Methylation associated transcriptional repression of ELOVL5 in novel colorectal cancer cell lines.

Arnoud Boot,Jan Oosting,Tom Van Wezel,Hans Morreau,Peter J K Kuppen,Jaap D H Van Eendenburg,Hiromu Suzuki

doi:10.1371/journal.pone.0184900

Arnoud Boot, Jan Oosting + Show 5 more

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https://doi.org/10.1371/journal.pone.0184900

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Journal: PloS one	Publication Date: Sep 20, 2017
Citations: 10	License type: CC BY 4.0

Affiliation: Leiden University Medical Center

Abstract

Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines. We generated global DNA methylation profiles with Infinium HumanMethylation450 BeadChips and analysed them in conjunction with matching gene expression profiles. Multidimensional scaling of the DNA methylation and gene expression datasets showed that BRAF mutated cell lines form a distinct group. In this group we investigated the 706 loci which we have previously identified to be hypermethylated in BRAF mutant CRC. We validated the significant findings in the The Cancer Genome Atlas colon adenocarcinoma dataset. Our analysis identified ELOVL5, FAM127B, MTERF1, ZNF606 to be subject to transcriptional downregulation through DNA hypermethylation in CRC. We further investigated ELOVL5 with qPCR and immunohistochemical staining, validating our results, but did not find a clear relation between ELOVL5 expression and tumor stage or relapse free survival. ELOVL5, FAM127B, MTERF1, ZNF606 are involved in important cellular processes such as apoptosis, lipogenesis and the downstream transcriptional effect of the MAPK-pathway. We have identified a DNA methylation profile regulating key cellular processes in CRC, resulting in a growth advantage to the tumor cells.

Highlights

Methylation of the C-5 carbon occurs at approximately 70–80% of all CpG dinucleotides in the human genome [1] and is associated with heterochromatin, a closed chromatin conformation
All 758 differentially methylated loci in BRAF-mutated primary tumor samples from this study were analysed in the cell line DNA methylation dataset. 706 of the 758 loci were covered by at least one probe in the 450k DNA methylation dataset when we identified the loci based on the same chromosomal positions
We found that ELOVL5, FAM127B, MTERF1 and ZNF606 all show a negative correlation with gene expression in the The Cancer Genome Atlas (TCGA) data smaller than -0.50

Summary

Introduction

Methylation of the C-5 carbon occurs at approximately 70–80% of all CpG dinucleotides in the human genome [1] and is associated with heterochromatin, a closed chromatin conformation. Heterochromatin at intergenic regions protects genomic stability by inactivation of transposable elements such as LINEs and SINEs. At gene regulatory elements the heterochromatin. DNA methylation in CRC cell lines state inhibitis gene expression by preventing the binding of transcription factors and transcription machinery. Addition of a methyl group to an individual CpG site can disrupt binding of transcription factors or chromatin remodelers [2]. 70% of all gene promoters contain CpG-islands (CpGI), loci with an elevated CG content. In normal tissues CpGI are generally unmethylated and often serve as sites of transcription initiation, including those located outside of promoter regions [3]. Many tumor types show a CpG island methylator phenotype (CIMP) [4]

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