Human papilloma virus as predictor of cancer prognosis

1. A method of treating a subject having a squamous cell carcinoma of the head and neck (HNSCC), comprising:

acquiring knowledge that the subject is positive for a human papillomavirus (HPV+); and

administering to the subject an anti-cancer agent other than a CDK inhibitor,

thereby treating the HNSCC in the subject.

2. The method of claim 1 , wherein the anti-cancer agent is cisplatin, cetuximab, fluorouracil (5-FU), carboplatin, or paclitaxel.

3. The method of claim 1 , wherein the subject has a mutation in a phosphoinositide-3-kinase, catalytic, alpha polypeptide (PIK3CA) gene; a phosphatase and tensin homolog (PTEN) gene; or a serine/threonine kinase 11 (STK11) gene.

4. The method of claim 1 , further comprising administering an mTOR inhibitor, a PI3K inhibitor, a PI3K/mTOR inhibitor, or a PI3K/Akt/mTOR inhibitor.

5. The method of claim 4 , wherein the mTOR inhibitor is rapamycin, a rapamycin derivative, resveratrol, or everolimus.

6. The method of claim 4 , wherein the PI3K/mTOR inhibitor is BEZ235, BGT226, BKM120, LY294002 or wortmannin.

7. A kit for assessing a subject having a squamous cell carcinoma of the head and neck (HNSCC), comprising one or more of the following detection agents:

(i) one or more PCR primers for detecting an HPV in a sample from the subject;

(ii) one or more probes for detecting an HPV in a sample from the subject; or

(iii) one or more antibodies for detecting an HPV protein in a sample from the subject; and

information for identifying a therapeutic agent to treat the HNSCC in the subject.

8. The kit of claim 7 , further comprising one or more of the following:

(i) an oligonucleotide that hybridizes specifically to a mutation in a functional domain of a mutant gene; or

(ii) an antibody which specifically binds to a mutant polypeptide associated with the HNSCC.

9. The kit of claim 7 , comprising:

a first antibody which binds specifically to the HPV protein or a mutant polypeptide associated with the HNSCC.

10. The kit of claim 9 , further comprising:

a second, different antibody which binds to either the mutant polypeptide or the first antibody,

wherein the second antibody is conjugated to a detectable agent.

11. A system or device for producing a report recording the presence or absence of HPV in a subject, said system or device comprising one or more of the following:

(i) a component for containing a sample from the subject;

(ii) a detection component capable of identifying the presence or absence of the HPV; and

(iii) a means for outputting the report.

12. The system or device of claim 11 , wherein the detection component is further capable of identifying the presence or absence of a mutant cell cycle gene.

13. The system or device of claim 12 , wherein the detection component identifies a gene or gene fragment described in Table 1 or Table 4.

14. The system or device of claim 12 , wherein the system or device is a sequencing device.

15. The system or device of claim wherein the mutant cell cycle gene is chosen from CDKN12A, CDKN2B, CCNE1, CCND1, CCND2, CCND3, CDK4 or CDK6.

16. The system or device of claim 15 , wherein the mutant cell cycle gene is detected in a nucleic acid molecule by one or more of: sequencing, a nucleic acid hybridization assay, an amplification-based assay, a PCR-RFLP assay, real-time PCR, screening analysis, FISH, spectral karyotyping, MFISH, comparative genomic hybridization, in situ hybridization, SSP, HPLC or mass-spectrometric genotyping.

17. A method for determining the likely effectiveness of a therapeutic option for a subject with a cancer, said method comprising:

(1) subjecting a sample from the subject to a sequencing device for producing a genotype report, said sequencing device comprising one or more of the following:

(i) a component for containing the sample;

(ii) a detection component capable of identifying the presence or absence of a mutant gene; and

(iii) a means for outputting the genotype report;

(2) identifying a sequence, an alteration, or a mutation of the mutant gene;

(3) determining the therapeutic option based on step (2); and

(4) providing a report of the therapeutic option based on the determination of step (3).

18. A method of evaluating a patient or a patient population, comprising:

identifying, selecting, or obtaining information or knowledge that the patient or the patient population has participated in a clinical trial;

acquiring information or knowledge of the presence of HPV in the patient or the patient population;

acquiring genotype information of the patient or the patient population that identifies a mutant gene as being present in the patient or the patient population;

acquiring a sequence for a nucleic acid molecule described in Table 1 or Table 4; or

detecting the presence of a mutant nucleic acid molecule or polypeptide in the patient or the patient population;

wherein the absence of HPV in the patient or the patient population identifies the patient or patient population as a candidate to receive treatment with a CDK inhibitor; and

wherein the presence of HPV identifies the patient or patient population as a candidate to receive treatment with an anti-cancer agent other than a CDK inhibitor.

19. The method of claim 1 , wherein the HNSCC is localized.

20. The method of claim 1 , wherein the subject has metastatic cancer.

21. A method for generating a personalized cancer treatment report, comprising:

acquiring a sample from a subject having an HNSCC,

determining whether the subject is HPV− or HPV+, and

selecting a treatment based on the whether the subject is HPV− or HPV+, wherein:

(i) if the subject is HPV+, an anti-cancer agent other than a CDK inhibitor is selected as a treatment, or

(ii) if the subject is HPV−, a CDK inhibitor is selected as a treatment.

22. The method of claim 21 , wherein the cancer treatment report comprises one or more of the following: (i) information on the HPV status of the subject;

(ii) information on prognosis, resistance, or potential therapeutic options;

(iii) information on the likely effectiveness of a therapeutic option;

(iv) the acceptability of a therapeutic option, or the advisability of applying the therapeutic option to the subject; or

(v) information on the administration of a drug.

23. The method of claim 21 , comprising generating the cancer treatment report to memorialize when the subject is tested for the presence of HPV.

24. The method of claim 1 , further comprising one or more of administering a radiation therapy to the subject or performing a surgery on the subject.

25. The method of claim 1 , wherein the anti-cancer agent is chosen from 4-hydroxyperoxycyclophosphoramide, 5-fluorodeoxyuridine (5-FUdR), 5-azacytidine, 6-mercaptopurine, 6-thioguanine, actinomycin D, amsacrine, bis-chloroethylnitrosurea, bleomycin, bryostatin-1, busulfan, chlorambucil, colchicine, cyclophosphamide, cytarabine, cytosine arabinoside, dacarbazine, daunorubicin, daunomycin, dactinomycin, deoxycoformycin, diethylstilbestrol (DES), doxorubicin, etoposide (VP-16), epirubicin, esorubicin, gemcitabine, hexamethylmelamine, hydroxyprogesterone, hydroxyurea, idarubicin, ifosfamide, irinotecan, mafosfamide, melphalan, methotrexate (MTX), methylcyclohexylnitrosurea, mithramycin, mitomycin C, mitoxantrone, nitrogen mustards, pentamethylmelamine, prednisone, procarbazine, tamoxifen, taxol, teniposide, testosterone, trimetrexate, topotecan, vincristine, or vinblastine.