Salivary transcriptomic and proteomic biomarkers for breast cancer detection
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 the presence of breast cancer in a subject at risk for developing breast cancer, the method comprising:
a) analyzing a saliva sample from the subject at risk for developing breast cancer with an assay that specifically detects at least nine biomarkers in the saliva sample, wherein the nine biomarkers are S100A8 (S 100 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);
b) detecting that the at least nine biomarkers are differentially expressed in the sample relative to a control sample from a subject without breast cancer, thereby detecting the presence of breast cancer in the subject; and
c) administering a breast cancer treatment regimen to the subject, wherein the treatment regimen is selected from the group consisting of chemotherapy, hormonal therapy, radiotherapy, immunotherapy, and surgical removal of breast tissue.
2. The method of claim 1 wherein the assay detects a nucleic acid encoding at least one of the biomarkers of a), and wherein the nucleic acid is detected by mass spectroscopy, PCR, microarray hybridization, thermal sequencing, capillary array sequencing, or solid phase sequencing.
3. The method of claim 1 wherein the assay detects a polypeptide of CA6, and wherein the polypeptide is detected by ELISA, Western blot, flow cytometry, immunofluorescence, immunohistochemistry, or mass spectroscopy.
4. The method of claim 1 , wherein the assay comprises a first and a second solid support, wherein the first solid support comprises capture binding probes selective for each of the following markers: S100A8, CSTA, GRM1, TPT1, GRIK1, H6PD, IGF2BP1 and MDM4, and wherein the second solid support comprises a capture binding probe selective for CA6.
5. The method of claim 4 , wherein the capture binding probe selective for CA6 is an antibody.