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.

Abstract

What's new?

DNA hypo- and hypermethylation both occur frequently in colorectal cancer, yet so far most attention has focused on the role of hypermethylation in silencing critical genes with CpG island promoters. This study provides evidence that hypomethylation of non-CpG island promoters deregulate gene expression nearly as frequently as does the hypermethylation of CpG island promoters. The authors identified 35 genes whose non-CpG island promoters were hypomethylated and expression levels inversely correlated. Hypomethylation of SRPX2 also correlated with poorly differentiated tumors, indicating its important role during CRC progression. The authors further identified miR-149 as a potential novel post-transcriptional regulator of SRPX2.

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References

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Citing Literature

Volume132, Issue10

15 May 2013

Pages 2303-2315

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IJC_27921_sm_SuppFig1.eps212.4 KB	Supporting Information Figure 1.
IJC_27921_sm_SuppFig2.eps1.5 MB	Supporting Information Figure 2.
IJC_27921_sm_SuppFig3.eps904.8 KB	Supporting Information Figure 3.
IJC_27921_sm_SuppFig4.eps216.3 KB	Supporting Information Figure 4.
IJC_27921_sm_SuppTab1.doc30.5 KB	Supporting Information Table 1.
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IJC_27921_sm_SuppTab3.doc34.5 KB	Supporting Information Table 3.
IJC_27921_sm_SuppTab4.xls61 KB	Supporting Information Table 4.
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IJC_27921_sm_SuppTab6.doc48.5 KB	Supporting Information Table 6.
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Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

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Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer

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