Salivary Transcriptomic and Microbial Biomarkers for Pancreatic Cancer

Abstract

The present invention relates to the identification of pancreatic cancer biomarkers for the detection of early pancreatic cancer. The present invention also provides methods of diagnosing pancreatic cancer and distinguishing between pancreatic cancer and chronic pancreatitis. The present invention additionally provides kits that find use in the practice of the methods of the invention.

1 . A method of diagnosing pancreatic cancer in a subject, the method comprising the steps of:
 (a) analyzing a saliva sample from the subject with an assay that specifically detects a marker selected from the group consisting of a nucleic acid or polypeptide encoded by a nucleic acid listed in  FIG. 4  and a microbe listed in  FIG. 5 ; and   (b) comparing the level of expression of the marker to a control to determine whether or not the marker is differentially expressed in the sample as compared to the control; thereby providing a diagnosis for pancreatic cancer.   
     
     
         2 . The method of  claim 1 , wherein the assay detects more than one marker. 
     
     
         3 . The method of  claim 1 , wherein the assay detects protein and is ELISA, Western blotting, flow cytometry, immunofluorescence, immunohistochemistry, or mass spectroscopy. 
     
     
         4 . The method of  claim 1 , wherein the assay detects nucleic acid and is mass spectroscopy, PCR, microarray hybridization, thermal cycle sequencing, capillary array sequencing, or solid phase sequencing. 
     
     
         5 . The method of  claim 1 , wherein the assay comprises a reagent that binds to a protein. 
     
     
         6 . The method of  claim 5 , wherein the reagent is an antibody. 
     
     
         7 . The method of  claim 6 , wherein the reagent is a monoclonal antibody. 
     
     
         8 . The method of  claim 1 , wherein the assay comprises a reagent that binds to a nucleic acid. 
     
     
         9 . The method of  claim 8 , wherein the reagent is a nucleic acid. 
     
     
         10 . The method of  claim 9 , wherein the reagent is an oligonucleotide. 
     
     
         11 . The method of  claim 10 , wherein the reagent is an RT-PCR primer set. 
     
     
         12 . The method of  claim 5 , wherein the assay is ELISA, Western blotting, flow cytometry, immunofluorescence, immunohistochemistry, or mass spectroscopy. 
     
     
         13 . The method of  claim 1 , wherein the analyzing step comprises analyzing the saliva sample from the subject with an assay that specifically detects the markers KRAS, MBD3L2, ACRV1, and DPMI, and wherein the comparing step comprises determining whether or not KRAS, MBD3L2, ACRV1, and DPMI are differentially expressed in the sample. 
     
     
         14 . The method of  claim 1 , wherein the marker distinguishes between chronic pancreatitis and pancreatic cancer. 
     
     
         15 . The method of  claim 14 , wherein the markers are CDKL, MBD3L2, and KRAS and they are all detected. 
     
     
         16 - 26 . (canceled) 
     
     
         27 . The method of  claim 1 , wherein the analyzing step comprises analyzing the saliva sample from the subject with an assay that specifically detects  Neisseria elongate  and  Streptococcus mitis  or  Granulicatella adiacens  and  Streptococcus mitis , and wherein the comparing step comprises determining whether or not the levels of  Neisseria elongate  and  Streptococcus mitis  or  Granulicatella adiacens  and  Streptococcus mitis  have increased or decreased in the sample relative to a control. 
     
     
         28 . (canceled) 
     
     
         29 . The method of  claim 28 , wherein the markers are  Granulicatella adiacens  and  Streptococcus mitis  and they are both detected. 
     
     
         30 . A kit for diagnosing pancreatic cancer in a subject, the kit comprising a reagent that specifically detects a marker selected from the group consisting of a nucleic acid or polypeptide encoded by a nucleic acid listed in  FIG. 4  and a microbe listed in  FIG. 5 . 
     
     
         31 . The kit of  claim 30 , wherein the kit comprises reagents that specifically detect the markers KRAS, MBD3L2, ACRV1, and DPMI. 
     
     
         32 . (canceled) 
     
     
         33 . The kit of  claim 30 , wherein the kit comprises reagents that specifically detect the markers  Granulicatella adiacens  and  Streptococcus mitis .