Genome‐wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT‐ROBO, ITGA2 and MET signaling

Abstract

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome‐wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high‐density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non‐malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5′ region of genes (including the proximal promoter, 5′UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF‐β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT‐ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT‐PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT‐ROBO signaling and up‐regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy.

HMGA2–FOXL2 Axis Regulates Metastases and Epithelial-to-Mesenchymal Transition of Chemoresistant Gastric Cancer

“…Ramirez and colleagues showed that integrin a 2 b 1 suppressed metastasis in human breast cancer and in mouse models (42), while Yoshimura and colleagues showed that ITGA2 contributed to the formation of hepatic metastasis in human colorectal cancer (43). ITGA2 regulation by miRNAs and epigenetic modifications is crucial in metastasis and EMT (44)(45)(46). Our data suggest that ITGA2 served as the effector of FOXL2 and that it was associated with metastasis and EMT in chemoresistant gastric cancer cells.…”

LIM-only protein FHL2 critically determines survival and radioresistance of pancreatic cancer cells

“…These resistances elicit from specific gene mutations and methylation patterns, which regulate proliferation, apoptosis and invasion as well as K-Ras, TGF-β, hedgehog and Wnt associated signal transduction pathways identified by genome and epigenome analysis [36,37]. Additionally, the large amount of ECM found in PDAC points at a strong impact of prosurvival FA signaling.…”

Tumor Heterogeneity in Pancreatic Adenocarcinoma

“…However, it has been reported that such an approach in breast cancer could work on formalin-fixed paraffin-embedded biopsies with a high sensitivity [27]. Additionally, impor-tant DNA methylation profile modifications have been reported in PDAC compared to normal tissue, but no subtypes have been individualized yet [28].…”