Inducible expression quantitative trait locus analysis of the MUC5AC gene in asthma in urban populations of children

Abstract

Background: Mucus plugging can worsen asthma control, lead to reduced lung function and fatal exacerbations. MUC5AC is the secretory mucin implicated in mucus plugging, and MUC5AC gene expression has been associated with development of airway obstruction and asthma exacerbations in urban children with asthma. However, the genetic determinants of MUC5AC expression are not established.

Objectives: This study sought to assess single-nucleotide polymorphisms (SNPs) that influence MUC5AC expression and relate to pulmonary functions in childhood asthma.

Methods: This study used RNA-sequencing data from upper airway samples and performed cis-expression quantitative trait loci (eQTL) and allele-specific expression analyses in 2 cohorts of predominantly Black and Hispanic urban children, a high asthma-risk birth cohort, and an exacerbation-prone asthma cohort. Inducible MUC5AC eQTLs were further investigated during incipient asthma exacerbations. Significant eQTLs SNPs were tested for associations with lung function measurements and their functional consequences were investigated in DNA regulatory databases.

Results: Two independent groups of SNPs in the MUC5AC gene that were significantly associated with MUC5AC expression were identified. Moreover, these SNPs showed stronger eQTL associations with MUC5AC expression during asthma exacerbations, which is consistent with inducible expression. SNPs in 1 group also showed significant association with decreased pulmonary functions. These SNPs included multiple EGR1 transcription factor binding sites, suggesting a mechanism of effect.

Conclusions: These findings demonstrate the applicability of organ-specific RNA-sequencing data to determine genetic factors contributing to a key disease pathway. Specifically, they suggest important genetic variations that may underlie propensity to mucus plugging in asthma and could be important in targeted asthma phenotyping and disease management strategies.

Keywords: Asthma; MUC5AC; expression quantitative trait.

Figure 1.

MUC5AC SNPs showed an eQTL effect in the URECA cohort a, The locus zoom plot for the URECA cohort showing eQTLs. Among the 86 cis SNPs detected, 43 showed significant association with MUC5AC expression (FDR< 0.05). Points are colored according to the minor allele frequency of the SNP and the point size reflects the percent of study subjects with a call at that SNP. b, An LD matrix shows the pairwise r² values among these 86 SNPs. c, For the block A representative SNP, rs1132436, MUC5AC gene expression was increased according to the number of minor alleles. d, ASE of heterozygotes at rs1132436 showed an increased proportion of minor allele reads. e, For the block B representative SNP, rs1292198170, MUC5AC gene expression was decreased in heterozygotes. f, ASE of heterozygotes at rs1292198170 showed a decreased proportion of minor allele reads. g, Genotypes at rs1132436 and rs1292198170 showed an additive effect on MUC5AC expression. Boxplots show mean values, interquartile ranges, and 1.5 interquartile ranges.

Figure 2.

MUC5AC SNPs showed an inducible eQTL effect during asthma exacerbations in the MUPPITS cohort a, The locus zoom plot for the MUPPITS cohort showing eQTLs. Among the 24 cis SNPs detected, 5 showed significant association with MUC5AC expression (FDR<0.05). Points are colored according to the minor allele frequency of the SNP and the point size reflects the percent of study subjects with a call at that SNP. b, An LD matrix shows the pairwise r² values among these 24 SNPs. c, For the block A representative SNP rs1132436, MUC5AC gene expression was increased according to the number of minor alleles and showed an inducible eQTL effect during exacerbations compared to non-exacerbation samples. d, ASE of heterozygotes at rs1132436 showed an increased proportion of minor allele reads. e, For the block B representative SNP, rs1292198170, MUC5AC gene expression showed a non-significant (FDR=0.24) decrease in heterozygotes relative to homozygotes and showed an inducible eQTL effect during exacerbations compared to non-exacerbation samples (p=3.9E-3). f, ASE of heterozygotes at rs1292198170 showed a decreased proportion of minor allele reads. g, Genotypes at rs1132436 and rs1292198170 showed an additive effect on MUC5AC expression. Boxplots show mean values, interquartile ranges, and 1.5 interquartile ranges.

Figure 3.

MUC5AC SNP rs1132436 showed a significant association with pulmonary function in both URECA and MUPPITS. a, The FEV₁/FVC ratio was significantly associated with the genotype at the block A representative SNP rs1132426 in the URECA cohort. b, Both the FEV₁/FVC ratio and FEV₁ % predicted were significantly associated with the genotype at the block A representative SNP rs1132426 in the MUPPITS cohort. Boxplots show mean values, interquartile ranges, and 1.5 interquartile ranges.