17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

Abstract

Asthma and autoimmune disease susceptibility has been strongly linked to genetic variants in the 17q21 haploblock that alter the expression of ORMDL3; however, the molecular mechanisms by which these variants perturb gene expression and the cell types in which this effect is most prominent are unclear. We found several 17q21 variants overlapped enhancers present mainly in primary immune cell types. CD4 þ T cells showed the greatest increase (threefold) in ORMDL3 expression in individuals carrying the asthma-risk alleles, where ORMDL3 negatively regulated interleukin-2 production. The asthma-risk variants rs4065275 and rs12936231 switched CTCF-binding sites in the 17q21 locus, and 4C-Seq assays showed that several distal cis-regulatory elements upstream of the disrupted ZPBP2 CTCF-binding site interacted with the ORMDL3 promoter region in CD4 þ T cells exclusively from subjects carrying asthma-risk alleles. Overall, our results suggested that T cells are one of the most prominent cell types affected by 17q21 variants.

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

“…S4 and Table S4 the cell types most susceptible to the potential effects of genetic variants associated with common immune-mediated diseases. rs12936231, a variant associated with several autoimmune diseases and asthma, whose functional effects have been previously described (Schmiedel et al, 2016), is associated with the modulation of expression of ORMDL3 and GSDMB in lymphocyte subsets and not in cells of myeloid origin. In contrast, the ERAP2 peak eQTL (rs2548540), which was also a lead GWAS SNP for multiple autoimmune diseases, caused genotype-dependent expression differences across all the immune cell types studied (Fig.…”

“…3H, top panel). Non-coding SNPs in general have previously been shown to perturb the function of cell-specific enhancers and thus affect gene expression in specific cell types (Schmiedel et al, 2016). As expected, several of the cis -eQTLs in the 12p13.2 locus directly overlapped many cell-specific DNase sites present in NK cells and naïve CD8 + T cells (Fig.…”

“…All siRNA knockdown studies were performed as previously described (Schmiedel et al, 2016). Primary immune cells were negatively pre-enriched for the cell populations of interest by MACS-based isolation (Miltenyi Biotec) following the manufacturer’s instructions, and cultured in Iscove’s Modified Dulbecco’s Medium (IMDM; Invitrogen) supplemented with 5% (vol/vol) heat-inactivated fetal bovine serum (FBS) and 2% (vol/vol) human AB serum (CellGro).…”

The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis

“…Further sustaining a possible role of GSDMB in the pathogenesis of MS, the knockdown of GSDMB in memory CD4 + T-cells was shown to augment the production of cytokines such as tumor necrosis factor (TNF), interleukin (IL)-13, and IL-16 [61]. In addition, Das and colleagues [62] demonstrated that the GSDMB Δ6 isoform overexpression in primary human bronchial epithelial cells can lead to increased expression levels, among others, of the transforming growth factor beta 1 ( TGFB1 ) and matrix metallopeptidase 9 ( MMP9 ) genes.…”

GSDMAdrives the most replicated association with asthma in naïve CD4+T cells

“…13,14 Several studies explored the complex interactions between SNPs, gene expressions and epigenetic modifications at this locus, primarily focusing on the levels of expressed ORMDL3 and GSDMB. 12,[15][16][17][18][19][20][21][22][23][24][25] Given that DNA methylation and gene expression signals are cell-type specific, 26,27 isolated materials such as lymphocytes from blood [17][18][19][20][21] and, to a lesser extent, bronchial epithelial cells from biopsies of bronchi or bronchoalveolar lavages 15,16 have been used in a number of studies to investigate such interactions.…”