title: Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer.
abstract: Gene silencing by DNA hypermethylation of CpG islands is a well-characterized phenomenon in cancer. The effect of hypomethylation in particular of non-CpG island genes is much less well described. By genome-wide screening, we identified 105 genes in microsatellite stable (MSS) colorectal adenocarcinomas with an inverse correlation (Spearman's ρ ≤ -0.40) between methylation and expression. Of these, 35 (33%) were hypomethylated non-CpG island genes and two of them, APOLD1 (Spearman's ρ = -0.82) and SRPX2 (Spearman's ρ = -0.80) were selected for further analyses. Hypomethylation of both genes were localized events not shared by adjacent genes. A set of 662 FFPE DNA samples not only confirmed that APOLD1 and SRPX2 are hypomethylated in CRC but also revealed hypomethylation to be significantly (p < 0.01) associated with tumors being localized in the left side, CpG island methylator phenotype negative, MSS, BRAF wt, undifferentiated and of adenocarcinoma histosubtype. Demethylation experiments supported SRPX2 being epigenetically regulated via DNA methylation, whereas other mechanisms in addition to DNA methylation seem to be involved in the regulation of APOLD1. We further identified miR-149 as a potential novel post-transcriptional regulator of SRPX2. In carcinoma tissue, miR-149 was downregulated and inversely correlated to SRPX2 (ρ = -0.77). Furthermore, ectopic expression of miR-149 significantly reduced SRPX2 transcript levels. Our study highlights that in colorectal tumors, hypomethylation of non-CpG island-associated promoters deregulate gene expression nearly as frequent as do CpG-island hypermethylation. The hypomethylation of SRPX2 is focal and not part of a large block. Furthermore, it often translates to an increased expression level, which may be modulated by miR-149.
authors.affiliation: Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. bodil.oster@ki.au.dk
authors.forename: Bodil
authors.initials: B
authors.lastname: Øster
authors.forename: Lene
authors.initials: L
authors.lastname: Linnet
authors.forename: Lise Lotte
authors.initials: LL
authors.lastname: Christensen
authors.forename: Kasper
authors.initials: K
authors.lastname: Thorsen
authors.forename: Halit
authors.initials: H
authors.lastname: Ongen
authors.forename: Emmanouil T
authors.initials: ET
authors.lastname: Dermitzakis
authors.forename: Juan
authors.initials: J
authors.lastname: Sandoval
authors.forename: Sebastian
authors.initials: S
authors.lastname: Moran
authors.forename: Manel
authors.initials: M
authors.lastname: Esteller
authors.forename: Torben F
authors.initials: TF
authors.lastname: Hansen
authors.forename: Philippe
authors.initials: P
authors.lastname: Lamy
authors.forename: Søren
authors.initials: S
authors.lastname: Laurberg
authors.forename: Torben F
authors.initials: TF
authors.lastname: Ørntoft
authors.forename: Claus L
authors.initials: CL
authors.lastname: Andersen
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000236:Adenoma / Q000235:genetics; D001053:Apolipoproteins / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000235:genetics*; D018899:CpG Islands; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008565:Membrane Proteins; D035683:MicroRNAs / Q000378:metabolism*; D053842:Microsatellite Instability; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D001053:Apolipoproteins; C551557:MIRN149 microRNA, human; D008565:Membrane Proteins; D035683:MicroRNAs; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; C116881:SRPX2 protein, human; C010681:apolipoprotein LDL, human; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf