African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

Abstract

Background: Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe disease in children with African ancestry.

Methods: We tested for association with haplotypes at the most replicated and significant childhood-onset asthma locus at 17q12-q21 and asthma in European American and African American children. Following this, we used whole-genome sequencing data from 1060 African American and 100 European American individuals to identify novel variants on a high-risk African American-specific haplotype. We characterized these variants in silico using gene expression and ATAC-seq data from airway epithelial cells, functional annotations from ENCODE, and promoter capture (pc)Hi-C maps in airway epithelial cells. Candidate causal variants were then assessed for correlation with asthma-associated phenotypes in African American children and adults.

Results: Our studies revealed nine novel African-specific common variants, enriched on a high-risk asthma haplotype, which regulated the expression of GSDMA in airway epithelial cells and were associated with features of severe asthma. Using ENCODE annotations, ATAC-seq, and pcHi-C, we narrowed the associations to two candidate causal variants that are associated with features of T2 low severe asthma.

Conclusions: Previously unknown genetic variation at the 17q12-21 childhood-onset asthma locus contributes to asthma severity in individuals with African ancestries. We suggest that many other population-specific variants that have not been discovered in GWAS contribute to the genetic risk for asthma and other common diseases.

Keywords: Asthma; Fine mapping; Health disparities; Integrated omics; Whole-genome sequencing.

Fig. 1

Common haplotypes at the 17q12-q21 locus. A Ten genes and their relative locations at the extended locus (chr17:37815888-38143768; build hg19). Genes at the core, proximal, and distal regions are color coded (modified from Stein et al. [11] and Ober et al. [17]). The five variants defining the core region haplotypes and their locations relative to each gene are shown. B Results of logistic regression analysis for haplotypes with frequencies ≥0.05; haplotype 1 is the reference haplotype. C Allelic composition of the five variants on four haplotypes. Yellow background corresponds to alleles on the non-risk haplotype (haplotype 1) and red background corresponds to alleles on the risk haplotype (haplotype 2 in European-ancestry populations). The purple star denotes the high-risk haplotype in African Americans. D Haplotype frequencies

Fig. 2

17q12-q21 haplotypes in whole-genome sequences from individuals with asthma and homozygous for the 5-SNP haplotype. A Bar graph of haplotypes present in 44 Europeans (88 chromosomes) and 177 African Americans (354 chromosomes). The allelic composition and color code of each 5-SNP haplotype are shown under the bars. The purple star designates the African American high-risk haplotype 4. B ChromoPainter display of the haplotypes (88 chromosomes) in European Americans. C ChromoPainter display of 89 randomly selected chromosomes from the 354 chromosomes in African Americans. All chromosomes are shown in Additional file 1: Fig. S3. The LD plots include 17 SNPs previously associated with asthma in GWAS or with expression of genes at this extended locus, as previously described [11], are shown below the ChromoPainter displays. LD data are from 1000 Genomes (CEU and ASW, respectively); r² values are shown in each diamond. The darker the diamond, the more LD; black diamonds are r² = 1.0

Fig. 3

Functional characteristics of the African-specific novel variants on the high-risk asthma haplotype. A rs113282230, as a representative of the novel variants, is an eQTL for GSDMA but no other genes in upper airway epithelial cells (see Table 3 for results with all nine variants and Additional file 2 for results with all genes). BUpper panel: Chromosomal region from the 26.3-kb critical region (thick black bar) to the GSDMA gene on chromosome 17q12-q21. Vertical lines at the top show the locations of all variants in the critical region. The location of the four genes in the region, showing pcHi-C interactions (red arc) from a region in intron 1 of ORMDL3 to GSDMA. H3K27ac peaks (read counts; light blue tracks) in primary normal human epidermal keratinocytes (NHEK) (ENCODE) are shown in a region overlapping with the pcHi-C capture. Lower panel: Close-up of the 26.3-kb critical region. The nine African-specific variants enriched on haplotype 4 and eQTLs for GSDMA are shown in red. The same HEK27ac peaks as in upper panel, in addition to tracks of DNase clusters across all ENCODE cell lines, are shown. The darker the tracks the denser the DNase cluster. Two of the nine variants, rs113282230 and rs113571956, overlap with the marks of an active enhancer (H3K27ac), open chromatin (DNAse), and a putative enhancer (pcHi-C). See Fig. 4 and Additional file 1: Table S7 for additional annotations in airway epithelial cells and Additional file 1: Fig. S13 and Table S8 for additional annotations in immune cells

Fig. 4

pcHi-C loops and ATAC-seq peaks at 17q12-q21 locus from IKZF3 to GSDMA. The region harboring the 9 novel variants is shown in yellow and the location of the variants are show as vertical lines under the genes. The two candidate variants are indicated by an orange arrow. H3K27ac marks in NHEK (skin) cells from ENCODE are shown as blue tracks (also see Fig. 3B and Additional file 1: Fig. S11). ATAC-seq tracks of open chromatin for two airway epithelial cell lines (16HBE and SAEC) are shown in green. All pcHi-C interactions within this view in airway epithelial cells are shown. Two interactions between GSDMA with three of the nine variants (±1kb) were observed (shown as red loops). Two of those variants (orange arrow) were also eQTLs for GSDMA. All genes showing pcHi-C interactions with the 9 variants (±1kb) are shown in Additional file 1: Table S7

Fig. 5

Clinical phenotype associations with the novel variants and haplotype 4. A Correlation plot of the seven asthma-associated quantitative phenotypes in African American children from the URECA and APIC cohorts and their association with rs113282230 genotypes. B Bar plot showing the frequency of the 5-SNP high-risk haplotype 4 by STEP classification categories (mild, moderate, and severe) [47] in African American adults from Chicago. Severity categories and sample sizes are shown on the x-axis and the frequency of haplotype 4 is shown on the y-axis. Haplotype 4 was used as a surrogate for the nine novel SNPs because neither whole-genome sequences nor imputed genotypes for these variants were available for these individuals. C Bar plot of the frequencies of asthma severity categories in African American adults with asthma who carry at least one rs2305480-G allele, stratified by the presence or absence of haplotype 4 (x-axis). None of these individuals were homozygous for haplotype 4