virus and host cell biomarkers associated with head and neck tumors in biological samples, like saliva, blood or biopsy tissue, obtained from a subject.

What is claimed is: 
     
         1 . A method of detecting biomarkers associated with head and neck tumors in a patient comprising:
 (a) providing a first patient sample from the patient, wherein the first patient sample is selected from the group consisting of saliva, whole blood, white blood cells, serum, plasma and biopsy tissue from the throat, oropharynx or mouth of the patient;   (b) contacting the first patient sample with:
 (1) a first reagent that specifically binds to one or more than one HPV (human papillomavirus) biomarker, and allowing the first reagent to bind to the one or more than one HPV biomarker if the HPV biomarker is present in the first patient sample; and 
 (2) a second reagent that specifically binds to one or more than one host cell biomarker, wherein the host cell biomarker is differentially expressed in head and neck tumor cells as compared to normal cells, and allowing the second reagent to bind to the one or more than one host cell biomarker; 
 where the first reagent binds to the one or more than one HPV biomarker if the HPV biomarker is present in the first patient sample, and the second reagent binds to the one or more than one host cell biomarker simultaneously; 
   (c) simultaneously detecting the presence or absence of the HPV biomarker in the first patient sample and determining the expression level of the host cell biomarker in the first patient sample; and   (d) comparing the expression level of the host cell biomarker in the first patient sample to an expression level of the host cell biomarker from at least one reference sample, wherein the reference sample is a comparable biological sample obtained from a disease-free subject.   
     
     
         2 . The method of  claim 1 , wherein the first reagent is an oligonucleotide and the HPV biomarker is an HPV-specific nucleic acid. 
     
     
         3 . The method of  claim 2 , wherein the HPV biomarker is an HPV mRNA or a complement thereof. 
     
     
         4 . The method of  claim 3 , wherein the HPV mRNA is selected from the group consisting of E2 mRNA, E6 mRNA and E7 mRNA. 
     
     
         5 . The method of  claim 1 , wherein the first reagent is an antibody and the HPV biomarker is a HPV polypeptide. 
     
     
         6 . The method of  claim 1 , wherein the first reagent is a HPV antigen and the HPV biomarker is an anti-HPV antibody. 
     
     
         7 . The method of  claim 1 , wherein the one or more than one HPV biomarker is a plurality of HPV biomarkers. 
     
     
         8 . The method of  claim 1 , wherein the one or more than one host cell biomarker is a plurality of host cell biomarkers. 
     
     
         9 . The method of  claim 1 , wherein the host cell biomarker is selected from the group consisting of: H3F3A, TPT1, FTH1, NCOA4, ARCR, IGF-II, IGF-BP3, soluble α chain of the IL-15 receptor, IL1B, OAZ1, SAT, IL-8, S100P, DUSP1, LAMC2, COL4A1, COL1A1, PADI1, HA3 and CD44. 
     
     
         10 . The method of  claim 1 , wherein the host cell biomarker is selected from the group consisting of AL833646, BF055370, BUB1B, CCDC5, CCNA1, CCNB1, CCND1, CCND2, CCNE2, CDC2, CDC7, CDK2, CDKN2A, CDKN2B, CDKN2C, CENPF, CHEK1, E2F2, E2F3, E2F7, EHHADH, EREG, FKSG14, 10 FLJ31952, F1137881, FLJ39749, FLJ42662, F114628, GADD45G, GAS1, HCAP-G, KIF2C, KIRREL, KLK10, KNTC1, MCM2, MCM3, MCM6, MCM7, MCM8, MCM10, MGC24665, MTB, MYNN, NAP1L2, NR1D2, ORC1L, ORC3L, PARC, PCNA, RFC4, RIBC2, RPA2, SESN3, SMC2L1, SMC4L1, STAG3, SYCP2, SYNGR3, TAF7L, TCAM1, TFDP1 and TP53. 
     
     
         11 . The method of  claim 1 , wherein the second reagent is an oligonucleotide and the host cell biomarker is a nucleic acid. 
     
     
         12 . The method of  claim 11 , wherein the host cell biomarker is a host cell mRNA or a complement thereof. 
     
     
         13 . The method of  claim 1 , wherein the HPV biomarker or the host cell biomarker is DNA. 
     
     
         14 . The method of  claim 13 , wherein the DNA is a CpG containing promoter, the method further comprising determining whether or not the CpG-containing promoter is aberrantly methylated by comparing the methylation of the CpG-containing promoter in the biological sample to the methylation of said CpG-containing promoter for at least one reference sample, wherein the reference sample is a comparable biological sample obtained from a disease-free subject. 
     
     
         15 . The method of  claim 14 , wherein the CpG containing promoter is selected from the group consisting of: DAPK1, RARB, TWIST1, TIMP3, APC, KLK10, TP73, CDH13, IGSF4, FHIT, ESR1, CHFR, NOL4, LHFPL4, SOX1, PAX1, LMX1A, NKX6-1, WT-1 and ONECUT1. 
     
     
         16 . The method of  claim 1 , wherein the HPV biomarker is DNA. 
     
     
         17 . The method of  claim 16 , further comprising distinguishing between a high risk strain of HPV and a low risk strain of HPV. 
     
     
         18 . The method of  claim 16 , further comprising identifying HPV16 DNA or HPV18 DNA. 
     
     
         19 . The method of  claim 1 , further comprising comparing the expression level of the host cell marker in the first patient sample to the expression level of the host cell marker for one or more than one additional reference sample, wherein the additional reference sample is a comparable biological sample obtained from a patient with an HPV positive head and neck tumor or a patient with an HPV negative head and neck tumor. 
     
     
         20 . The method of  claim 1 , further comprising:
 (e) contacting a second patient sample from the patient with:
 (1) a reagent that specifically binds to a HPV biomarker, and 
 (2) a reagent that specifically binds to a host cell marker differentially expressed in head and neck tumor cells as compared to normal cells; 
   (f) detecting the presence or absence of the HPV marker; and   (g) determining the expression level of the host cell biomarker in the second patient sample;   wherein the first patient sample is saliva and the second patient sample is selected from the group consisting of whole blood, blood cells, serum, plasma, or a tissue sample from the throat, oropharynx or mouth.   
     
     
         21 . A method of detecting a human papillomavirus positive head and neck cancer in a patient comprising detecting biomarkers associated with head and neck tumors in the patient according to  claim 1 , and wherein the presence of the HPV biomarker and an expression level of the host cell biomarker from the first patient sample above the expression level from the at least one reference sample indicates the presence of human papillomavirus positive head and neck cancer in the patient. 
     
     
         22 . A method of detecting biomarkers associated with head and neck tumors in a patient comprising:
 (a) providing a patient sample from the patient, wherein the patient sample is selected from the group consisting of saliva, whole blood, white blood cells, serum, plasma and biopsy tissue from the throat, oropharynx or mouth of the patient;   (b) contacting the patient sample with:
 (1) a first reagent that specifically binds to one or more than one HPV (human papillomavirus) biomarker, and allowing the first reagent to bind to the one or more than one HPV biomarker if the HPV biomarker is present in the patient sample; and 
 (2) a second reagent that specifically binds to one or more than one host cell biomarker, wherein the host cell biomarker is differentially expressed in HPV positive head and neck tumor cells as compared to HPV negative head and neck tumor cells, and allowing the second reagent to bind to the one or more than one host cell biomarker; 
 where the first reagent binds to the one or more than one HPV biomarker if the HPV biomarker is present in the patient sample, and the second reagent binds to the one or more than one host cell biomarker simultaneously; 
   (c) simultaneously detecting the presence or absence of the HPV biomarker in the patient sample and determining the expression level of the host cell biomarker in the patient sample; and   (d) comparing the expression level of the host cell biomarker in the patient sample to an expression level of the host cell biomarker from at least one reference sample, wherein the reference sample is a comparable biological sample obtained from a patient with an HPV negative head and neck tumor.   
     
     
         23 . The method of  claim 22 , wherein the first reagent is an oligonucleotide and the HPV biomarker is an HPV-specific nucleic acid. 
     
     
         24 . The method of  claim 23 , wherein the HPV biomarker is an HPV mRNA or a complement thereof. 
     
     
         25 . The method of  claim 24 , wherein the HPV mRNA is selected from the group consisting of E2 mRNA, E6 mRNA and E7 mRNA. 
     
     
         26 . The method of  claim 22 , wherein the first reagent is an antibody and the HPV biomarker is a HPV polypeptide. 
     
     
         27 . The method of  claim 22 , wherein the first reagent is a HPV antigen and the HPV biomarker is an anti-HPV antibody. 
     
     
         28 . The method of  claim 22 , wherein the one or more than one HPV biomarker is a plurality of HPV biomarkers. 
     
     
         29 . The method of  claim 22 , wherein the second reagent is an oligonucleotide and the host cell biomarker is a nucleic acid. 
     
     
         30 . The method of  claim 29 , wherein the host cell biomarker is a host cell mRNA or a complement thereof. 
     
     
         31 . The method of  claim 22 , wherein the HPV biomarker or the host cell biomarker is DNA. 
     
     
         32 . The method of  claim 31 , wherein the DNA is a CpG containing promoter, the method further comprising determining whether or not the CpG-containing promoter is aberrantly methylated by comparing the methylation of the CpG-containing promoter in the biological sample to the methylation of said CpG-containing promoter for at least one reference sample, wherein the reference sample is a comparable biological sample obtained from a disease-free subject. 
     
     
         33 . The method of  claim 32 , wherein the CpG containing promoter is selected from the group consisting of: DAPK1, RARB, TWIST1, TIMP3, APC, KLK10, TP73, CDH13, IGSF4, FHIT, ESR1, CHFR, NOL4, LHFPL4, SOX1, PAX1, LMX1A, NKX6-1, WT-1 and ONECUT1. 
     
     
         34 . The method of  claim 22 , wherein the HPV biomarker is DNA. 
     
     
         35 . The method of  claim 34 , further comprising distinguishing between a high risk strain of HPV and a low risk strain of HPV. 
     
     
         36 . The method of  claim 34 , further comprising identifying HPV16 DNA or HPV18 DNA. 
     
     
         37 . The method of  claim 22 , further comprising comparing the expression level of the host cell marker in the patient sample to the expression level of the host cell marker for one or more than one additional reference sample, wherein the additional reference sample is a comparable biological sample obtained from a patient with an HPV positive head and neck tumor or a patient with an HPV negative head and neck tumor. 
     
     
         38 . The method of  claim 22 , further comprising:
 (e) contacting a second patient sample from the patient with:
 (1) a reagent that specifically binds to a HPV biomarker, and 
 (2) a reagent that specifically binds to a host cell marker differentially expressed in head and neck tumor cells as compared to normal cells; 
   (f) detecting the presence or absence of the HPV marker; and   (g) determining the expression level of the host cell biomarker in the second patient sample;   wherein the first patient sample is saliva and the second patient sample is selected from the group consisting of whole blood, blood cells, serum, plasma, or a tissue sample from the throat, oropharynx or mouth.   
     
     
         39 . The method of  claim 22 , wherein the host cell biomarker is selected from the group consisting of AL833646, BF055370, BUB1B, CCDC5, CCNA1, CCNB1, CCND1, CCND2, CCNE2, CDC2, CDC7, CDK2, CDKN2A, CDKN2B, CDKN2C, CENPF, CHEK1, E2F2, E2F3, E2F7, EHHADH, EREG, FKSG14, 10 FLJ31952, FLJ37881, FLJ39749, F1142662, F114628, GADD45G, GAS1, HCAP-G, KIF2C, KIRREL, KLK10, KNTC1, MCM2, MCM3, MCM6, MCM7, MCM8, MCM10, MGC24665, MTB, MYNN, NAP1L2, NR1D2, ORC1L, ORC3L, PARC, PCNA, RFC4, RIBC2, RPA2, SESN3, SMC2L1, SMC4L1, STAG3, SYCP2, SYNGR3, TAF7L, TCAM1, TFDP1 and TP53. 
     
     
         40 . A method of detecting a human papillomavirus negative head and neck cancer in a patient comprising detecting biomarkers associated with head and neck tumors in the patient according to  claim 22 , and wherein the absence of the HPV biomarker and an expression level of the host cell biomarker from the patient sample at the same as the expression level from the reference sample indicates the presence of human papillomavirus negative head and neck cancer in the patient.