An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line

Our plain-English summary of An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line, by M.C. Kim, N.Y. Kim, Y.R. Seo, et al (Journal of Cancer, 2016).

The study

• Authors: M.C. Kim, N.Y. Kim, Y.R. Seo, Y. Kim
• Journal: Journal of Cancer
• Published: 2016;7(12):1668-1679
• Cited by: 17 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity.

In plain English

This was a laboratory study of one human malignant mesothelioma cell line, MS-1. It did not study people or asbestos exposure. The authors used dye staining and cell sorting to separate a small 'side population', 0.2% to 3.2% of the cells, from the rest. They compared the groups for DNA methylation, a chemical marking that can switch genes off, and gene activity. The side population had 6,400 genes with regions of more methylation than the other cells and 3,483 with regions of less; 2,161 genes had both. It also had 1,130 genes differing in activity: 795 more active, 335 less active. Combined, the analyses identified 122 genes where methylation and activity changed together. In 118, methylation was higher and activity lower. In 4, methylation was lower and activity higher. Four genes, BNC1, RPS6KA3, TWSG1 and DUSP15, showed methylation differences in the switch region at the gene's start. The authors concluded that DNA methylation may play a pivotal role in creating differences between cells within a tumor. They noted more cell lines or patient samples would strengthen this.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory (in vitro) study comparing side population and non-side population cells sorted from one cell line, using genome-wide DNA methylation sequencing (MeDIP-seq) and gene-expression sequencing (RNA-seq) analyzed together
• Who was studied: One human malignant mesothelioma cell line, MS-1, provided by a researcher at the University of California San Francisco. Side population (SP) and non-side population (NSP) cells were sorted from it. The article does not state the tumor site (pleural or peritoneal) of the cell line.
• Exposure: No asbestos or other exposure was studied. The comparison was between side population cells and non-side population cells of the same cell line. Asbestos appears only in the introduction and discussion, describing other studies.
• Main results:
  • Side population cells made up 0.2% to 3.2% of the total MS1 cells.
  • In SP cells compared to NSP cells, 6,400 genes were differentially hypermethylated and 3,483 genes were differentially hypomethylated. These groups overlap: 2,161 genes had both hypermethylated and hypomethylated regions.
  • 1,130 of 17,122 mRNAs differed in expression between SP and NSP cells. In SP cells, 795 were up-regulated and 335 were down-regulated.
  • 122 genes were considered candidates regulated by aberrant DNA methylation. These were 118 hypermethylated genes with lower expression and 4 hypomethylated genes with higher expression in SP cells.
  • 10 of the candidate genes showed altered methylation in CpG islands. TWSG1, BNC1, RPS6KA3 and DUSP15 showed differential methylation in CpG islands of the promoter region.
  • In gene ontology analysis of the 122 genes, the three most significantly enriched biological process terms were stem cell maintenance, stem cell development and stem cell differentiation.
  • Methylation results for 4 selected genes were confirmed by methylation-specific PCR. Expression results for 6 selected genes were generally concordant with real-time RT-PCR, with small differences in the degree of fold changes.
• The authors' conclusion: The authors concluded that genes defining subpopulations of mesothelioma cells could be regulated epigenetically. They suggested that DNA methylation may play a pivotal role in the genesis of intratumoral heterogeneity, possibly by regulating the more aggressive properties of cancer stem cells.
• Limitations the authors state:
  • Only one cell line was used. The authors state that additional mesothelioma cell lines or human disease samples would solidify the conclusion.
  • Gene ontology terms could not be obtained for the hypomethylated, up-regulated genes because there were too few of them.
  • The suggested biological functions of the highlighted genes were not tested and require further study.

Topics

Medical terms in this study, explained in our Lexicon: Mesothelioma, STEM.

Related studies

• A subset of microRNAs defining the side population of a human malignant mesothelioma cell line — M.C. Kim, N.Y. Kim, et al. (2017)
• Inhibition of hedgehog signaling reduces the side population in human malignant mesothelioma cell lines — H.A. Kim, M.C. Kim, et al. (2015)
• Integrated Analysis of Dysregulated ncRNA and mRNA Expression Profiles in Humans Exposed to Carbon Nanotubes — A.A. Shvedova, N. Yanamala, et al. (2016)
• Characterization of side population cells in human malignant mesothelioma cell lines — K. Kai, S. D'Costa, et al. (2010)
• Asbestos-associated genome-wide DNA methylation changes in lung cancer — E. Kettunen, H. Hernandez-Vargas, et al. (2017)
• Genome-wide profile of pleural mesothelioma versus parietal and visceral pleura: the emerging gene portrait of the mesothelioma phenotype — O.D. Røe, E. Anderssen, et al. (2009)

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