Impact of mechanical unloading on genome-wide DNA methylation profile of the failing human heart

Xianghai Liao; Peter J. Kennel; Bohao Liu; Trevor R. Nash; Richard Z. Zhuang; Amandine F. Godier-Furnemont; Chenyi Xue; Rong Lu; Paolo C. Colombo; Nir Uriel; Muredach P. Reilly; Steven O. Marx; Gordana Vunjak-Novakovic; Veli K. Topkara

doi:10.1172/jci.insight.161788

Impact of mechanical unloading on genome-wide DNA methylation profile of the failing human heart

Xianghai Liao,¹ Peter J. Kennel,¹ Bohao Liu,² Trevor R. Nash,² Richard Z. Zhuang,² Amandine F. Godier-Furnemont,² Chenyi Xue,¹ Rong Lu,¹ Paolo C. Colombo,¹ Nir Uriel,¹ Muredach P. Reilly,⁴ Steven O. Marx,¹ Gordana Vunjak-Novakovic,² and Veli K. Topkara¹

Published January 19, 2023 - More info

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Abstract

Heart failure (HF) is characterized by global alterations in myocardial DNA methylation, yet little is known about epigenetic regulation of the non-coding genome and potential reversibility of DNA methylation with left ventricular assist device (LVAD) therapy. Genome-wide mapping of myocardial DNA methylation in 36 HF patients at LVAD implantation, 8 patients at LVAD explantation, and 7 non-failing donors using a high-density bead array platform identified 2079 differentially methylated positions (DMPs) in ischemic cardiomyopathy and 261 DMPs in non-ischemic cardiomyopathy. LVAD support resulted in normalization of only 3.2% of HF-associated DMPs. Methylation-expression correlation analysis yielded several protein-coding genes that are hypomethylated and upregulated (HTRA1, FBXO16, EFCAB13, AKAP13) or hypermethylated and downregulated (TBX3) in HF. A novel cardiac-specific super-enhancer lncRNA (LINC00881) is hypermethylated and downregulated in human HF. LINC00881 is an upstream regulator of sarcomere and calcium channel gene expression including MYH6, CACNA1C, and RYR2. LINC00881 knockdown reduces peak calcium amplitude in the beating human iPS cell derived cardiomyocytes. Collectively, these data suggest that HF-associated changes in myocardial DNA methylation within coding and non-coding genome are minimally reversible with mechanical unloading. Epigenetic reprogramming strategies may be necessary to achieve sustained clinical recovery from heart failure.

Impact of mechanical unloading on genome-wide DNA methylation profile of the failing human heart

Xianghai Liao,¹ Peter J. Kennel,¹ Bohao Liu,² Trevor R. Nash,² Richard Z. Zhuang,² Amandine F. Godier-Furnemont,² Chenyi Xue,¹ Rong Lu,¹ Paolo C. Colombo,¹ Nir Uriel,¹ Muredach P. Reilly,⁴ Steven O. Marx,¹ Gordana Vunjak-Novakovic,² and Veli K. Topkara¹

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Impact of mechanical unloading on genome-wide DNA methylation profile of the failing human heart

Xianghai Liao,1 Peter J. Kennel,1 Bohao Liu,2 Trevor R. Nash,2 Richard Z. Zhuang,2 Amandine F. Godier-Furnemont,2 Chenyi Xue,1 Rong Lu,1 Paolo C. Colombo,1 Nir Uriel,1 Muredach P. Reilly,4 Steven O. Marx,1 Gordana Vunjak-Novakovic,2 and Veli K. Topkara1

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Xianghai Liao,¹ Peter J. Kennel,¹ Bohao Liu,² Trevor R. Nash,² Richard Z. Zhuang,² Amandine F. Godier-Furnemont,² Chenyi Xue,¹ Rong Lu,¹ Paolo C. Colombo,¹ Nir Uriel,¹ Muredach P. Reilly,⁴ Steven O. Marx,¹ Gordana Vunjak-Novakovic,² and Veli K. Topkara¹