Biomarkers for Reducing Mortality of Cancers of the Colon and Esophagus

The goal of this EDRN renewal proposal is the discovery and validation of biomarkers for reducing mortality from gastrointestinal cancers. We particularly target cancers of the colon (CRC), the second leading cause of U.S. cancer deaths, and adenocarcinomas of the esophagus (EAC), the fastest increasing cause of U.S. cancer deaths. In our first funding period, our group prominently advanced early detection of colon cancers through detection of aberrantly methylated tumor DNA in stools. Our work testing methylated VIM (M-VIM) DNA in stools led to an EDRN prospective validation study (GLNE-10), a commercial colon cancer test (ColoSure, from Exact Sciences & LabCorp), and to proof of principal for the Exact Cologuard test of methylated stool DNA that is now FDA approved. Our work studying the 15-PGDH tumor suppressor gene identified the first biomarker for personalized chemoprevention, showing NSAIDs lower colon cancer risk only in individuals with high, but not low, colon 15-PGDH expression. And our further studies of M-VIM showed this biomarker to also be highly sensitive and specific for detecting Barrett's esophagus (BE) and EAC, specifically in tests using esophageal brushings. In this renewal application, for colon cancer we propose EDRN phase 2 validation studies testing biomarkers that identify individuals at high risk of developing colon cancer by testing normal colon mucosa for RNA and DNA markers of elevated cancer risk that are: a) low levels of 15-PGDH transcript expression, and/or b) high levels of DNA methylation at specific colon cancer risk loci. For EAC, we first propose an EDRN phase 2 validation study testing sensitivity and specificity of a panel of candidate DNA methylation biomarkers for identifying BE, the currently best recognized marker of EAC susceptibility, in assays of samples collected from esophageal brushings. We follow these BE assays by then proposing an EDRN phase 2 study of a set of markers that detect EAC, and its precursor lesion HGD, while not detecting BE, thus providing surveillance markers for catching early BE progression, again by testing samples from esophageal brushings. Our candidate progression marker panel includes DNA loci we find aberrantly methylated in HGD and EAC (but not BE); novel non-coding lincRNAs we find highly expressed in EAC (but not in BE); and mutations in TP53. We also further test the ability of this panel to discriminate low grade BE dysplasias (LGD) that are or are not associated with progression to HGD and EAC. Last, we propose new biomarker discovery to identify methylated DNA and/or RNA biomarkers that, in esophageal brushings, will detect the minority subset of EAC or HGD that are negative for our current EAC/HGD marker panel. Our goals are to: 1) develop effective risk stratification assays to optimize primary prevention of CRC; and 2) replace the current ineffective paradigm for preventing EAC deaths by developing inexpensive biomarker based tests of non-endoscopic esophagus brushings, thus: enabling cost-effective population screening to detect BE, enabling cost effective surveillance to catch early progression of BE to HGD and EAC, reducing EAC deaths, and reducing over-treatment of LGD.