Developing ATAC-array as a novel epigenetic biomarker to guide personalized therapy in pancreatic cancer - ABSTRACT: Although chemotherapy remains the mainstay of systemic therapy, a large number of cancer patients fail to respond to. About half of surgically resected pancreatic ductal adenocarcinoma (PDAC) patients relapse within a year despite adjuvant chemotherapy. Using genome-wide ATAC-Seq to comprehensively analyze tumor cell-intrinsic chromatin accessibility patterns of resected PDAC, we discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Based on this signature, we developed “ATAC-array” – a novel, clinically applicable microarray platform that reads chromatin accessibility without the time and cost associated with Next Generation Sequencing. Using this novel platform, we developed a chromatin-based Prognosis Score, derived from the ATAC-array results from our training set samples, which was further validated on an independent cohort of PDAC patient-derived 3D organoids. By analyzing over-represented transcription factor binding sites among chromatin loci found to be accessible in patients with prolonged DFS, we also identified HNF1b as a transcription factor displaying differential nuclear localization between patients with short vs. long DFS. Combining these two simple methodologies (i.e., the ATAC-array “Prognosis Score” and immunohistochemical determination or HNF1b nuclear localization), we have developed an algorithm that at the time of diagnosis stratifies PDAC patients into prognostic groups with more than seven-fold differences in DFS. Our stratification algorithm provides a simple and clinically achievable prediction of favorable vs unfavorable epigenetic states in PDAC. Based on this work, we now hypothesize that ATAC-array based analysis of chromatin accessibility will provide a clinically relevant means of predicting prognosis in both localized and metastatic pancreatic cancer, and further allow rational selection of patients for clinical trials of epigenetic therapy. Through this R21 grant, we now aim to optimize ATAC-array for clinical use and expand it to all stages of pancreatic cancer. Our goal is to optimize methodologies allowing ATAC-array to be applied to scant tumor specimens retrieved from needle biopsies. We additionally plan to screen epigenetic drugs in vitro in patient-derived 3D organoids to determine whether adverse patterns of chromatin accessibility might be amenable to epigenetic “reprogramming” therapy, such that ATAC- array could provide a therapeutic biomarker selecting patients for epigenetic therapy. The long-term goal of this project is to enhance the feasibility of genome-wide assessment of chromatin accessibility as a clinically relevant indicator of outcome in PDAC patients, and to facilitate the rational inclusion of epigenetic drugs into the therapeutic regimens of patients displaying poor-prognosis epigenetic signatures.
