Salivary Biomarkers for Gastric Cancer Detection

Abstract

Disclosed herein are biomarkers related to gastric cancer. The presently identified salivary biomarkers create the basis for a gastric cancer detection bioassay with sensitivity and specificity. Means and methods for evaluating the data generated using multiple biomarkers in order to validate findings and further use of the multiplexed gastric cancer assay in clinical, diagnostic and therapeutic uses is also included.

1 . A method for diagnosing gastric cancer in a subject, the method comprising:
 a) providing a saliva sample from the subject;   b) analyzing the saliva sample with an assay that specifically detects at least one biomarker in the saliva sample, wherein at least one biomarker is selected from the group consisting of Annexin 1 (ANXA1), Cystatin/Stefin B (CSTB), Semaphorin 4B (SEMA4B), S100 calcium binding protein A10 (S100A10), Periplakin (PPL), Serine peptidase inhibitor, Kazal type 7 (SPINK7), EROL-like, RAN binding protein 9 (RANBP9), CD24, Keratin 6A (KRT6A), Keratin 4 (KRT4), eukaryotic translation initiation factor 3 subunit G (EIF3G), triophosphate isomerase 1 (TPL1), deleted in malignant brain tumors 1 protein (DMBT1),  Neisseria  sp strain (B33KA_ot020_Y56),  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98),  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99), miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, and miR-301a;   c) comparing the subject biomarker profile with a control biomarker profile wherein a statistically significant difference between the subject biomarker profile and the control biomarker profile is indicative of gastric cancer; and   d) effectuating a treatment regimen based thereon.   
     
     
         2 . The assay of  claim 1 , wherein the control biomarker profile is derived from a patient with gastric cancer. 
     
     
         3 . The method of  claim 1 , wherein the biomarker types comprise mRNA biomarkers. 
     
     
         4 . The method of  claim 1 , wherein the mRNA is detected by mass spectroscopy, PCR, microarray hybridization, thermal sequencing, capillary array sequencing, or solid phase sequencing. 
     
     
         5 . The method of  claim 1 , the method comprising:
 a) providing a saliva sample from the subject;   b) analyzing the saliva sample with an assay that specifically detects at least three biomarkers in the saliva sample, wherein the three biomarkers are triophosphate isomerase 1 (TPL1), Cystatin-B (CSTB), deleted in malignant brain tumors 1 protein (DMBT1);   c) comparing the subject biomarker profile with a control biomarker profile wherein a statistically significant difference between the subject biomarker profile and the control biomarker profile is indicative of gastric cancer; and   d) effectuating a treatment regimen based thereon.   
     
     
         6 . The method of  claim 5 , wherein the control biomarker profile is derived from a patient with gastric cancer. 
     
     
         7 . The method of  claim 5 , wherein the biomarker types comprise polypeptide biomarkers. 
     
     
         8 . The method of  claim 5 , wherein the polypeptide is detected by ELISA, Western blot, flow cytometry, immunofluorescence, immunohistochemistry, or mass spectroscopy. 
     
     
         9 . The method of  claim 1 , the method comprising:
 a) providing a saliva sample from the subject;   b) analyzing the saliva sample with an assay that specifically detects at least four biomarkers in the saliva sample, wherein the four biomarkers are  Neisseria  sp strain (B33KA_ot020_Y56),  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98),  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99);   c) comparing the subject biomarker profile with a control biomarker profile wherein a statistically significant difference between the subject biomarker profile and the control biomarker profile is indicative of gastric cancer; and   d) effectuating a treatment regimen based thereon.   
     
     
         10 . The method of  claim 9 , wherein the control biomarker profile is derived from a patient with gastric cancer. 
     
     
         11 . The method of  claim 9 , wherein the biomarker types comprise bacterial markers. 
     
     
         12 . The method of  claim 1 , the method comprising:
 a) providing a saliva sample from the subject;   b) analyzing the saliva sample with an assay that specifically detects at least six biomarkers in the saliva sample, wherein the six biomarkers are miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, and miR-301a;   c) comparing the subject biomarker profile with a control biomarker profile wherein a statistically significant difference between the subject biomarker profile and the control biomarker profile is indicative of gastric cancer; and   d) effectuating a treatment regimen based thereon.   
     
     
         13 . The method of  claim 12 , wherein the control biomarker profile is derived from a patient with gastric cancer. 
     
     
         14 . The method of  claim 12 , wherein the biomarker types comprise bacterial markers. 
     
     
         15 . (canceled) 
     
     
         16 . A method of assessing the efficacy of a therapy on a subject comprising:
 (a) analyzing a first saliva sample from the subject with an assay that specifically detects at least two biomarkers selected from the group consisting of Annexin 1 (ANXA1), Cystatin/Stefin B (CSTB), Semaphorin 4B (SEMA4B), S100 calcium binding protein A10 (S100A10), Periplakin (PPL), Serine peptidase inhibitor, Kazal type 7 (SPINK7), EROL-like, RAN binding protein 9 (RANBP9), CD24, Keratin 6A (KRT6A), Keratin 4 (KRT4), eukaryotic translation initiation factor 3 subunit G (EIF3G), triophosphate isomerase 1 (TPL1), Cystatin-B (CSTB), deleted in malignant brain tumors 1 protein (DMBT1),  Neisseria  sp strain (B33KA_ot020_Y56,  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98,  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99), miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, or miR-301a, thereby providing a first profile;   (b) effecting a therapy on the subject;   (c) analyzing a second sailva from the subject with an assay that specifically detects at least two biomarkers selected from the group consisting of Annexin 1 (ANXA1), Cystatin/Stefin B (CSTB), Semaphorin 4B (SEMA4B), S100 calcium binding protein A10 (S100A10), Periplakin (PPL), Serine peptidase inhibitor, Kazal type 7 (SPINK7), EROL-like, RAN binding protein 9 (RANBP9), CD24, Keratin 6A (KRT6A), Keratin 4 (KRT4), eukaryotic translation initiation factor 3 subunit G (EIF3G), triophosphate isomerase 1 (TPL1), Cystatin-B (CSTB), deleted in malignant brain tumors 1 protein (DMBT1),  Neisseria  sp strain (B33KA_ot020_Y56,  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98,  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99), miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, or miR-301a; thereby providing a second expression profile;   (e) comparing the first and second expression profile, thereby assessing the efficacy of a therapy.   
     
     
         17 . A kit selected from the group consisting of:
 a) a kit comprising a solid support, wherein the solid support comprises a capture binding probe selective for at least two biomarkers selected from the group consisting of Annexin 1 (ANXA1), Cystatin/Stefin B (CSTB), Semaphorin 4B (SEMA4B), S100 calcium binding protein A10 (S100A10), Periplakin (PPL), Serine peptidase inhibitor, Kazal type 7 (SPINK7), EROL-like, RAN binding protein 9 (RANBP9), CD24, Keratin 6A (KRT6A), Keratin 4 (KRT4), eukaryotic translation initiation factor 3 subunit G (EIF3G), triophosphate isomerase 1 (TPL1), Cystatin-B (CSTB), deleted in malignant brain tumors 1 protein (DMBT1),  Neisseria  sp strain (B33KA_ot020_Y56,  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98,  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99), miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, or miR-301a; and   b) a kit comprising one or more primers for the selective amplification of at least two biomarkers selected from the group consisting of Annexin 1 (ANXA1), Cystatin/Stefin B (CSTB), Semaphorin 4B (SEMA4B), S100 calcium binding protein A10 (S100A10), Periplakin (PPL), Serine peptidase inhibitor, Kazal type 7 (SPINK7), EROL-like, RAN binding protein 9 (RANBP9), CD24, Keratin 6A (KRT6A), Keratin 4 (KRT4), eukaryotic translation initiation factor 3 subunit G (EIF3G),  Neisseria  sp strain (B33KA_ot020_Y56,  Eikenella corrodens  and  Kingella dentriflicans  and sp clone (DE012_0t012_577_582_AD98,  Streptococcus australis  and sp clone (FN04_ot65_073_Ab83),  Fusobacterium  all species (AD99), miR-140-5p, miR-374a, miR-454, miR-15b, miR-28-5p, or miR-301a, wherein each of the primers optionally comprises a detectable label.   
     
     
         18 . The kit of  claim 17 , wherein the capture binding probe is an antibody. 
     
     
         19 . (canceled)