A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis

Abstract

Background Genetic variants in the chromosomal region 17q21 are consistently associated with asthma. However, mechanistic studies have not yet linked any of the associated variants to a function that could influence asthma, and as a result, the identity of the asthma gene(s) remains elusive. Objectives We sought to identify and characterize functional variants in the 17q21 locus. Methods We used the Exome Aggregation Consortium (ExAC) browser to identify coding (amino acid-changing) variants in the 17q21 locus. We obtained asthma association measures for these variants in both the GERA cohort (16,274 cases and 38,269 matched controls) and the EVE Consortium study (5,303 asthma cases and 12,560 individuals). Gene expression and protein localization were determined by quantitative RT-PCR and fluorescence immunostaining, respectively. Molecular and cellular studies were performed to determine the functional effects of coding variants. Results Two coding variants (rs2305480 and rs11078928) of the gasdermin B (GSDMB) gene in the 17q21 locus were associated with lower asthma risk in both GERA (OR = 0.92; P= 1.01 × 10−6) and EVE (OR= 0.85; Joint PEVE = 1.31 ×10−13). In GERA, rs11078928 had a minor allele frequency (MAF) of 0.45 in unaffected (non-asthmatic) controls and 0.43 in asthma cases. For European Americans in EVE the MAF of rs2305480 was 0.45 for controls and 0.39 for cases; for all EVE subjects the MAF was 0.32 for controls and 0.27 for cases. GSDMB is highly expressed in differentiated airway epithelial cells, including the ciliated cells. We found that when the GSDMB protein is cleaved by inflammatory caspase-1 to release its N-terminal fragment, potent pyroptotic cell death was induced. The splicing variant rs11078928 deletes the entire exon 6, which encodes 13 amino acids in the critical N-terminus, and abolishes the pyroptotic activity of the GSDMB protein. Conclusions Our study identified a functional asthma variant in the GSDMB gene of the 17q21 locus and implicates GSDMB-mediated epithelial cell pyroptosis in pathogenesis.

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

“…298 The GSDMB locus (17q21) has been consistently identified as a contributor to genetic susceptibility to 299 asthma 42 and other autoimmune diseases, such as type 1 diabetes 51 , ulcerative colitis 52 or rheumatoid 300 arthritis 53 . Although its exact function is unknown, GSDMB is highly expressed in human bronchial ep-301 ithelial cells in asthma 54,55 , and it is known that overexpression of the human GSDMB transgene in mice 302 induces an asthma phenotype 55 . In addition, the lipid-binding N-terminal domain of GSDMB and other 303 gasdermins causes pyroptotic cell death 56 , potentially leading to the release of inflammatory molecules 304 that trigger the asthma pathophysiology.…”

“…307 5d). Allele C of the splice acceptor variant rs11078928 (chr17:38064469, T/C) has been shown to lead to 308 the skipping of exon 6, which encodes 13 amino acids in the N-terminal domain, disrupting its pyroptotic 309 activity 54 . While the major allele (T) is associated with a higher incidence of asthma, the C allele confers 310 a lower asthma risk 54 .…”

“…Allele C of the splice acceptor variant rs11078928 (chr17:38064469, T/C) has been shown to lead to 308 the skipping of exon 6, which encodes 13 amino acids in the N-terminal domain, disrupting its pyroptotic 309 activity 54 . While the major allele (T) is associated with a higher incidence of asthma, the C allele confers 310 a lower asthma risk 54 . We have identified rs11078928 as an sQTL for GSDMB, whose alternative allele 311 C precisely promotes expression of isoforms GSDMB-001 and GSDMB-002 (exon 6 skipping) vs isoform 312 GSDMB-003 (exon 6 inclusion) ( Fig.…”

“…Pairs failing this test (FDR 52 across all nominal tests > 0.05) were still assessed for significance and taken into account for multiple 53 testing correction, but they were not reported as significant sQTLs. 54 Cell type heterogeneity 55 We employed xCell 25 to estimate the enrichment of 64 reference cell types from the bulk expression profile 56 of each GTEx sample. We applied the xCellAnalysis function in the xCell R package to the full gene 57 expression TPM matrix (56,205 genes × 11,688 samples), in order to maximize tissue heterogeneity.…”

Specific type 1 diabetes risk genes underpin age-at-diagnosis and indicate joint defects in immunity, beta-cell fragility and responses to viral infections in early-onset disease

“…IKZF3 is a transcriptional repressor with a key role in B-cell activation and differentiation 20 and T cell differentiation 21 . ORMDL3 is a central regulator of sphingolipid biosynthesis 22 and has also been proposed to negatively regulate store-operated calcium, lymphocyte activation and cytokine production 18,23 , while GSDMB can act as a pyroptotic protein 24 . Therefore one or more of these genes may be causal for T1D risk.…”