Comprehensive sequence-based DNA methylation analysis suggests that PanIN lesions are acinar-derived and epigenetically primed for carcinogenesis

Pancreatic ductal adenocarcinoma (PDAC) is believed to arise from the accumulation of a series of somatic mutations and is also frequently associated with pancreatic intraepithelial neoplasia (PanIN) lesions. However, there is still debate as to whether the cell-type-of-origin of PanINs and PDACs is acinar or ductal. As cell type identity is maintained epigenetically, DNA methylation changes during pancreatic neoplasia can provide a compelling perspective to examine this question, but DNA methylation sequencing has not yet been performed genome-wide on purified exocrine and neoplastic cell types in the pancreas. Thus, we performed genome-wide DNA methylation sequencing on acini, non-neoplastic ducts, PanIN lesions, and PDAC lesions. We found that: 1) both global methylation profiles and block DMRs clearly implicate an acinar origin for PanINs; 2) at the gene level, PanIN lesions exhibit an intermediate acinar-ductal phenotype resembling acinar-to-ductal metaplasia (ADM); and 3) PanINs are epigenetically primed to progress to PDAC. Thus, epigenomic analysis complements histopathology to define molecular progression toward PDAC. Here, we performed laser-capture microdissection on surgically resected specimens from 18 patients to isolate, with high purity, DNA from four relevant cell types: acini (n=8), non-neoplastic ducts (n=7), PanIN lesions (n=14), and PDAC lesions (n=6). We then performed whole-genome bisulfite sequencing and identified differentially methylated regions (DMRs) using two complementary analytical approaches: bsseq, which identifies any DMRs but is particularly useful for large block-like DMRs; and informME which profiles the potential energy landscape across the genome and is particularly useful for identifying differential methylation entropy.