Combinatorial interactions of genetic variants in human cardiomyopathy

Abstract

Dilated cardiomyopathy (DCM) is a leading cause of morbidity and mortality worldwide; yet how genetic variation and environmental factors impact DCM heritability remains unclear. Here, we report that compound genetic interactions between DNA sequence variants contribute to the complex heritability of DCM. By using genetic data from a large family with a history of DCM, we discovered that heterozygous sequence variants in the TROPOMYOSIN 1 (TPM1) and VINCULIN (VCL) genes cosegregate in individuals affected by DCM. In vitro studies of patient-derived and isogenic human-pluripotent-stem-cell-derived cardiomyocytes that were genome-edited via CRISPR to create an allelic series of TPM1 and VCL variants revealed that cardiomyocytes with both TPM1 and VCL variants display reduced contractility and sarcomeres that are less organized. Analyses of mice genetically engineered to harbour these human TPM1 and VCL variants show that stress on the heart may also influence the variable penetrance and expressivity of DCM-associated genetic variants in vivo. We conclude that compound genetic variants can interact combinatorially to induce DCM, particularly when influenced by other disease-provoking stressors.

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Fig. 1: Novel TPM1 and VCL variants together cosegregate with family members exhibiting cardiomyopathy.
Fig. 2: hPSC-derived cardiomyocytes harbouring TEK; VCL genetic variants exhibit functional and sarcomeric organization defects.
Fig. 3: ECM and muscle contraction genes are coordinately upregulated in TV-Dhet hiPSC cardiomyocytes.
Fig. 4: TV-Dhet mouse hearts exhibit reduced contractility and respond worse than WT control mouse hearts to TAC.

Code availability

All custom code used in this study can be found at http://github.com/englea52/Englerlab or https://github.com/enfarah/digital_karyotype.

Data availability

The authors declare that all data supporting the findings of this study are available within the paper and its Supplementary Information. The materials and data of this study are available from the corresponding author on reasonable request, with the exception of patient DNA and tissue, which is limited and protected by local and federal privacy regulations. Microarray study and RNA-seq data are available via dbGaP with GEO accession numbers GSE121844 and GSE121559.

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Acknowledgements

We thank the patients who participated in this study. K. DeMali (Univ. Iowa) provided the truncated Gallus gallus VCL peptide. Various experiments were conducted with the assistance, expertise and support of the following UCSD core facilities: Institute for Genomic Medicine Core, Mouse Transgenic Core, Histology and Immunohistochemistry Core, Seaweed Canyon Cardiovascular Physiology Laboratory, Microscopy Core and Human Embryonic Stem Cell Core facilities. We also thank P. Mali and H. Taylor-Weiner for assistance with hPSC culture, members of the Bruce Hamilton laboratory for helpful discussions and experimental design and members of the Chi lab for comments on the manuscript. This work was supported in part by grants from the NIH to N.C.C., J.C., R.S.R., E.D.A. and grant no. R01AG045428 to A.J.E. D.C.D. was supported by a CIRM pre-doctoral fellowship (grant no. TG2-01154) and an NIH pre-doctoral training grant (grant no. T32 GM008666). C.L.H. was supported by post-doctoral fellowships from the American Heart Association (grant no. 15POST25720070) and NIH (grant no. F32HL131424). J.C. is an American Heart Association Endowed Chair. E.N.F. was supported by a NIH pre-doctoral training grant (grant no. 4T32HL007444-34).

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Authors

Contributions

D.C.D., C.L.H., C.C., A.J.E., R.S.R. and N.C.C. conceived the project. D.C.D., C.L.H., C.C., N.T., A.M.M., T.L., N.D.D., Q.P., E.N.F., Y.G., K.P.T., V.D.T., J.C. and K.L.P. planned the design of studies and conducted experiments. D.C.D. and E.D.A. recruited patients and generated human fibroblast lines. D.C.D. generated CRISPR-edited mouse lines and C.L.H. generated CRISPR-edited hESC lines. Q.P., J.C., K.L.P. and N.J.S. assisted in data interpretation and provided experimental advice. D.C.D., C.L.H., C.C., A.J.E., R.S.R. and N.C.C. prepared and wrote the manuscript.

Corresponding authors

Correspondence to Adam J. Engler or Robert S. Ross or Neil C. Chi.

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Supplementary information

Supplementary Information

Supplementary figures, tables, references and video captions.

Reporting summary

Supplementary Video 1

Representative parasternal short axis left ventricular views of mouse echocardiography pre-surgery for WT mice.

Supplementary Video 2

Representative parasternal short axis left ventricular views of mouse echocardiography post-TAC for WT mice.

Supplementary Video 3

Representative parasternal short axis left ventricular views of mouse echocardiography pre-surgery for VclVFS/+ mice.

Supplementary Video 4

Representative parasternal short axis left ventricular views of mouse echocardiography post-TAC for VclVFS/+ mice.

Supplementary Video 5

Representative parasternal short axis left ventricular views of mouse echocardiography pre-surgery for Tpm1TEK/+ mice.

Supplementary Video 6

Representative parasternal short axis left ventricular views of mouse echocardiography post-TAC for Tpm1TEK/+ mice.

Supplementary Video 7

Representative parasternal short axis left ventricular views of mouse echocardiography pre-surgery for TV-Dhet mice.

Supplementary Video 8

Representative parasternal short axis views of TV-Dhet mouse echocardiography reveals grossly decreased left ventricular function post-TAC.

Supplementary Table 2

Differentially expressed genes revealed by RNA-seq of TV-Dhet, and control hiPSC-cardiomyocytes.

Supplementary Table 8

Primers, guideRNA (gRNA), and single strand DNA oligonucleotide (ssDNA) sequences.

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Deacon, D.C., Happe, C.L., Chen, C. et al. Combinatorial interactions of genetic variants in human cardiomyopathy. Nat Biomed Eng 3, 147–157 (2019). https://doi.org/10.1038/s41551-019-0348-9

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