Epigenome‐Wide Analysis of Methylation Changes in the Sequence of Gallstone Disease, Dysplasia, and Gallbladder Cancer

Abstract

Background & aims: Gallbladder cancer (GBC) is a highly aggressive malignancy of the biliary tract. Most cases of GBC are diagnosed in low-and middle-income countries and research into this disease has long been limited. In this study we therefore investigate the epigenetic changes along the model of GBC carcinogenesis represented by the sequence gallstone disease → dysplasia → GBC in Chile, the country with the highest incidence of GBC worldwide.Approach: To perform epigenome-wide methylation profiling, genomic DNA extracted from sections of FFPE gallbladder tissue was analyzed using Illumina Infinium MethylationEPIC BeadChips. Pre-processed, quality-controlled data from 82 samples (gallstones n=32, lowgrade dysplasia n=13, high-grade dysplasia n=9, GBC n=28) were available to identify differentially methylated markers, regions, and pathways as well as changes in copy number variations (CNVs). Main results:The number and magnitude of epigenetic changes increased with disease development and predominantly involved the hypermethylation of CpG islands and gene promoter regions. The methylation of genes implicated in Wnt signaling, Hedgehog signaling, and tumor suppression increased with tumor grade. CNVs also increased with GBC development and affected CDKN2A, MDM2, TP53, and CCND1. Gains in the targetable ERBB2 were detected in 14% of the GBC samples. Conclusions:Our results indicate that GBC carcinogenesis comprises three main methylation stages: early (gallstone disease and low-grade dysplasia), intermediate (highgrade dysplasia), and late (GBC). The identified gradual changes in methylation and CNVs may help to enhance our understanding of the mechanisms underlying this aggressive disease and eventually lead to improved treatment and early diagnosis of GBC.

Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications

“…These mechanisms involve various structures (e.g., intercellular desmosome, gap, tight, and adherens junctions; extracellular matrix hemidesmosomes and focal contact), interacting protein families (e.g., integrins, actins, connexins, claudins, occludin, catenins, cadherins, fibronectin), and signaling pathways (TGFβ-SMAD3, WNT-β CATENIN, and NOTCH) inducing the expression of transcription factors (e.g., ZEB1, ZEB2, SNAIL, SLUG, TWIST) to downregulate or upregulate the expression of epithelial (e.g., E-CADHERIN, CLAUDINS, OCCLUDIN), and mesenchymal markers (e.g., N-CADHERIN, VIMENTIN, FIBRONECTIN). There is an increasing number of studies on different cancers highlighting epigenetic modifications and changes in gene expression that have already occurred by the stage of dysplasia [558][559][560][561][562], and later during EMT [557]. Therefore, monitoring epigenetic deregulation may assist in better predicting the potential adversity of cellular transformation processes.…”

Epigenetic activation of the elongator complex sensitizes gallbladder cancer to gemcitabine therapy

“…Genetic and epigenetic alterations in GBC have been extensively reported [ 31 – 33 ]. Recent studies have shown that hypermethylation induces silencing of tumour suppressor genes in GBC, and the progression of GBC is accompanied by an increased frequency of methylation [ 34 , 35 ].…”

Biliary Tract Cancers: Treatment Updates and Future Directions in the Era of Precision Medicine and Immuno-Oncology

“…Comparing 103 IHCs with matched controls, Zhou et al identified three pathways (transforming growth factor-b/ S m a d s i g n a l i n g p a t h w a y a l o n g w i t h k n o w n R a s / phosphatidylinositol-4,5-bisphosphate 3-kinase signaling and p53/cell cycle signaling) along with genes involved in epigenetic regulation and oxidative phosphorylation more frequent in IHCs (30). Using samples from patients in Chile (which has the highest incidence of GBC), Brägelmann et al were able to identify methylation changes during the progression from gallstone disease to dysplasia and then to GBC (37). They identified stages of progression through a sequence of early (gallstone disease and low-grade dysplasia), intermediate (highgrade dysplasia), and late (GBC) stages.…”