Ionizing radiations induce shared epigenomic signatures unraveling adaptive mechanisms of cancerous cell lines with or without methionine dependency

Clinical Epigenetics

Pierre Rouyer¹  Sébastien Hergalant¹  Jérémie Raso¹  Youssef Siblini¹  Amélia Julien¹  Céline Chéry²  Jean-Louis Guéant²  Abderrahim Oussalah²  Aurélie François³  Lina Bezdetnaya⁴  Guillaume Vogin⁵ 

[1] INSERM, UMR_S1256, NGERE (Nutrition, Genetics, and Environmental Risk Exposure), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Vandoeuvre-lès-Nancy, Nancy, France;INSERM, UMR_S1256, NGERE (Nutrition, Genetics, and Environmental Risk Exposure), Faculty of Medicine of Nancy, University of Lorraine, 9 Avenue de la Forêt de Haye, 54000, Vandoeuvre-lès-Nancy, Nancy, France;Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism, University Hospital of Nancy, 54000, Vandoeuvre-lès-Nancy, France;Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, 54000, Vandoeuvre-lès-Nancy, France;Lorraine Institute of Oncology, 54000, Nancy, France;Lorraine Institute of Oncology, 54000, Nancy, France;CNRS, UMR_7039, CRAN (Centre de Recherche en Automatique de Nancy), Faculty of Medicine of Nancy, University of Lorraine, 54000, Vandoeuvre-lès-Nancy, France;UMR_7365, IMoPA (Ingénierie Moléculaire Et Ingénierie Articulaire), Faculty of Medicine of Nancy, CNRS-UL, University of Lorraine, 54000, Vandoeuvre-lès-Nancy, France;

关键词: Epigenome-wide association study;    Epigenome alterations;    Aberrant methylation;    Radioresistance;    Radiation therapy;    Ionizing radiation;    Metabolic adaptation in cancer;    Methionine dependency;    Hepatocellular carcinoma;    Melanoma;    Glioblastoma;   

DOI  :  10.1186/s13148-021-01199-y

来源: Springer

【 摘 要 】

BackgroundAlthough radiation therapy represents a core cancer treatment modality, its efficacy is hampered by radioresistance. The effect of ionizing radiations (IRs) is well known regarding their ability to induce genetic alterations; however, their impact on the epigenome landscape in cancer, notably at the CpG dinucleotide resolution, remains to be further deciphered. In addition, no evidence is available regarding the effect of IRs on the DNA methylome profile according to the methionine dependency phenotype, which represents a hallmark of metabolic adaptation in cancer.MethodsWe used a case–control study design with a fractionated irradiation regimen on four cancerous cell lines representative of HCC (HepG2), melanoma (MeWo and MeWo-LC1, which exhibit opposed methionine dependency phenotypes), and glioblastoma (U251). We performed high-resolution genome-wide DNA methylome profiling using the MethylationEPIC BeadChip on baseline conditions, irradiated cell lines (cumulative dose of 10 Gy), and non-irradiated counterparts. We performed epigenome-wide association studies to assess the effect of IRs and methionine-dependency-oriented analysis by carrying out epigenome-wide conditional logistic regression. We looked for epigenome signatures at the locus and single-probe (CpG dinucleotide) levels and through enrichment analyses of gene ontologies (GO). The EpiMet project was registered under the ID#AAP-BMS_003_211.ResultsEWASs revealed shared GO annotation pathways associated with increased methylation signatures for several biological processes in response to IRs, including blood circulation, plasma membrane-bounded cell projection organization, cell projection organization, multicellular organismal process, developmental process, and animal organ morphogenesis. Epigenome-wide conditional logistic regression analysis on the methionine dependency phenotype highlighted several epigenome signatures related to cell cycle and division and responses to IR and ultraviolet light.ConclusionsIRs generated a variation in the methylation level of a high number of CpG probes with shared biological pathways, including those associated with cell cycle and division, responses to IRs, sustained angiogenesis, tissue invasion, and metastasis. These results provide insight on shared adaptive mechanisms of the epigenome in cancerous cell lines in response to IR. Future experiments should focus on the tryptic association between IRs, the initiation of a radioresistance phenotype, and their interaction with methionine dependency as a hallmark of metabolic adaptation in cancer.Graphical abstract

【 授权许可】

CC BY