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Updated: Jun 24, 2025
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Genome-wide DNA methylation in relation to ARID1A deficiency in ovarian clear cell carcinoma
Shang Li1, Gert Jan Meersma1,2, Jolanta Kupryjanczyk3
1Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
Background:
The poor chemo-response and high DNA methylation of ovarian clear cell carcinoma (OCCC) have attracted extensive attentions. Recently, we revealed the mutational landscape of the human kinome and additional cancer-related genes and found deleterious mutations in ARID1A, a component of the SWI/SNF chromatin-remodeling complex, in 46% of OCCC patients. The present study aims to comprehensively investigate whether ARID1A loss and genome-wide DNA methylation are co-regulated in OCCC and identify putative therapeutic targets epigenetically regulated by ARID1A.
Methods:
DNA methylation of ARID1Amt/ko and ARID1Awt OCCC tumors and cell lines were analyzed by Infinium MethylationEPIC BeadChip. The clustering of OCCC tumors in relation to clinical and mutational status of tumors were analyzed by hierarchical clustering analysis of genome-wide methylation. GEO expression profiles were used to identify differentially methylated (DM) genes and their expression level in ARID1Amt/ko vs ARID1Awt OCCCs. Combining three pre-ranked GSEAs, pathways and leading-edge genes epigenetically regulated by ARID1A were revealed. The leading-edge genes that passed the in-silico validation and showed consistent ARID1A-related methylation change in tumors and cell lines were regarded as candidate genes and finally verified by bisulfite sequencing and RT-qPCR.
Results:
Hierarchical clustering analysis of genome-wide methylation showed two clusters of OCCC tumors. Tumor stage, ARID1A/PIK3CA mutations and TP53 mutations were significantly different between the two clusters. ARID1A mutations in OCCC did not cause global DNA methylation changes but were related to DM promoter or gene-body CpG islands of 2004 genes. Three pre-ranked GSEAs collectively revealed the significant enrichment of EZH2- and H3K27me3-related gene-sets by the ARID1A-related DM genes. 13 Leading-edge DM genes extracted from the enriched gene-sets passed the expression-based in-silico validation and showed consistent ARID1A-related methylation change in tumors and cell lines. Bisulfite sequencing and RT-qPCR analysis showed promoter hypermethylation and lower expression of IRX1, TMEM101 and TRIP6 in ARID1Amt compared to ARID1Awt OCCC cells, which was reversed by 5-aza-2'-deoxycytidine treatment.
Conclusions:
Our study shows that ARID1A loss is related to the differential methylation of a number of genes in OCCC. ARID1A-dependent DM genes have been identified as key genes of many cancer-related pathways that may provide new candidates for OCCC targeted treatment.
Insights
ARID1A loss in ovarian clear cell carcinoma (OCCC) is linked to differential DNA methylation of key cancer genes. These ARID1A-dependent genes offer potential new therapeutic targets for OCCC treatment.
Area of Science:
- Oncology
- Epigenetics
- Genomics
Background:
- Ovarian clear cell carcinoma (OCCC) exhibits poor chemo-response and high DNA methylation.
- Deleterious mutations in ARID1A, a SWI/SNF complex component, occur in 46% of OCCC patients.
Purpose of the Study:
- To investigate the co-regulation of ARID1A loss and genome-wide DNA methylation in OCCC.
- To identify potential therapeutic targets epigenetically regulated by ARID1A.
Main Methods:
- Genome-wide DNA methylation analysis using Infinium MethylationEPIC BeadChip.
- Hierarchical clustering of OCCC tumors based on methylation status.
- Identification of differentially methylated (DM) genes and pathways using GEO expression profiles and GSEA.
- Validation of candidate genes via bisulfite sequencing and RT-qPCR.
Main Results:
- Hierarchical clustering revealed two distinct OCCC tumor clusters with significant differences in tumor stage and mutations (ARID1A, PIK3CA, TP53).
- ARID1A mutations were associated with differential methylation of 2004 genes, particularly affecting CpG islands.
- ARID1A-related DM genes were enriched in EZH2- and H3K27me3-related pathways, identifying 13 leading-edge genes.
Conclusions:
- ARID1A loss in OCCC is associated with differential methylation of numerous genes.
- ARID1A-dependent DM genes are involved in key cancer pathways, presenting novel therapeutic targets for OCCC.
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