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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Functional epigenomics approach to identify methylated candidate tumour suppressor genes in renal cell carcinoma
M R Morris1, D Gentle, M Abdulrahman
1Cancer Research UK Renal Molecular Oncology Group, University of Birmingham, Birmingham B15 2TT, UK.
Abstract:
Promoter region hypermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many human cancers. Previously, to identify candidate epigenetically inactivated TSGs in renal cell carcinoma (RCC), we monitored changes in gene expression in four RCC cell lines after treatment with the demethylating agent 5-azacytidine. This enabled us to identify HAI-2/SPINT2 as a novel epigenetically inactivated candidate RCC TSG. To identify further candidate TSGs, we undertook bioinformatic and molecular genetic evaluation of a further 60 genes differentially expressed after demethylation. In addition to HAI-2/SPINT2, four genes (PLAU, CDH1, IGFB3 and MT1G) had previously been shown to undergo promoter methylation in RCC. After bioinformatic prioritisation, expression and/or methylation analysis of RCC cell lines+/-primary tumours was performed for 34 genes. KRT19 and CXCL16 were methylated in RCC cell lines and primary RCC; however, 22 genes were differentially expressed after demethylation but did not show primary tumour-specific methylation (methylated in normal tissue (n=1); methylated only in RCC cell lines (n=9) and not methylated in RCC cell lines (n=12)). Re-expression of CXCL16 reduced growth of an RCC cell line in vitro. In a summary, a functional epigenomic analysis of four RCC cell lines using microarrays representing 11 000 human genes yielded both known and novel candidate TSGs epigenetically inactivated in RCC, suggesting that this is valid strategy for the identification of novel TSGs and biomarkers.
Insights
Epigenetic silencing of tumor suppressor genes (TSGs) is common in cancer. This study identified novel epigenetically inactivated TSGs in renal cell carcinoma (RCC) using a functional epigenomic approach, revealing potential new biomarkers.
Area of Science:
- Cancer epigenetics
- Molecular oncology
- Renal cell carcinoma (RCC) research
Background:
- Promoter hypermethylation and transcriptional silencing frequently inactivate tumor suppressor genes (TSGs) in human cancers.
- Identifying epigenetically silenced TSGs is crucial for understanding cancer development and finding therapeutic targets.
- Previous work identified HAI-2/SPINT2 as a candidate epigenetically inactivated TSG in renal cell carcinoma (RCC).
Purpose of the Study:
- To identify novel epigenetically inactivated candidate TSGs in renal cell carcinoma (RCC).
- To evaluate the functional impact of candidate TSG re-expression in RCC.
- To validate the utility of functional epigenomic analysis for TSG discovery in RCC.
Main Methods:
- Treatment of four RCC cell lines with a demethylating agent (5-azacytidine) to monitor gene expression changes.
- Bioinformatic and molecular genetic evaluation of 60 differentially expressed genes.
- Expression and methylation analysis of 34 candidate genes in RCC cell lines and primary tumors.
Main Results:
- Identified HAI-2/SPINT2, KRT19, and CXCL16 as epigenetically inactivated candidate TSGs in RCC.
- Demonstrated that re-expression of CXCL16 inhibited RCC cell line growth in vitro.
- 22 genes showed differential expression after demethylation but lacked primary tumor-specific methylation.
Conclusions:
- Functional epigenomic analysis is a valid strategy for identifying novel epigenetically inactivated TSGs in RCC.
- The study identified both known and novel candidate TSGs implicated in RCC pathogenesis.
- These findings suggest potential for novel TSGs and biomarkers in renal cell carcinoma.
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