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

Heart failure is a major public health problem affecting over 23 million people worldwide. In this study, we present the results of a large scale meta-analysis of heart failure GWAS and replication in a comparable sized cohort to identify one known and two novel loci associated with heart failure. Heart failure sub-phenotyping shows that a new locus in chromosome 1 is associated with left ventricular adverse remodeling and clinical heart failure, in response to different initial cardiac muscle insults. Functional characterization and fine-mapping of that locus reveal a putative causal variant in a cardiac muscle specific regulatory region activated during cardiomyocyte differentiation that binds to the ACTN2 gene, a crucial structural protein inside the cardiac sarcolemma (Hi-C interaction p-value = 0.00002). Genome-editing in human embryonic stem cell-derived cardiomyocytes confirms the influence of the identified regulatory region in the expression of ACTN2. Our findings extend our understanding of biological mechanisms underlying heart failure.


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Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A list of figures that have associated raw data -A description of any restrictions on data availability in the Gene Expression Omnibus under the accession number GSE116862 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116862] whereas the sequencing raw reads for ATAC-seq and H3K4me1-seq as well as all processed epigenetic, RNA-seq and HiC data in hESC-CMs for our loci of interest were made available at the following Zenodo repository (https://zenodo.org/record/3612522#.XiSE_i2ZOgA). Lastly, the source data underlying Figures 1b, 3a, c, 4c and Supplementary Figures 2, 6a, c, 10a are provided as a Source Data file.
We performed a large scale GWAS meta-analysis of five cohorts that study cardiovascular disease and two population genetics cohorts, all of European ancestry comprising a total of 10,976 heart failure cases and 437,573 controls For each individual study we performed sample level filtering (excluding samples with assigned and genotype sex discrepancy, extreme deviations from heterozygosity or missingness). We also excluded individuals that were not of European Ancestry and for every group of individuals that were related (Identity by descent (IBD) >0.125) we randomly selected one.
We replicated our findings in an independent cohort of 24,829 Heart failure cases and 1,614,513 controls of European ancestry within the 23andMe research cohort.
Not applicable. This is not a randomized trial Not applicable. This is not an intervention trial.
H9 hESC MLC2v:H2B-GFP reporter transgenic line was generated in Sylvia Evans's lab (Veevers et al. PMID: 30122443) from a wild-type H9 hESC cell line purchased by WiCell. H9 hESC with and without deletion of an identified 1400 bp enhancer region in chromosome 1 were generated in Emmanouil Tampakakis' lab from a wild-type H9 hESC cell line purchased by WiCell.
H9 hESC MLC2v:H2B-GFP reporter transgenic line was generated and authenticated in Sylvia Evans's lab by Short Tandem Repeat (STR) profiling analysis. Enhancer-deleted H9 hESC cell lines were authenticated using target PCR experiments in Emmanouil Tampakakis' lab All cell lines used in this study tested negative for Mycoplasma contamination.
No commonly misidentified lines were used.