Genetic and Epigenetic Alterations of CDH1 Regulatory Regions in Hereditary and Sporadic Gastric Cancer

E-cadherin is a key player in gastric cancer (GC) and germline alterations of CDH1, its encoding gene, are responsible for Hereditary Diffuse Gastric Cancer (HDGC) syndrome. This study aimed at elucidating the role of genetic variants and DNA methylation of CDH1 promoter and enhancers in the regulation of gene expression. For this purpose, we analyzed genetic variants of the CDH1 gene through Next-Generation Sequencing (NGS) in a series of GC cell lines (NCI-N87, KATO-III, SNU-1, SNU-5, GK2, AKG, KKP) and the corresponding CDH1 expression levels. By bisulfite genomic sequencing, we analyzed the methylation status of CDH1 regulatory regions in 8 GC cell lines, in a series of 13 sporadic GC tissues and in a group of 20 HDGC CDH1-negative patients and 6 healthy controls. The NGS analysis on CDH1 coding and regulatory regions detected genetic alterations in 3 out of 5 GC cell lines lacking functional E-cadherin. CDH1 regulatory regions showed different methylation patterns in patients and controls, GC cell lines and GC tissues, expressing different E-cadherin levels. Our results showed that alterations in terms of genetic variants and DNA methylation patterns of both promoter and enhancers are associated with CDH1 expression levels and have a role in its regulation.

[1]  A. Jemal,et al.  Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries , 2021, CA: a cancer journal for clinicians.

[2]  Fidel Ramírez,et al.  pyGenomeTracks: reproducible plots for multivariate genomic datasets , 2020, Bioinform..

[3]  A. Sporle,et al.  Hereditary diffuse gastric cancer: updated clinical practice guidelines. , 2020, The Lancet. Oncology.

[4]  P. Lollini,et al.  Epigenetic Mechanisms in Gastric Cancer: Potential New Therapeutic Opportunities , 2020, International journal of molecular sciences.

[5]  Maria Sofia Fernandes,et al.  S100P is a molecular determinant of E-cadherin function in gastric cancer , 2019, Cell Communication and Signaling.

[6]  B. Shirts,et al.  Comparison of CDH1 Penetrance Estimates in Clinically Ascertained Families vs Families Ascertained for Multiple Gastric Cancers. , 2019, JAMA oncology.

[7]  D. Calistri,et al.  E-cadherin Downregulation and microRNAs in Sporadic Intestinal-Type Gastric Cancer , 2019, International journal of molecular sciences.

[8]  D. Amadori,et al.  Multigene Panel Testing Increases the Number of Loci Associated with Gastric Cancer Predisposition , 2019, Cancers.

[9]  Carla Oliveira,et al.  Hereditary gastric cancer: what’s new? Update 2013–2018 , 2019, Familial Cancer.

[10]  Marzieh Ebrahimi,et al.  Histone Modification Marks Strongly Regulate CDH1 Promoter in Prostospheres as A Model of Prostate Cancer Stem Like Cells , 2019, Cell journal.

[11]  Y. Yuasa,et al.  Identification of selective inhibitors for diffuse-type gastric cancer cells by screening of annotated compounds in preclinical models , 2018, British Journal of Cancer.

[12]  Yutaka Suzuki,et al.  Necessity of p53-binding to the CDH1 locus for its expression defines two epithelial cell types differing in their integrity , 2018, Scientific Reports.

[13]  Doron Lancet,et al.  GeneHancer: genome-wide integration of enhancers and target genes in GeneCards , 2017, Database J. Biol. Databases Curation.

[14]  P. Ding,et al.  Clinicopathological significance and potential drug target of CDH1 in breast cancer: a meta-analysis and literature review , 2015, Drug design, development and therapy.

[15]  R. van Hillegersberg,et al.  Hereditary diffuse gastric cancer: updated clinical guidelines with an emphasis on germline CDH1 mutation carriers , 2015, Journal of Medical Genetics.

[16]  B. Fernandez,et al.  Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond. , 2015, JAMA oncology.

[17]  R. Seruca,et al.  Familial gastric cancer: genetic susceptibility, pathology, and implications for management. , 2015, The Lancet. Oncology.

[18]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[19]  D. Aran,et al.  DNA Methylation of Transcriptional Enhancers and Cancer Predisposition , 2013, Cell.

[20]  Sivan Sabato,et al.  DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes , 2013, Genome Biology.

[21]  Raquel Seruca,et al.  Somatic mutations and deletions of the E-cadherin gene predict poor survival of patients with gastric cancer. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[22]  Manuel A. S. Santos,et al.  Lack of microRNA‐101 causes E‐cadherin functional deregulation through EZH2 up‐regulation in intestinal gastric cancer , 2012, The Journal of pathology.

[23]  D. Huntsman,et al.  Characterization of the intronic portion of cadherin superfamily members, common cancer orchestrators , 2012, European Journal of Human Genetics.

[24]  D. Huntsman,et al.  Allele-specific CDH1 downregulation and hereditary diffuse gastric cancer. , 2010, Human molecular genetics.

[25]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[26]  Thomas D. Schmittgen,et al.  Analyzing real-time PCR data by the comparative CT method , 2008, Nature Protocols.

[27]  R. Kemler,et al.  E-cadherin intron 2 contains cis-regulatory elements essential for gene expression , 2005, Development.

[28]  F. Graziano,et al.  The role of the E-cadherin gene (CDH1) in diffuse gastric cancer susceptibility: from the laboratory to clinical practice. , 2003, Annals of oncology : official journal of the European Society for Medical Oncology.

[29]  R. Kemler,et al.  Analysis of regulatory elements of E‐cadherin with reporter gene constructs in transgenic mouse embryos , 2003, Developmental dynamics : an official publication of the American Association of Anatomists.

[30]  Jun Yu,et al.  Promoter hypermethylation of tumor‐related genes in gastric intestinal metaplasia of patients with and without gastric cancer , 2002, International journal of cancer.

[31]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[32]  C. Caldas,et al.  E-cadherin gene (CDH1) promoter methylation as the second hit in sporadic diffuse gastric carcinoma , 2001, Oncogene.

[33]  J. Willis,et al.  Methylation of the CDH1 promoter as the second genetic hit in hereditary diffuse gastric cancer , 2000, Nature Genetics.

[34]  S. Nishizuka,et al.  E-Cadherin gene promoter hypermethylation in primary human gastric carcinomas. , 2000, Journal of the National Cancer Institute.

[35]  G. Christofori,et al.  The role of the cell-adhesion molecule E-cadherin as a tumour-suppressor gene. , 1999, Trends in biochemical sciences.

[36]  Anthony E. Reeve,et al.  E-cadherin germline mutations in familial gastric cancer , 1998, Nature.

[37]  F. Molemans,et al.  Cloning and characterization of the human invasion suppressor gene E-cadherin (CDH1). , 1995, Genomics.

[38]  S. Hirohashi,et al.  E-cadherin gene mutations in human gastric carcinoma cell lines. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[39]  P. Laurén,et al.  THE TWO HISTOLOGICAL MAIN TYPES OF GASTRIC CARCINOMA: DIFFUSE AND SO-CALLED INTESTINAL-TYPE CARCINOMA. AN ATTEMPT AT A HISTO-CLINICAL CLASSIFICATION. , 1965, Acta pathologica et microbiologica Scandinavica.

[40]  H. Espejo,et al.  [Gastric cancer]. , 1996, Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru.