Salivary Transcriptomics and Proteomic Biomarkers for Breast Cancer Detection

Abstract

Presented herein are biomarkers related to breast cancer. The presently identified salivary biomarkers create the basis for a breast 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 breast cancer assay in clinical, diagnostic and therapeutic uses is also included.

1 . A method for diagnosing breast cancer status in a subject, the method comprising:
 a) analyzing a saliva sample from the subject with an assay that specifically detects at least two biomarkers in the saliva sample, wherein at least one biomarker is selected from the group consisting of the biomarkers S100A8 (S100 calcium binding protein A8) (SEQ ID NO: 1), CSTA (cystatin A) (SEQ ID NO:2), GRM1 (glutamate receptor, metabotropic 1) (SEQ ID NO: 3), TPT1 (tumor protein, translationally-controlled 1)(SEQ ID NO:4), GRIK1 (glutamate receptor, ionotropic, kainate 1) (SEQ ID NO: 5), H6PD (hexose-6-phosphate dehydrogenase) (SEQ ID NO: 6), IGF2BP1 (insulin-like growth factor 2 mRNA binding protein 1) (SEQ ID NO: 7), MDM4 (3T3 cell double minute 4) (SEQ ID NO: 8), and CA6 (carbonic anhydrase VI) (SEQ ID NO: 9); and   b) determining whether or not the at least two biomarkers are differentially expressed in the sample relative to a control; thereby providing breast cancer status.   
     
     
         2 . The method of  claim 1 , wherein one of the at least two biomarkers is cystatin A (CSTA). 
     
     
         3 . The method of  claim 1 , wherein one of the at least two biomarkers is CSTA and the other biomarker of the at least two biomarkers is transformed 3T3 cell double minute 4 (MDM4). 
     
     
         4 . The method of  claim 1 , wherein at least three biomarkers are measured. 
     
     
         5 . The method of  claim 1 , wherein one of the at least two biomarkers is anhydrase VI (CA6) polypeptide. 
     
     
         6 . The method of  claim 1  wherein the assay detects a nucleic acid encoding at least one biomarker, and wherein the nucleic acid is detected by mass spectroscopy, PCR, microarray hybridization, thermal sequencing, capillary array sequencing, or solid phase sequencing. 
     
     
         7 . The method of  claim 1 , wherein the assay detects a polypeptide of at least one biomarker, and wherein the polypeptide is detected by ELISA, Western blot, flow cytometry, immunofluorescence, immunohistochemistry, or mass spectroscopy. 
     
     
         8 . 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 S100A8 (SEQ ID NO: 1), CSTA (cystatin A) (SEQ ID NO:2), GRM1 (glutamate receptor, metabotropic 1) (SEQ ID NO: 3), TPT1 (tumor protein, translationally-controlled 1) (SEQ ID NO:4), GRIK1 (glutamate receptor, ionotropic, kainate 1) (SEQ ID NO: 5), H6PD (hexose-6-phosphate dehydrogenase) (SEQ ID NO: 6), IGF2BP1 (insulin-like growth factor 2 mRNA binding protein 1) (SEQ ID NO: 7), MDM4 (3T3 cell double minute 4) (SEQ ID NO: 8), and CA6 (carbonic anhydrase VI) (SEQ ID NO: 9), thereby providing a first expression profile;   (b) effecting a therapy on the subject;   (c) analyzing a second saliva from the subject with an assay that specifically detects at least two biomarkers selected from the group consisting of S100A8, CSTA, GRM1, TPT1, GRIM, H6PD, IGF2BP1, MDM4, and CA6; thereby providing a second expression profile;   (e) comparing the first and second expression profile, thereby assessing the efficacy of a therapy.   
     
     
         9 . 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 S100A8, CSTA, GRM1, TPT1, H6PD, IGF2BP1, MDM4. 
     
     
         10 . A kit comprising a first and a second solid support, wherein the first solid support comprises a capture binding probe selective for at least two biomarkers selected from the group consisting of S100A8, CSTA, GRM1, TPT1, GRIK1, H6PD, IGF2BP1, MDM4, and wherein the second solid support comprises a capture binding ligand for CA6. 
     
     
         11 . The kit of  claim 10 , wherein the capture binding ligand is an antibody. 
     
     
         12 . A kit comprising one or more primers for the selective amplification of at least two biomarkers selected from the group consisting of S100A8, CSTA, GRM1, TPT1, GRIK1, H6PD, IGF2BP1, MDM4, wherein each of the primers optionally comprises a detectable label. 
     
     
         13 . A method for diagnosing breast cancer status in a subject, the method comprising:
 a) analyzing a saliva sample from the subject with an assay that specifically detects at least nine biomarkers in the saliva sample, wherein the at least nine biomarkers are selected from the group consisting of the biomarkers S100A8 (S100 calcium binding protein A8) (SEQ ID NO: 1), CSTA (cystatin A) (SEQ ID NO:2), GRM1 (glutamate receptor, metabotropic 1) (SEQ ID NO: 3), TPT1 (tumor protein, translationally-controlled 1) (SEQ ID NO:4), GRIK1 (glutamate receptor, ionotropic, kainate) (SEQ ID NO: 5), H6PD (hexose-6-phosphate dehydrogenase) (SEQ ID NO: 6), IGF2BP1 (insulin-like growth factor 2 mRNA binding protein 1) (SEQ ID NO: 7), MDM4 (3T3 cell double minute 4) (SEQ ID NO: 8), and CA6 (carbonic anhydrase VI) (SEQ NO: 9); and   b) determining whether or not the at least nine biomarkers are differentially expressed in the sample relative to a control; thereby providing breast cancer status