Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure

Figures

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  Fig. 1. Summary GWAS and genetic correlation plots. a Manhattan plot of the GWAS meta-analysis. The black dotted line denotes the genome-wide significance threshold (p-value < 5e-8) while the red dotted line denotes the suggestive threshold (p-value < 1e-6). N = 448,549 independent participants. b Genetic correlation values between heart failure and other complex traits. The x-axis shows the genetic correlation r-value. Traits are color coded based on the group in which they belong. Stars denote the Bonferroni adjusted z-test p-value: (*) 0.001 < p-value < 0.01, (**) 0.0001 < p-value < 0.001, (***) p-value < 0.0001. N = 1,171,562 SNPs. Source data are provided as a Source Data file.

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  Fig. 2. Epigenetic overview of the ACTN2 locus. Manhattan plot of the ACTN2 locus and the corresponding Roadmap ChromHMM 25-state model annotations in cardiac and muscle cell-types and tissues, H3K4me1, H3K4me3, H3K27ac peaks in left ventricle, and phyloP and phastCons evolutionary conservation values. The blue box highlights the region that contains all 111 credible set variants identified by CAVIAR.

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  Fig. 3. Fine-mapping of the ACTN2 locus. a A zoomed in view of the credible set region for the ACTN2 locus in Roadmap Epigenomics. b ATAC-seq, ChIP-seq (H3K27ac, H3K4me1), and RNA-seq peaks in the hESC-to-cardiomyocyte differentiation model for the fine-mapped SNPs that overlap cardiac-specific active chromatin states. We see that one SNP (rs535411) is overlapping an ATAC-seq peak that starts to develop on Day 7 of cardiomyocyte differentiation and remains active until Day 80. Ranges for peak values: ATAC-seq: 0–127, H3K27ac-seq: 0–127, H3K4me1-seq:0–10. b was created using the UCSC genome browser (http://genome.ucsc.edu/).

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  Fig. 4. The fine-mapped regulatory element in chromosome 1 affects ACTN2 gene expression. a HiC data from cardiomyocytes on Day 80 of differentiation for the interaction between the 5 Kb region containing rs535411 and the promoters of nearby (within 1 Mb) genes. Significant interactions after Bonferroni adjustment are colored red, while non-significant interactions (Bonferroni Poisson test p > 0.05, n = 2 independent biological replicates) are colored blue. b HiC data in different stages of cardiomyocyte differentiation centered at rs535411. Black lines/dots: expected interaction counts, which follow distance-based decay, red crosses: observed interaction counts, Blue dashed line: 5 Kb region containing rs535411, cyan dashed line: 5 Kb region containing ACTN2 promoter, p-value indicates the upper-tailed Poisson probability with the expected counts as lambda. N = 2 independent biological replicates. c Boxplot of relative expression of the ACTN2 gene in cardiomyocytes edited to produce a deletion of the identified putative enhancer element and isogenic controls (n = 4 independent biological replicates). We see that expression of ACTN2 is reduced by 47% in the cardiomyocytes carrying the…

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  Fig. 5. Functional characterization of the ABO locus. a Phenome-wide association of the rs9411378 SNP across over 4000 GWAS from the GWAS Atlas. b Manhattan plot of the ABO locus overlaying a similar Manhattan plot for the ABO gene eQTL in eQTLGen. r2 is the 1000 Genomes phase 3 Europeans LD. We see that the signal colocalizes that is confirmed by coloc (posterior probability of colocalization 96%). c Expression transcripts per million for the ABO gene in GTEx whole-blood stratified by the genotype of rs8176719 (variant defining blood group O) and rs550057 (variant tagging our sentinel variant rs9411378 (LD r2 = 0.92 in 1000 Genomes Europeans)) (n = 670 independent samples). We see that the T allele for rs550057 is associated with non-O blood group, leads to decreased expression of ABO in individuals that are not blood group O and denotes increased risk of heart failure in our GWAS (GWAS beta = 0.0961, score test p-value = 6.1e-8, n = 448,549 independent participants). Boxplot center line represents the median, the bounds represent the interquartile range (IQR) (25–75%) and the whiskers extend from the bounds to the largest value no further than 1.5*IQR from the bound. Data beyond the…