Methods for detecting human papillomavirus and providing prognosis for head and neck squamous cell carcinoma

Abstract

Methods and kits for diagnosing and determining prognosis of head and neck squamous cell carcinoma are described. An exemplary method for diagnosing head and neck squamous cell carcinoma (HNSCC) in a subject may comprise assaying a saliva sample from the subject for the presence of total protein, solCD44, and HPV, and using the combination of total protein, HPV, and CD44 levels in a multivariate analysis to determine a combined score, whereby an increase in score above a cut-off point distinguishes subjects with HNSCC, or an elevated risk of future occurrence thereof, from subjects without HNSCC or at low risk of future occurrence thereof.

What is claimed is: 
     
         1 . A method for diagnosing head and neck squamous cell carcinoma (HNSCC) in a subject, comprising assaying a saliva sample from the subject for the presence of total protein, solCD44, and HPV, and using the combination of total protein, HPV, and CD44 levels in a multivariate analysis to determine a combined score, whereby an increase in score above a cut-off point distinguishes subjects with HNSCC, or an elevated risk of future occurrence thereof, from subjects without HNSCC or at low risk of future occurrence thereof. 
     
     
         2 . A method for determining the prognosis of a subject diagnosed with (HNSCC), comprising assaying a saliva sample from the subject for the presence of total protein, solCD44, and HPV, using the combination of total protein, HPV, and CD44 levels in a multivariate analysis to determine a combined score, whereby an increase in score above a cut-off point is associated with worse prognosis. 
     
     
         3 . The method of any one of  claims 1  to  2 , further comprising treating the subject diagnosed with HNSCC or determined to have a poor prognosis with surgery, radiation therapy, chemotherapy, photodynamic therapy, targeted therapy, or any combination thereof. 
     
     
         4 . The method of any one of  claims 1  to  3 , wherein HPV is detected by detecting p16 INK4a . 
     
     
         5 . The method of any one of  claims 1  to  3 , wherein HPV is detected by detecting HPV DNA or RNA, HPV protein, or epigenetic changes. 
     
     
         6 . The method of any one of  claims 1  to  5 , further comprising assessing the subject for one or more risk factors or demographic factors selected from the group consisting of tobacco exposure, alcohol exposure, race, ethnicity, oral health, gender, level of education, and age, and using the one or more risk factors or demographic factors in the multivariate analysis to determine the combined score. 
     
     
         7 . The method of any one of  claims 1  to  6 , wherein the saliva sample is an oral rinse. 
     
     
         8 . A kit, comprising:
 at least one antibody that specifically binds p16 INK4a ;   at least one antibody that specifically binds CD44; and   a reagent for determining total protein concentration in a sample.   
     
     
         9 . The kit of  claim 8 , wherein the at least one antibody that specifically binds p16 INK4a  comprises the idiotype of the E6H4 antibody clone. 
     
     
         10 . The kit of  claim 8  or  9 , further comprising a CD44 reference sample, a p16 reference sample, or a combination thereof. 
     
     
         11 . The kit of any one of  claims 8  to  10 , further comprising one or more colorimetric agents for the detection of the antibody that specifically binds p16 INK4a , the antibody that specifically binds CD44, or a combination thereof. 
     
     
         12 . The kit of any one of  claims 8  to  11 , wherein the kit is a lateral flow immunoassay. 
     
     
         13 . The kit of any one of  claims 8  to  11 , wherein the kit comprises a multi-well plate optionally coated with the antibody that specifically binds p16 INK4a , the antibody that specifically binds CD44, or a combination thereof.