Epigenetic Regulation in Dilated Cardiomyopathy

Abstract

Dilated cardiomyopathy (DCM) is a non-ischemic heart muscle disease characterized by impaired contractility, cardiac dilation, and heart failure, with both genetic and non-genetic causes. Emerging evidence highlights epigenetic mechanisms, including deoxyribonucleic acid (DNA) methylation, histone modifications, chromatin remodeling, and noncoding RNAs, as critical regulators of gene expression in DCM pathogenesis. This article explores familial DCM linked to pathogenic variants in genes like LMNA and TTN, as well as non-genetic forms such as diabetic and autoimmune DCM. By summarizing recent discoveries, it highlights the epigenetic factors in bridging genetic and environmental influences, offering potential biomarkers and therapeutic targets for improved DCM management.

1. Introduction

Dilated cardiomyopathy (DCM) is a non-ischemic heart muscle disease characterized by reduced systolic function and cardiac dilation in the absence of coronary artery disease, hypertension, valvular disease, or congenital heart disease.¹ This condition leads to impaired contractility and reduced cardiac output, which can ultimately result in heart failure (HF). The causes of DCM are diverse, including both genetic and non-genetic factors. For genetic (familial) DCM, pathogenic variants (particularly those encoding structural proteins of the heart muscle) can lead to DCM, even though their penetrance and phenotypes can vary widely. Other non-genetic causes include infections, inflammation, and immune-mediated diseases.¹ DCM is a common cause of HF in adults younger than 50 and is often associated with significant morbidity and mortality, affecting the quality of life of patients and imposing substantial healthcare burdens.² However, a considerable portion of DCM cases is classified as idiopathic DCM, where the exact cause remains initially unknown. Understanding DCM has expanded from focusing solely on pathogenic variants to encompassing a more complex interaction between genetic and environmental factors.

Epigenetics modulates DCM by altering the expression of genes involved in cardiac function, which can lead to abnormal cardiac hypertrophy, fibrosis, and impaired contractility, contributing to the development of cardiomyopathies like DCM and hypertrophic cardiomyopathy. Epigenetics functions at multiple levels, including DNA methylation, chromatin remodeling, histone modifications, and noncoding RNAs, which work together to regulate gene expression. DNA methylation typically represses gene transcription, depending on the site of methylation, while histone modifications can either promote or inhibit transcription based on the specific type of modification. Long-range and high-degree chromatin interactions forming topologically associating domains (TADs) play a crucial role in mediating essential cellular functions, including the regulation of gene expression. Additionally, noncoding RNAs, such as microRNAs and lncRNAs, play critical roles in fine-tuning gene expression. Collectively, these epigenetic mechanisms provide a dynamic regulatory network that significantly contributes to the onset and progression of DCM, eventually leading to HF. In essence, epigenetic changes can modify gene expression without changing the underlying DNA sequence, impacting the heart's ability to respond to stress and maintain normal function. Hence, epigenetics represents a layer of regulation that bridges these genetic and environmental influences, controlling how genes are expressed without altering the DNA sequence. Exploring epigenetic mechanisms in DCM may reveal new therapeutic opportunities, offering insights into how gene expression patterns contribute to disease progression and potential interventions.³

Over the past decades, with the advent of cutting-edge technologies such as High-throughput Chromosome Conformation Capture (Hi-C) and proximity ligation-assisted ChIP-Seq (PLAC-Seq, also known as Hi-ChIP) for analyzing higher-order chromatin structures and chromosome spatial organization, transposase-accessible chromatin sequencing (ATAC-seq) for assessing chromatin accessibility, DNA methylation sequencing, and RNA-seq, miRNA-seq, and single-cell RNA-seq (scRNA-seq) for transcriptome profiling, numerous research groups, including ours, have explored the effects of epigenetic regulation on gene expression at various levels in human heart tissues or human-derived cardiac cells. ^4–10 We have summarized these findings in Table 1.

Table 1:

Overview of epigenetic study on DCM using human cardiac tissues from 2019–2024

Epigenetic regulation	Methods	Key findings	References
DNA Methylation	Whole genome bisulfite sequencing	• Differential methylation found in promoter CpG islands regulating downstream genes. • Hypermethylation linked to oxidative metabolism; hypomethylation to glycolysis. • NRF1 motif hypermethylation disrupts mitochondrial biogenesis regulation.	Pepin et al, 2019
DNA Methylation	Whole genome bisulfite sequencing	• TTN-AS1 shows disease-dependent differential DNA methylation affecting alternative splicing.	Gi, et al, 2020; Pepin et al, 2019
Histone Modification & chomatin remodeling	ChIP-seq; PLAC-seq/Hi-ChIP	• H3K4me3 active promoter signatures are significantly reduced in the DCM cardiac genome. • Super-enhancers are enriched in genomic regions with long-range chromatin interactions. • Identified potential novel factors contributing to DCM.	Liu, et al, 2020
Histone Modification & chomatin remodeling	ChIP-seq; PLAC-seq/Hi-ChIP	• Identified differential H3K27ac between nonfailing and HF hearts and histone acetylation quantitative trait loci (haQTLs) • Identified 62 novel cardiac causal genes and their association with haQTL.	Tan et al,, 2020
Histone Modification & chomatin remodeling	HiChIP(H3K27ac); in situ Hi-C; ChIP-seq; ATAC-seq	• High-resolution 3D epigenomic mapping and computational analysis were conducted in human DCM hearts. • Enhancer-promoter connections are extensively rewired and found in pre-accessible chromatin regions in DCM. • The transcription factor HAND1 is highly enriched at DCM-specific H3K27ac loop anchors.	Feng, et al, 2022
ncRNA	Methylation 450K Bead Chip and EPIC Bead Chip	• Identified a potential novel cardiac-specific super-enhancer long noncoding RNA (lncRNA) (LINC00881). LINC00881 is downregulated in ICM and NICM hearts compared to NF hearts.	Liao, et al, 2023
Chromatin Remodeling	ChIP-seq	• TRIM35 directly monoubiquitinate H2BK120 in mature crdiomhocytes. • P53 is elevated at promoter sites for PUMA and P21 in DCM LV samples compared to NF controls.	Lorenzana-Carrillo, et al, 2024

This article aims to provide an updated and comprehensive overview of the current understanding of both genetic (familial) and non-genetic forms of dilated cardiomyopathy (DCM), with a particular emphasis on the role of epigenetic modifications in its pathophysiology. We will first discuss the current findings associated with the epigenetic regulation of idiopathic dilated cardiomyopathy, describing each layer of epigenetic regulation linked to iDCM. Following this, we will focus on studies examining how epigenetic regulation interacts with pathogenic variants associated with familial DCM, and highlight specific epigenetic modifications linked to these genetic drivers. Next, we will discuss the mechanisms underlying non-genetic DCM, focusing primarily on diabetic and autoimmune factors. We hope to underscore the importance of such epigenetic factors in the development and disease progression of DCM and how targeting epigenetic modifications could pave the way for innovative therapeutic strategies.

2. Idiopathic DCM

More than 50% of DCM cases have no known cause and are classified as idiopathic DCM (iDCM). With the advances in genetic sequencing technology, many idiopathic DCMs are increasingly linked to genetics. In this section, we will summarize the important epigenetic studies that have utilized human heart tissues or genetic mouse models for DCM in the past five years.

2.1. DNA Methylation and Demethylation

DNA methylation usually occurs on the fifth carbon atom of cytosine (5mC).¹¹ Another important epigenetic mark is 5-Hydroxymethylcytosine (5hmC), which is known as the “sixth base” in mammalian DNA, converting from 5-mc by the ten-eleven translocation proteins.¹² Their effect on gene activity depends on genomic regions, including CpG islands, intergenic regions, and genomic regions. The details of its regulation on gene activity have been reviewed previously in detail.³ Using human left ventricle (LV) samples from DCM patients without severe coronary artery stenosis or hypertension and an immunostaining method for methylated DNA 5mC, Watanabe et al. observed that nuclear DNA methylation was significantly increased in cardiomyocytes but not in other cell types.¹³ Immunoelectron microscopy revealed the increased DNA methylation was mostly present in the heterochromatin, which was significantly related to LV structure and function. Tabish et al. performed genome-wide 5mc and 5hmc profiling in an MYBPC3 (myosin binding protein-C) mutated DCM mouse model using methylated DNA immunoprecipitation-sequencing (MeDIP-seq).¹⁴ They identified 957 5mC-altered genes and 2,022 5hmC-altered genes in DCM, and differential 5mc and 5hmc were linked to sarcomere genes, especially at Mhy6 and Myh7 loci. Pepin et al. analyzed genome-wide DNA methylation profiles in LV tissues from pre-LV assist device (LVAD) patients and identified differential methylation localized to promoter-associated CpG islands, key regulatory regions for downstream genes. Hypermethylated promoters were linked to genes involved in oxidative metabolism, while hypomethylated promoters enriched glycolytic pathways. Additionally, hypermethylation of the nuclear respiratory factor 1 (NRF1) motif suggested binding-site competition, potentially disrupting its role as a regulator of mitochondrial biogenesis.⁴

2.2. Histone Modification and Chromatin Remodeling

Histone modifiers have been shown to play crucial roles in DCM development and cardiac metabolism over recent decades.^3,15 A recent study using a cardiac-specific pathogenic variant mouse model found that histone lysine demethylase 8 (KDM8) may regulate cardiac metabolism in DCM. KDM8 demethylates H3K36me2, a mark typically linked to active transcription.¹⁶ Ahmed et al. demonstrated that KDM8 controls cardiac mitochondrial activity and metabolism by suppressing Tbx15 expression and maintaining metabolic gene expression, preventing DCM. Deregulation of the KDM8-TBX15 axis contributes to myocardial remodeling and DCM initiation, suggesting it is a potential target for early intervention in DCM.¹⁷

Recent studies have uncovered additional mechanisms of DCM involving chromatin remodeling. Lorenzana-Carrillo et al. demonstrated that TRIM35, an E3-ubiquitin ligase, is upregulated early in DCM pathogenesis. Using TRIM35-overexpressing mice and DCM heart samples, they showed that TRIM35 monoubiquitinates lysine-120 (K120) on histone H2B in postnatal cardiomyocytes, leading to chromatin remodeling and increased p53 accessibility, enhancing transcription.¹⁰ Feng et al. constructed 3D epigenome and transcriptome maps of human DCM and non-failing hearts using HiChIP (H3K27ac), in situ Hi-C, ChIP-seq, ATAC-seq, and RNA-seq.⁸ These maps revealed extensive reprogramming of active regulatory elements (H3K27ac peaks) and connectomes (H3K27ac loops) in DCM hearts, contributing to transcriptional dysregulation. For example, decreased H3K27 acetylation at the MYH6 locus corresponded with reduced MYH6 expression in DCM hearts, consistent with previous genome-wide studies.^6,7 (See section 3.4 for detail) Further analysis identified HAND1 as a key transcription factor enriched in H3K27ac loops, driving enhancer/promoter reprogramming and promoting DCM pathogenesis.

2.3. Non-coding RNA (ncRNA)

Although numerous ncRNAs have been discovered to play an important role in DCM, more and more findings are uncovering novel ncRNAs that lead to potential new mechanistic explanations, drug targets, or potential biomarkers of DCM. Luo et. al. aimed to discover novel lncRNA biomarkers to be associated with DCM using existing datasets. ¹⁸ Using bioinformatics analysis with samples from 108 DCM patients and 16 non-failing control samples, they identified differentially expressed lncRNAs. Among these lncRNAs, Isopentenyldiphsophate delta isomerase 2 antisense (IDI2-AS1) and X inactive-specific transcript (XIST) were identified to be differentially expressed in DCM samples and were deemed to have potential diagnostic values in DCM. IDI2-AS1 was upregulated in DCM samples, and XIST was downregulated. A genome-wide DNA methylation analysis of failing human hearts from non-ischemic cardiomyopathy, ischemic cardiomyopathy, and donor controls revealed differential methylation patterns. A novel cardiac-specific super-enhancer lncRNA, LINC00881, was found to be hypermethylated and downregulated in DCM.⁹ As an upstream regulator of genes like MYH6 and CACNA1C, LINC00881 influences sarcomere and calcium channel function. Knockdown of LINC00881 in hiPSC-derived cardiomyocytes reduced peak calcium amplitude. These findings highlight that HF-associated DNA methylation changes in coding and noncoding regions are not fully reversible with mechanical unloading, suggesting the need for epigenetic reprogramming for lasting clinical recovery.

Epigenetic modifications of RNA, including structural changes at cytosine and adenine bases, have been reported to influence RNA stability in the heart under normal and pathological conditions. For a detailed discussion, readers are referred to previously reviewed studies.^19,20

3. Epigenetic Regulation in Familial DCM

Familial DCM refers to cases of DCM with a genetic basis, often involving pathogenic variants in genes that play key roles in maintaining the structure and function of heart muscle cells. These pathogenic variants can result in impaired contractility, abnormal heart rhythms, and a predisposition to HF. Below, we discuss several specific forms of familial DCM and the genes involved, and their involvement at the epigenetic level.

3.1. Lamin A/C (LMNA) Cardiomyopathy

Lamin A/C-related DCM, caused by pathogenic variants in the LMNA gene, is the most studied form of DCM at the epigenetic level. LMNA encodes nuclear Lamins A and C, which maintain nuclear integrity and regulate gene expression. Pathogenic variants in LMNA are responsible for 5%–8% of familial DCM cases. Patients with LMNA cardiomyopathy experience heart block and atrial arrhythmia, with progressive replacement fibrosis and progressive cardiac dysfunction often resulting in poor prognosis due to malignant arrhythmias and sudden cardiac death.²¹

The nuclear lamina anchors large heterochromatic regions, known as lamina-associated domains (LADs), to the nuclear periphery, influencing chromatin structure and gene regulation. LADs are enriched with repressive histone marks (e.g., H3K9me3, H3K27me3), silencing nearby genes.^22–24 However, the dynamic interaction between chromatin, epigenetic modifiers, and genomic organizers in the nuclear lamina likely plays an additional role in gene regulation. For instance, histone deacetylase 3 (HDAC3) directly represses cardiomyocyte differentiation by anchoring cardiomyocyte-specific genes to the nuclear lamina. In the absence of HDAC3 in cardiac progenitor cells, these genomic regions are released from the nuclear periphery, leading to the premature expression of cardiac genes and the promotion of differentiation.²⁵

Another example of lamin interaction with epigenetic modifiers is its association with the Polycomb repressive complex 2 (PRC2), which catalyzes the methylation H3K27, leading to gene repression. Loss of this interaction with PRC2 can decrease H3K27me3 levels, impairing the repression of gene activity.²⁶ Additionally, disruption of LADs due to the loss of lamins or LMNA pathogenic variants can increase permissive modifications at fourth lysin at H3 (e.g., H3K4me). These changes result in abnormal gene regulation and altered chromatin accessibility. For example, in embryonic stem cells lacking the LMNA gene, the chromatin architecture required for cardiac specification is disrupted, leading to altered chromatin compaction and mislocalization of cardiac-specific genes. This disruption ultimately promotes premature differentiation of cardiomyocytes by activating cardiac transcription factors such as Gata4, Wnts, and Bmps.^25,27 Thus, LMNA-dependent chromatin organization is critical in maintaining a primordial pluripotent state and preventing aberrant cardiovascular cell fate and function.

Given that LMNA pathogenic variant affects epigenetic modifiers' activity or expression, researchers have tried to target the affected epigenetic receptor to activate LMNA-DCM.^28,29 In a laminopathy model with Lmna H222P variants, lysine-specific histone demethylase 1 (LSD1) inhibition via GSK1-LSD restored cardiac function by reversing H3K4 demethylation.²⁹ In a recent study, Du et al. showed that overexpressing sirtuin 1 (SIRT1) via adeno-associated virus (AAV) in Lmna^−/− mice significantly improved mitochondrial function, enhanced cardiac systolic performance, reduced ventricular dilation and fibrosis, and ultimately extended the lifespan of these mice.²⁸ However, these proof-of-concept animal models may not fully reflect human LMNA-DCM diversity. Future studies with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are warranted to better model the genotype-phenotype spectrum of LMNA-related DCM. This approach will allow a more clinically relevant evaluation of therapies targeting SIRT1 and LSD1 or other epigenetic regulators. Indeed, recent studies have already used hiPSC-CMs derived from patients with LMNA-DCM to investigate the role of lamin A/C in chromatin organization.^30–37 A summary of these studies is provided in Table 2.

Table 2:

Summary of current hiPSC-Cardiac cells study in Lamin A/C

Mutation site on LMNA	Mutation Type	Key findings	References
K117fs	Frameshift	• Aberrant calcium homeostasis led to arrhythmias. • Increased open chromatin in mutant iPSC-CMs. • PDGF signaling pathway activation. • Inhibition PDFG signaling pathway he arrhythmic phenotypes of mutant iPSC-CMs.	Lee et al.2019
K219T	Missense point mutations	• The expression of sodium channel was affected via epigenetic regulation. • Mutant iPSC-CM cooperate with PRC2 in downregulating SCN5A.	Salvarani et al. 2019
R225X	Premature truncation of both lamin A and lamin C splicing isoforms	• Increased expression of non-cardiac genes in mutant iPSC. • Upregulated the neuronal P/Q-type calcium channel gene CACNA1A	Bertero et al., 2019
R216C; R335Q;R377H; R541C	Missense point mutations	• Reduction of migration rate. • Abnormal calcium handling, arrhythmic phenotype, and electrophysiological and ion channel alterations.	Yang et al., 2021(a) ;Yang et al., 2021(b)
T10I	Defective filament formation	• Disrupt peripheral chromatin in a cell-type-specific manner in LMNA mutant • Maintain cell fate identity	Shah et al,, 2021
R249Q	Reduction of LMNA expression	• Increased nuclear-envelope rupture • Reduced nuclear stiffness	Wallace et al., 2023
P120L	Splice-site mutation	• High quality cells from Single-cell RNAseq • DEGs related to metabolism , proliferation and homeostasis and development of cardiac progenitor and cardiomyocytes	Zaragoza et al., 2024
A388fs	Frameshift	• Abnormal Ca2+ handling, arrhythmia. • Deformed nuclear envelop • Mitochondrial dysfunction and ROS elevation • Accelerated degradation of SIRT1 • Activated ROS-CAMKII-RYR2 pathway in mutant iPSC-CMs	Qiu et al., 2024

PDFG:Platelet-derived growth factor; iPSC-CMs: PRC2: Polycomb repressive complex 2 ;SCN5A: Sodium voltage-gated channel alpha subunit 5; iPSC-CM; Induced pluripotent stem cell-derived cardiomyocytes; ROS:reactive oxygen species; SIRT1:sirtuin1; DEGs: Differentially expressed genes.

In summary, LMNA-DCM is tightly linked to epigenetic regulation. Understanding the interplay between LMNA pathogenic variants, histone modifiers, and LADs offers insights into disease progression and potential therapeutic targets.

3.2. Titin Cardiomyopathy

Titin (TTN) is a giant protein (2.97–3.7 MDa) and an essential component of the sarcomere, responsible for the contractility machinery of cardiomyocytes. Pathogenic or likely pathogenic TTN variants (especially truncated variants) are most commonly identified familial DCM (~20–25% of all cases), making it the primary genetic cause of familial DCM.³⁸

Alternative splicing plays a significant role in TTN, resulting in three main isoforms: N2A, N2B, and N2BA, which primarily vary in the lengths of their extensible I-band domains. In adult cardiomyocytes, N2B and N2BA are the predominant isoforms. N2BA is longer and less rigid compared to N2B, leading to differences in their extensibility and mechanical properties.³⁹ Pathogenic variants or truncations of this protein have been shown to be associated with a large proportion of DCM. Truncating pathogenic variants in the TTN gene contribute to 15%–25% of familial DCM cases and 10%–18% of sporadic DCM occurrences.⁴⁰ Alternative splicing is a critical process in the production of the TTN protein and the most frequently dysregulated mechanism at the TTN locus. This dysregulation is primarily linked to the RNA-binding splicing factor, RNA binding motif protein 20 (RBM20). (See section 3.3 for details)

Although alternative splicing may not directly regulate gene expression, it may significantly influence epigenetic mechanisms. Using data generated from the Care4DCM multi-omics project, Gi et al. investigated the association between epigenome-wide DNA methylation and alternative splicing. They found a strong association between intronic DNA methylation and adjacent exon usage, affecting sarcomeric protein and related pathways, including those involving the TTN locus.⁵ Furthermore, the authors observed inverse regulation of TTN and TTN antisense RNA 1 (TTN-AS1), a long noncoding RNA (lncRNA) that produces an estimated 80 different transcripts. These transcripts display a DCM-dependent differential regulation of DNA methylation, affecting alternative splicing. The study suggests that the epigenetic landscape, including DNA methylation, plays a critical role in regulating alternative splicing of TTN, which may contribute to the pathogenesis of TTN-related DCM. The differential methylation at intronic regions and its impact on exon usage indicate that epigenetic modifications could serve as potential therapeutic targets. Targeting specific epigenetic changes may help restore normal splicing patterns and potentially ameliorate the effects of pathogenic TTN truncations. For instance, inhibition of mir-208b improves cardiac function in titin-based dilated cardiomyopathy.⁴¹ These findings open up new avenues for understanding the complexity of DCM and for developing targeted interventions to manage TTN-cardiomyopathy.

3.3. RBM20 Cardiomyopathy

Pathogenic variants in RBM20 are a common cause of familial DCM, accounting for 2 to 6% of patients with familial DCM.^42,43 RMB20 is a striated muscle-specific splicing protein that regulates alternative splicing for many essential cardiac genes such as TTN and Ca2+/calmodulin-dependent kinase IIδ (CAMK2D). Although the defect in RNA alternative splicing may not be directly related to epigenetic regulation, it was shown that RMB20 regulates the formation of circular RNAs (circRNAs), a type of noncoding RNA . It is known that circRNA production is achieved by back-splicing of pre-mRNA exons in the canonical spliceosome machinery, thereby forming single-strand RNA molecules lacking poly A tails. ^44,45 The formation of cirRNAs can potentially affect gene expression by altering splicing, serving as a microRNA sponge⁴⁶, or by interacting with RNA polymerase II.⁴⁷ Using circRNA profiling from human hearts, Khan et al. reported that 80 circRNAs are expressed from the TTN gene, and RBM20 is required for the production of these circRNAs. In addition, they confirmed that alternative splicing and circRNA production are intimately connected. However, the biological function of these circRNAs in DCM remains to be determined. Nevertheless, due to the long-term stability of circRNAs, these RBM20-related circRNAs may serve as biomarkers for detecting splicing aberrations in DCM.

The TADs in mammalian genomes also play a role in RMB20-dependent RNA splicing.⁴⁸ A study using human embryonic stem cells, combined with multiple next-generation sequencing methods, including Hi-C, ATAC-seq, and RNA-seq, found that TTN pre-mRNA binds and accumulates RBM20 foci near its genomic locus.⁴⁸ This RBM20 accumulation mediates spatial proximity between the TTN locus and other inter-chromosomal RBM20 targets, such as CAMK2D and CACNA1C. Disruption of this TADs assembly of RBM20 targets can reduce the spatial concentration of RBM20 at genomic foci, resulting in altered RBM20-dependent alternative splicing of other targets. Thus, RBM20-dependent alternative splicing may be influenced by a cardiac-specific trans-interacting chromatin domain.

3.4. Myosin heavy chain-related Cardiomyopathy

The Myh6 gene encodes the α-myosin heavy chain (α-MHC), whereas the Myh7 gene encodes the β-myosin heavy chain (β-MHC). During heart development, there is a ratio switch between these two isoforms, with β-MHC being predominantly expressed in the fetal heart and α-MHC becoming the primary isoform in the adult heart. This switch is crucial for the heart to adapt to differing functional demands at various stages of development. Furthermore, during the progression of HF, the MYH6/MYH7 ratio undergoes a shift, marked by reduced MYH6 expression and elevated MYH7 expression.^49,50 Several recent genome-wide epigenetic studies have shown that epigenetic changes frequently occur at the Myh6 or Myh7 loci in heart failure.^6,8,14 The Myh6-to-Myh7 expression switch is regulated by Brahma-related gene 1 (Brg1), a chromatin remodeling factor, during cardiac development and pathological conditions.^3,51 In the fetal heart, high Brg1 levels suppress Myh6 and maintain Myh7 expression, while in adults, Brg1 downregulation allows the switch. Reactivation of Brg1 in HF models triggers a similar Myh6-to-Myh7 switch. Thyroid hormone T3 also plays a role, exerting opposing effects on Myh6 and Myh7 expression through epigenetic modifications^52–54. Studies in hypothyroid models show reduced activation marks (H3K4me3) and increased repression marks (H3K9me) at the Myh6 promoter, resembling patterns seen in fetal or stressed hearts.^52–55 These findings suggest an interplay between T3 and Brg1 in regulating cardiac myosin isoforms. Future studies are needed to confirm the mechanisms of T3-Brg1 interaction and their role in epigenetic regulation.

Additionally, the McNally group integrated published epigenomic analyses with functional validation in iPSC-derived cardiomyocytes to identify enhancer regions linked to the Myh7 locus, which regulate Myh7 expression and may be associated with cardiomyopathy progression.⁵⁶

4. Epigenetic Regulation of Non-familial DCM

Non-genetic DCM can arise from various conditions, including inflammation, viral infections, toxins, and autoimmune diseases. In the following sections, we will focus on two major forms of non-genetic DCM: diabetic cardiomyopathy (DbCM) and autoimmune-related DCM.

4.1. Diabetic cardiomyopathy

Diabetic cardiomyopathy is a non-ischemic form of DCM, which is associated with diabetes and is the leading cause of HF in patients with diabetes. Often distinct from idiopathic DCM, DbCM develops as a result of abnormal glucose metabolism that leads to structural heart defects and dysfunction presenting without typical cardiac risk factors such as hypertension, severe valvular disease, or coronary artery disease.⁵⁷

In recent years, many studies have shown that noncoding mechanisms are involved in the mechanisms behind DbCM. For example, miR-21, has been highlighted as playing a significant role in cardiac dysfunction in DbCM.^58,59 Dai et al. found that miR-21 was downregulated in the hearts of leptin receptor-deficient (db/db) diabetic mice.⁵⁸ Further studies on miR-12 found that circulating levels of miR-21 in type 2 diabetic patients with DCM were significantly lower compared to those of type 2 diabetic patients without DCM.⁵⁹ The role of miR-21 in DbCM was further elucidated and it was found that overexpression of exogenous miR-21 improved mitochondrial biogenesis and decreased cell apoptosis, and that expression of miR-21 is significantly correlated with cardiac diastolic function, further indicating its protective role in the diabetic heart.⁵⁹

Another miRNA, miR-30c, has recently been found to play a protective role in DbCM.⁶⁰ Yin et al. demonstrated that miR-30c plays a protective role by mitigating cardiac metabolic derangement and dysfunction in diabetic mice. Overexpression of miR-30c was shown to target peroxisome proliferator-activated receptor-γ coactivator 1β (PGC-1β), which is upregulated in the hearts of db/db mice. This effect was mediated, at least in part, by the PPAR-α (peroxisome proliferator-activated receptor-α) signaling pathway.⁶⁰ Similarly, Yang et al. identified miR-203 as another protective miRNA in DbCM. Their findings revealed that miR-203 inhibits myocardial fibrosis and oxidative stress by targeting the PI3K/Akt signaling pathway through the PIK3CA gene, thereby offering cardioprotective effects.⁶¹ Tang et al. explored the role of miR-22 in DbCM and found it to be highly protective against oxidative stress injury. In both in vitro and in vivo experiments, overexpression of miR-22 significantly reversed cardiac dysfunction and structural abnormalities in diabetic mice. Mechanistically, this protective effect was attributed to the upregulation of Sirt1, a key regulator of cellular stress responses.⁶² Collectively, these studies emphasize the potential of miRNAs, such as miR-30c, miR-203, and miR-22, as therapeutic targets for managing DbCM.

Feng et al. identified a long noncoding RNA (lncRNA) that was significantly upregulated in rats with DbCM.⁶³ This lncRNA was TCONS_00069849 on chromosome 2 and was referred to as DCM-related factor (DCRF). DCRF was upregulated in the myocardium of diabetic rats and in cardiomyocytes treated with high glucose. Interestingly, a knockdown of DCRF in diabetic rats resulted in improved cardiac function.⁶³ Bioinformatic analysis revealed that DCRF contained the binding site for miR551b-5p. A direct target for miR551b-5p is PCDH17, which is involved in cardiomyocyte autophagy. Since miR551b-5p can bind to DCRF, it is posited that DCRF may play a role in increasing cardiomyocyte autophagy in the progression of DbCM, by sponging miR-551b-5p and increasing PCDH17 expression.⁶³

Another lncRNA found to play a role in autophagy in DbCM is lncRNA H19.⁶⁴ In rats with DbCM, H19 was downregulated, and overexpression of H19 improved left ventricular function and reduced cardiomyocyte autophagy. LncRNA can have an influence on histone modifiers and modifications. It was shown that H19 could directly bind to EZH2 in cardiomyocytes, and EZH2 could directly bind to the promoter region of DIRAS3, a GTP binding protein, mediating H3K27me3 modification. They concluded that H19, therefore, can inhibit autophagy by silencing DIRAS3 in DbCM.⁶⁴

Inhibition of HDACs is associated with the prevention of DbCM.⁶⁵ Xu et al. aimed to uncover which specific HDAC plays the pivotal role in DbCM by investigating the specific inhibition of HDAC3.⁶⁶ To do this, they utilized a type I diabetic mouse model and found evidence that the administration of the selective HDAC3 inhibitor RGFP966 improved cardiac dysfunction, fibrosis, and dysfunction induced by diabetes. Furthermore, they elucidated possible mechanisms behind this improvement. Chromatin precipitation assay analysis revealed that HDAC3 inhibition elevated histone H3 acetylation on the DUSP5 gene promoter, which is an ERK1/2 nuclear phosphatase. They concluded that the HDAC3 activity activated by diabetes inhibits DUSP5 expression through deacetylating histone H3 on the primer region of DUSP5, leading to the de-repression of ERK1/2 and the initiation of DCM.

DNA methylation is also highly linked to DbCM.⁶⁷ Hussain et al. observed that JunD expression was decreased in the heart tissues of diabetic patients and in DCM mouse models.⁶⁸ Overexpression of JunD specifically in cardiac tissue helped improve heart function by reducing oxidative stress, inflammation, and overall cardiac damage in DCM. They also showed that JunD expression is influenced by multiple epigenetic modifications.⁶⁸

It is evident that epigenetic regulation plays a significant role in the development of DbCM. However, most of the research has been conducted in rodent models, with only limited studies involving genome-wide histone modifications and DNA CpG methylation analysis in human cardiac mesenchymal cells from patients with type 2 diabetes. More comprehensive studies using human tissue samples are needed to understand better the complex epigenetic mechanisms underlying DbCM and to identify potential therapeutic targets.

4.2. Autoimmune cardiomyopathy

Autoimmune diseases arise when the immune system attacks healthy cells, tissues, and organs, often causing inflammation and leading to secondary health issues like myocarditis. Conditions such as giant cell myocarditis, diabetes mellitus, sarcoidosis, systemic lupus erythematosus, and inflammatory bowel disease can all lead to myocarditis, which, when linked to DCM, is sometimes referred to as “inflammatory DCM.”^69,70

Bromodomain and extra-terminal domain (BET) proteins are epigenetic readers that bind acetylated chromatin. Antolic et al. studied BET proteins BRD2, BRD3, and BRD4 in a mouse model, finding that their inhibition reduced the expression of pathological genes dominated by inflammatory and profibrotic signaling pathways, delaying DCM progression. This suggests BET proteins as promising therapeutic targets for DCM.⁷¹

At the DNA methylation level, FKBP5 hypomethylation in DCM patients suggests an epigenetic regulation role in DCM pathogenesis. Wada et al. found reduced methylation at specific CpG sites in FKBP5, with increased FKBP5 and IL-1B mRNA levels in DCM patients, indicating a potential inflammatory response mechanism and the viability of FKBP5 methylation as a DCM biomarker.^72,73

RNA methylation is also implicated in DCM. A recent study showed that IGFBP2 regulates N6-methyladenosine (m6A) patterns, which increased immune cell infiltration and activation of signaling pathways involved in DCM's immune microenvironment, raising the risk of DCM.⁷⁴

Long non-coding RNA can also contribute to the development and progression fof autoimmune myocarditis. In a mouse model of experimental autoimmune myocarditis, Gan et al. identified lncRNA MAAMT as a key pro-inflammatory regulator. Knocking down MAAMT reduced macrophage activation, decreased myocardial injury, and improved cardiac function, indicating its potential as a therapeutic target for DCM.⁸

Recent advances in epigenetic regulation have enhanced our understanding of autoimmune DCM mechanisms, offering new biomarkers and therapeutic targets. However, further research is necessary to elucidate these mechanisms and improve patient outcomes fully.

5. Conclusion and Future Prospects

The understanding of DCM has expanded from genetics to include epigenetic mechanisms, bridging genetic and environmental factors. Epigenetic modifications play a key role in both familial and non-genetic forms of DCM, influencing disease onset and progression. Human-derived models, such as hiPSC-CMs, better reflect human phenotypes and are essential for exploring the genotype-phenotype spectrum and evaluating clinically relevant treatments. Integrating multi-omics approaches, including epigenomics, transcriptomics, and proteomics, offers a comprehensive understanding of the molecular mechanisms for DCM. This integration can help identify novel biomarkers for diagnosis and targeted therapies, even though it is unclear whether some of these changes are reversible or not and whether they pose unintended consequences. Targeting specific epigenetic regulators, such as SIRT1, through small molecule inhibitors or AAV-mediated gene delivery has shown promise in preclinical studies. Nevertheless, epigenetic biomarkers are diverse and often non-specific. While the gene lists are large and pathways are complex, comparative data are few, and disagreements in published papers are frequent. Future efforts should focus on interventions targeting specific epigenetic pathways to confirm no off-target consequences, while adopting stratified approaches that account for individual genetic and epigenetic profiles. This personalized strategy could significantly improve patient outcomes by tailoring treatments to the unique molecular landscape of each patient. Ultimately, advancing epigenetic research and translating these findings into clinical practice will pave the way for precision medicine in DCM care.

Fig. 1.

Epigenetic regulation in dilated cardiomyopathy (DCM). Epigenetic mechanisms including DNA methylation and demethylation, histone modifications and chromatin remodeling, and noncoding RNAs such as lncRNAs, miRNAs, and circRNAs collectively influence gene expression and cardiac remodeling. Alterations in these pathways, as shown in LMNA, TTN, and RBM20 related cardiomyopathies as well as Idiopathic DMC and Non-Gentic DCM, contribute to the development and progression of DCM and ultimately heart failure.

Key points:

• Deoxyribonucleic acid (DNA) methylation, histone modifications, and noncoding RNAs regulate gene expression in DCM.

• Targeting epigenetic regulators (e.g., SIRT1, HDAC inhibitors) shows promise in preclinical DCM models.

• Human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes offer a platform to study epigenetic changes in DCM, reflecting patient-specific phenotypes.