Abstract LB-238: Genome wide cis-regulatory elements accessibility signature predicts early recurrence of the treatment-naïve resected subset of PDAC: A new paradigm for precision oncology

Abstract

Abstract We have recently discovered a set of 1092 cis-regulatory elements in the human genome that are differentially accessible in the treatment-naïve resected subset of pancreatic ductal adenocarcinoma (PDAC) recurring within first 12 months of surgery. Recurrence, even after complete removal of the primary tumor, is a pressing issue in PDAC. We hypothesized that malignant cells of the recurrent and the non-recurrent PDAC tumors possessed differential accessibility patterns of cis-regulatory elements in the genome. To test this hypothesis, we interrogated genome wide chromatin accessibility landscape of EpCAM-sorted “pure” PDAC malignant cells (KRAS mutant allele frequency 45+22%) from 54 freshly resected tumors followed by the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). We identified a near-saturating total number of 126661 open chromatin peaks from duplicate ATAC-seq libraries from each of 40 (out of 54) patients (80 libraries with Irreproducible Discovery Rate (IDR)-cut-off <0.01). We found 1092 peaks differentially represented (p<0.001) in patients who recurred within first 12 months of surgery compared to the patients who didn't. We identified 62 transcription-factor binding motifs by MEME curated CisBP transcription factor binding motifs (TBFM) and FIMO that were differentially enriched in recurrent and non-recurrent patients (P < 1x10-4). We selected the top listed two transcription factors, HNF1b and ZKSCAN1, from the non-recurrent and recurrent groups respectively, for further validation by immunohistochemistry (IHC) and immunofluorescence (IF) staining of tissue microarrays (TMA) prepared from formalin-fixed paraffin blocks of these tumors (N=40). With the blinded subjective scoring (0-3 scale) method using the combination of HNF1b and ZKSCAN1 we could predict recurrence with 83.33% accuracy. HNF1b nuclear staining pattern was completely absent from 7, weak in 4 and strong in 1 out of 12 recurrent patients. As opposed to that, strong nuclear staining of ZKSCAN1 in 3, moderate staining in 5, weak to moderate in 3 and no staining in 1 out of 12 patients was observed. Among the rest 28 patients, only 3 (10.7%) showed a clear cut opposite staining pattern, i.e., strong HNF1b and weak ZKSCAN1 nuclear staining, 7 patients showed the recurrence signature of staining and other 18 patients showed ambivalent patterns. Altogether, from the current study we conclude that epigenetic reprogramming, by increasing or decreasing accessibility of the cis-regulatory elements in the genome, regulates binding of the specific transcription factors, which in turn might control the PDAC heterogeneity of recurrence and chemoresistance. Citation Format: Surajit Dhara, Sagar Chhangawala, Gokce Askan, Zhang Liguo, Smrita Sinha, Danielle Glassman, Kenneth Yu, Vinod Balachandran, Christina Leslie, Steven Leach. Genome wide cis-regulatory elements accessibility signature predicts early recurrence of the treatment-naïve resected subset of PDAC: A new paradigm for precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-238.