Salivary Biomarkers for Lung Cancer Detection

Abstract

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

We claim: 
     
         1 . A method for diagnosing lung cancer status in a subject, the method comprising:
 a) analyzing a saliva sample from the subject with an assay that specifically detects a biomarker selected from the group consisting of CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, ANXA1, Haptoglobin Hp2, Zinc Alpha2-Glycoprotein, Calprotectin, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA; and   b) determining whether or not the biomarker is differentially expressed in the sample relative to a control; thereby providing lung cancer status.   
     
     
         2 . The method of  claim 1 , wherein at least two biomarkers are measured. 
     
     
         3 . The method of  claim 2 , wherein one of the at least two biomarkers is Porphyromonas catoniae 16S rRNA and wherein one of the at least two biomarkers is Campylobacter showae 16S rRNA. 
     
     
         4 . The method of  claim 1 , wherein at least three biomarkers are measured. 
     
     
         5 . The method of  claim 4 , wherein one of the at least three biomarkers is GREB1 , wherein one of the at least three biomarkers is CCNI, and wherein one of the at least three biomarkers is FRS2. 
     
     
         6 . The method of  claim 4 , wherein one of the at least three biomarkers is Haptoglobin 2, wherein one of the at least three biomarkers is Annexin A1, and wherein one of the at least three biomarkers is Zinc alpha2-protein. 
     
     
         7 . 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. 
     
     
         8 . The method of  claims 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. 
     
     
         9 . 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 a biomarker selected from the group consisting of CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, ANXA1, Haptoglobin Hp2, Zinc Alpha2-Glycoprotein, Calprotectin, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA, 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 CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, ANXA1, Haptoglobin Hp2, Zinc Alpha2-Glycoprotein, Calprotectin, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA; thereby providing a second expression profile;   (e) comparing the first and second expression profile, thereby assessing the efficacy of a therapy.   
     
     
         10 . A kit comprising a solid support, wherein the solid support comprises a capture binding probe selective for a biomarker selected from the group consisting of CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA. 
     
     
         11 . 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 CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA and wherein the second solid support comprises a capture binding ligand for ANXA1, Haptoglobin Hp2, Zinc Alpha2-Glycoprotein, Calprotectin. 
     
     
         12 . The kit of  claim 11 , wherein the capture binding ligand is an antibody. 
     
     
         13 . A kit comprising one or more primers for the selective amplification of at least two biomarkers selected from the group consisting of CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA, wherein each of the primers optionally comprises a detectable label. 
     
     
         14 . A method for diagnosing lung cancer status in a subject, the method comprising:
 a) analyzing a saliva sample from the subject with an assay that specifically detects at least seventeen biomarkers in the saliva sample, wherein the at least seventeen biomarkers are selected from the group consisting of CCNI, EGFR, FGF9, GREB1 protein, LZTS, BRAF, FRS2, ANXA1, Haptoglobin Hp2, Zinc Alpha2-Glycoprotein, Calprotectin, Porphyromonas catoniae 16S rRNA, Campylobacter showae 16S rRNA, Streptococcus salivaris 16S rRNA, Campylobacter rectus 16S rRNA, Veillonella parvula 16S rRNA, Kigella oralis 16S rRNA, and Granulicatella adiacens 16S rRNA; and   b) determining whether or not the at least seventeen biomarkers are differentially expressed in the sample relative to a control; thereby providing lung cancer status.