Role of DNA methylation in expression control of the IKZF3-GSDMA region in human epithelial cells.

Sanny Moussette,Raquel Farias,Samar Elzein,Julie Bérubé,Bianca Ho,Cynthia G Goodyer,Abeer Al Tuwaijri,Hamid-Reza Kohan-Ghadr,Catherine Laprise,Simon Rousseau,Anna K Naumova,Aamir Ahmad

doi:10.1371/journal.pone.0172707

Abstract

Chromosomal region 17q12-q21 is associated with asthma and harbors regulatory polymorphisms that influence expression levels of all five protein-coding genes in the region: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermins A and B (GSDMA, GSDMB). Furthermore, DNA methylation in this region has been implicated as a potential modifier of the genetic risk of asthma development. To further characterize the effect of DNA methylation, we examined the impact of treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC) that causes DNA demethylation, on expression and promoter methylation of the five 17q12-q21 genes in the human airway epithelium cell line NuLi-1, embryonic kidney epithelium cell line 293T and human adenocarcinoma cell line MCF-7. 5-aza-dC treatment led to upregulation of expression of GSDMA in all three cell lines. ZPBP2 was upregulated in NuLi-1, but remained repressed in 293T and MCF-7 cells, whereas ORMDL3 was upregulated in 293T and MCF-7 cells, but not NuLi-1. Upregulation of ZPBP2 and GSDMA was accompanied by a decrease in promoter methylation. Moreover, 5-aza-dC treatment modified allelic expression of ZPBP2 and ORMDL3 suggesting that different alleles may respond differently to treatment. We also identified a polymorphic CTCF-binding site in intron 1 of ORMDL3 carrying a CG SNP rs4065275 and determined its methylation level. The site’s methylation was unaffected by 5-aza-dC treatment in NuLi-1 cells. We conclude that modest changes (8–13%) in promoter methylation levels of ZPBP2 and GSDMA may cause substantial changes in RNA levels and that allelic expression of ZPBP2 and ORMDL3 is mediated by DNA methylation.

Highlights

Genome-wide association studies (GWAS) have identified thousands of loci associated with human disease
The 17q12-q21 common polymorphisms associated with asthma delineate a genomic interval that encompasses five protein-coding genes: IKAROS family zinc finger 3 (Aiolos) (IKZF3), zona pellucida binding protein 2 (ZPBP2), gasdermin B (GSDMB), ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3), and gasdermin A (GSDMA)
IKZF3, GSDMA and GSDMB proteins are detected in human airway epithelial cells, whereas ZPBP2 appears in the glandular epithelium of the bronchus, albeit at very low levels[14]

Summary

Introduction

Genome-wide association studies (GWAS) have identified thousands of loci associated with human disease. The genetic association alone cannot accurately predict whether an individual carrier of the risk allele will develop the disease. Such an uncertain heritability is explained by differences in environmental exposures or epigenetic variation between individuals [1]. Two common haplotypes associated with expression levels and spanning about 160 kb were first delineated in studies of lymphoblastoid cell lines (LCLs) and termed HapA and HapB [7, 9]. Haplotype HapA is associated with higher expression levels of ORMDL3 and GSDMB in cells from peripheral blood, LCLs, mammary tissue, lungs and several other tissues; ZPBP2 in testes and IKZF3 in the aorta [7]. Potential involvement of these genes in predisposition to airway disease cannot be completely ruled out [7]

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Conclusion