Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte

Xianghai Liao; Peter J. Kennel; Bohao Liu; Trevor R. Nash; Richard Z. Zhuang; Amandine Godier-Furnémont; Chenyi Xue; Rong Lü; P.C. Colombo; Nir Y. Uriel; Muredach P. Reilly; Steven O. Marx; Gordana Vunjak‐Novakovic; Veli Kemal Topkara

doi:10.1172/jci.insight.161788

GenomicsJCI InsightJan 19, 2023

Peer-reviewed journal article

Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte

Xianghai Liao, Peter J. Kennel iD, Bohao Liu iD, Trevor R. Nash iD, Richard Z. Zhuang iD, Amandine Godier-Furnémont iD, Chenyi Xue iD, Rong Lü iD, P.C. Colombo iD, Nir Y. Uriel iD, Muredach P. Reilly iD, Steven O. Marx iD, Gordana Vunjak‐Novakovic iD, Veli Kemal Topkara iD

Abstract

BackgroundHuman heart failure is characterized by global alterations in the myocardial DNA methylation profile, yet little is known about epigenetic regulation of non-coding transcripts and potential reversibility of DNA methylation with left ventricular assist device (LVAD) support. MethodGenome-wide mapping of myocardial DNA methylation was performed in 36 patients with end-stage heart failure at the time of LVAD implant, 8 patients at the time of LVAD explant, and 7 non-failing controls using high-density bead array platform. Transcriptomic and functional studies were performed in human induced pluripotent stem cell derived cardiomyocytes (iPSCs). ResultsEtiology-specific analysis revealed 2079 differentially methylated positions (DMPs) in ischemic cardiomyopathy (ICM) and 261 DMPs in non-ischemic cardiomyopathy (NICM). 192 DMPs were common to ICM and NICM. Analysis of paired samples before and after LVAD support demonstrated reverse methylation of only 3.2% of HF-specific DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FAM65A, FBXO16, EFCAB13, AKAP13, RPTOR) or hypermethylated and downregulated (TBX3) in ICM and NICM patients. A novel cardiac-specific super-enhancer lncRNA (LINC00881) is hypermethylated and downregulated in the failing human heart. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown significantly reduced peak calcium amplitude in the beating human iPSCs. ConclusionsFailing human heart exhibits etiology-specific changes in DNA methylation including coding and non-coding regions, which are minimally reversible with mechanical unloading. Epigenetic reprogramming may be necessary to achieve transcriptional normalization and sustained clinical recovery from heart failure.

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