Identification of high grade or ≧ CIN2 for early stages and late stages detection, screening, and diagnosis of human papillomavirus (HPV) and HPV-associated cancers

1. A method for determining a disease stage of human papillomavirus (HPV) infection in a human subject comprising:

contacting a tissue sample or a cell sample with a first one or more monoclonal antibodies, wherein

the tissue sample or the cell sample comprises protein, and the sample is obtained from a human subject;

the first one or more monoclonal antibodies specifically bind to two or more viral proteins, and the one or more monoclonal antibodies are capable of binding in situ to the viral proteins in the tissue sample or the cell sample, wherein

the viral proteins comprise two or more HPV E6 proteins from different HPV types in a clinical sample and/or two or more HPV E7 proteins from different HPV types in a clinical sample; and

said contacting takes place under conditions that promote specific binding of said one or more monoclonal antibodies;

contacting the tissue sample or the cell sample with a second one or more antibodies that specifically binds to a cellular protein;

determining presence, absence, or an amount of the two or more viral proteins in said sample that specifically binds to the first one or more monoclonal antibodies based at least in part on a measure of specific binding of the first one or more monoclonal antibodies to the sample contacted by the one or more monoclonal antibodies;

determining presence, absence, or an amount of the cellular protein in said sample that specifically binds to the second one or more antibodies based at least in part on a measure of specific binding of the second one or more antibodies to the sample contacted by the second one or more antibodies; and

determining said disease stage of papillomavirus infection in said human subject based on said determined presence, absence, or amount of the viral proteins and the cellular protein in said sample.

2. The method of claim 1 wherein said sample comprises a tissue sample, or a cell sample, and said determining comprises an immunocytochemistry assay, a immunohistochemistry assay or a flow cytometry assay.

3. The method of claim 1 wherein said determining said disease stage comprises determining the presence or absence of HSIL.

4. The method of claim 1 wherein said determining said disease stage comprises determining the presence or absence of late stage HPV infection.

5. The method of claim 1 wherein said determining said disease stage comprises determining the presence or absence of high grade dysplasia.

6. The method of claim 1 wherein said determining said disease stage comprises determining the presence or absence of a disease stage ≧CIN2.

7. The method of claim 1 wherein said disease stage is ≧CIN2 or <CIN2.

8. The method of claim 7 wherein said ≧CIN2 is CIN2/3.

9. The method of claim 1 wherein said disease stage is HSIL.

10. The method of claim 1 wherein said different HPV types comprises HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, HPV-33, HPV-39, HPV-44, HPV-45, HPV-51, HPV-52, HPV-53, HPV-58, HPV-59, and HPV-66.

11. The method of claim 10 wherein said papillomavirus comprises one or more viruses selected from the group consisting of HPV-16 and HPV-18.

12. The method of claim 1 wherein said cell sample comprises normal cells, ASC-US cells, ASC-H cells, LSIL cells, HSIL cells, ADC cells, AGC cells or SCC cells.

13. The method of claim 1 wherein said tissue sample is benign, CIN1, CIN2, CIN3, SCC, AGC or ADC.

14. The method of claim 1 further comprising:

obtaining a second sample from said human subject, said sample comprising a cell sample; and

performing a cytological Papanicolaou smear assay on said sample.

15. The method of claim 1 further comprising:

obtaining a second sample from said human subject, said sample comprising a nucleic acid; and

performing a nucleic acid hybridization assay for human papillomavirus on said sample.

16. The method of claim 1 , wherein the cellular protein is p16 INK4a .

17. The method of claim 1 , wherein the cellular protein is selected from a group comprising p16 INK4a , pRB, p53, E2F, E2F activated cell cycle protein, cyclin dependent kinase, CDK4, CDK6, Ki-67 (MIB-1), MYC protein, cyclin-A, cyclin-B, cyclin-E, telomerase-TERC, MCM2, TOP2A, heat shock protein 40 (HSP40), heat shock protein 60 (HSP60), heat shock protein 70 (HSP70), CA9/MN, Iaminin5, brn-3a, CDK N2, topoisomerase 2A, microsome maintenance protein-2, microsome maintenance protein-4, microsome maintenance protein-5, survivin, VEGF, p27 (kip1), and p21 (waf).

18. A kit for determining a disease stage of papillomavirus infection in a human subject comprising a first one or more monoclonal antibodies, wherein

the first one or more monoclonal antibodies specifically bind to two or more HPV E7 proteins from different HPV types and/or two or more HPV E6 proteins from different HPV types, and the first one or more monoclonal antibodies is capable of binding in situ to the protein in a clinical sample, wherein

the clinical sample is a tissue sample comprising proteins or a cell sample comprising proteins and the sample is obtained from a human, and

a second one or more antibodies that specifically binds to a cellular protein.

19. The method of claim 18 , wherein the cellular protein is p16 INK4a .

20. The method of claim 18 , wherein the cellular protein is selected from a group comprising p16 INK4a , pRB, p53, E2F, E2F activated cell cycle protein, cyclin dependent kinase, CDK4, CDK6, Ki-67 (MIB-1), MYC protein, cyclin-A, cyclin-B, cyclin-E, telomerase-TERC, MCM2, TOP2A, heat shock protein 40 (HSP40), heat shock protein 60 (HSP60), heat shock protein 70 (HSP70), CA9/MN, Iaminin5, brn-3a, CDK N2, topoisomerase 2A, microsome maintenance protein-2, microsome maintenance protein-4, microsome maintenance protein-5, survivin, VEGF, p27 (kip1), and p21 (waf).

21. The method of claim 18 wherein said different HPV types comprises HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, HPV-33, HPV-39 HPV-44, HPV-45, HPV-51, HPV-52, HPV-53, HPV-58, HPV-59, and HPV-66.