Abstract
Non-ischemic cardiomyopathy (NICM) is a devastating diagnosis with a wide array of phenotypes, ranging from mild cardiac hypertrophy to end-stage heart failure. Single-cell/nucleus RNA sequencing technologies have expanded and become a necessary tool to unravel the transcriptome across thousands to millions of cells. Studies incorporating these technologies to examine pediatric and adult myocardium have improved our understanding of underlying pathophysiology in cardiomyopathy, identified novel gene and genetic pathway associations, and paved the way for precision medicine therapeutics in cardiovascular medicine. We compiled the recent literature that showcase single cell/nucleus technologies in NICM in adult and pediatric populations and describe cell type-specific changes, ultimately setting the stage for future targeted gene manipulation/precision medicine.
Keywords: Gene expression, non-ischemic cardiomyopathy, pediatrics, single cell/nuclei RNA sequencing
Graphical Abstract

I. Introduction
Single cell/nuclei RNA sequencing (scRNA-seq) has exploded in the recent era and now allows for the characterization of the transcriptome within a tissue of interest.1,2 Further, toolkits like the Seurat R package, have expanded accessibility to researchers.3 Through established isolation and capture methods and analysis pipelines, we can define both cell subtypes and states in the heart.2 This allows us to test for differentially expressed genes (DEGs), perform gene set enrichment using functional databases, and to employ advanced modalities like trajectory/pseudotime, drug-to-gene prediction, and ligand-to-receptor analyses.2 In turn, this has accelerated the development of precision therapeutics to target genes or pathways implicated in disease. Building on this, recent efforts have turned toward applying scRNA approaches to inheritable cardiomyopathies.
Inheritable cardiomyopathies have a prevalence of one in 250–500 individuals in the adult population, and clinical features can range from mild to more severe phenotypes like sudden cardiac death and end-stage heart failure.4,5 The most common include dilated cardiomyopathy (DCM), hypertrophic cardiomyopathy (HCM), and arrhythmogenic cardiomyopathy (ACM). More rare forms in children include syndromic causes of cardiomyopathy like Noonan Syndrome associated HCM. The etiology is thought to be genetic, although testing yields range from 30% in DCM to 80% in ACM.4,5 Since prognostication is vital for counseling and clinical care, studies have established genotype-phenotype correlations, although phenotypic heterogeneity remains significant.6,7 As such, scRNA technologies can provide a more meticulous avenue for determining genotype-to-transcriptome correlations that provide deep insight into disease cell states.
Here, we summarize the core literature (Supplemental Figure) describing the use of scRNA-seq technologies in non-ischemic cardiomyopathies (NICM) in adults and children, describe commonalities across datasets, and discuss future directions of this field.
II. Baseline Cardiac Cell States Revealed by Single-Cell Transcriptomics
Recent scRNA-seq studies outline the inherent cellular heterogeneity in the heart.8,9 Litvinukova et al profiled nearly half a million cells across 14 donors and defined various cell states in atrial and ventricular cardiomyocytes.8 They identified enrichment of genes in ventricular cardiomyocytes expected to reflect their functional role of contraction. Although some cell states were more left ventricle (LV) specific, the LV and right ventricle (RV) had similar underlying gene programs.8 Also, early studies did not exhibit significant sex-based differences across cardiomyocytes; a significant amount of DEGs were autosomal, suggesting differences can be seen outside of sex chromosomes.9 Some DEGs noted are associated with hormonal regulation like CRISPLD2 and UGT2B4.9 Although making up less than 20% of LV cells, a stress-response cell state was identified.8 The characterization of other cell populations identified cell states that are highly interactive in the microtissue environment. Vascular cell states identified include arterial, capillary, and venous endothelial cells, as well as unique immune gene enriched endothelial cells that interact with pericyte and smooth muscle cells.8 Regarding fibroblasts, quiescent cell states involved in homeostasis were predominant but populations enriched in extracellular matrix (ECM) remodeling and cytokine regulation were identified.8 Finally, macrophage populations identified included resident populations enriched in LYVE1 and pathways associated with tissue remodeling and homeostasis, as well as monocyte-derived macrophages enriched in antigen-presenting and inflammatory genes.8 These findings define the predominant cell states in the healthy heart and show rare cell states associated with stress responses or maladaptive remodeling; their limited abundance suggests they reflect transient physiological adaptations rather than chronic pathological processes. These exhibit the complex myocardial transcriptome and provide a reference point for comparison to disease.
III. Hypertrophic Cardiomyopathy
HCM is characterized by LV hypertrophy, often secondary to sarcomere gene mutations, and has a prevalence of 1 in 500 people.10 It is associated with diastolic dysfunction, arrhythmias, and an increased risk of sudden cardiac death. scRNA-seq studies focus on patients with end-stage HCM, with severe diastolic and/or systolic dysfunction at the time of transplant 11–13 and in patients with severe LV outflow tract obstruction (LVOTO) undergoing surgical myectomy (Table 1).12,14–17 In this section, we discuss cell types and states that play primary roles in HCM, genes that drive disease cell states, and cell interactions upregulated in disease (Figure 1A).
Table 1:
Characteristics for studies incorporating single cell/nuclei testing in non-ischemic cardiomyopathy
| Study | Number of Patients* | Age of Patients** | Tissue Location | Time of Collection | Sequencing Platform | Primary Comparisons | Genotype/Top 3 Genes Identified |
|---|---|---|---|---|---|---|---|
| Hypertrophic Cardiomyopathy (HCM) or HCM Phenocopies | |||||||
| Chaffin et al.11 | 16 | Adult | LV | Transplant | 10x Genomics | DCM/NF | WGS in 15/16 patients 1. MYBPC3 2. MYH7 3. A2ML1 |
| Liu et al.15 | 10 | Adult | IVS | Surgical Myectomy | 10x Genomics | DCM/NF | Sequencing in 10/10 patients☨ 1. MYBPC3 2. MYH7 |
| Lu et al.16 | 7 | Adult | IVS | Surgical Myectomy | STRT-seq | DCM/NF | Sequencing in 2/7 patients☨ 1. MYBPC3 2. MYH7 |
| Wehrens et al.17 | 5 | Adult | IVS | Surgical Myectomy | 10x Genomics | NF | Sequencing in 2/5 patients☨ 1. MYBPC3 |
| Codden et al.13 | 6 | Adult | LV☨☨ | Transplant | 10x Genomics | NF | Sequencing in 6/6 patients☨ 1. MYH7 |
| Larson et al.14 | 9 | Adult | IVS | Surgical Myectomy | 10x Genomics | NF | Sequencing in 9/9 patients☨ 1. MYBPC3 2. KRAS |
| Ali et al.87 | 5 | Adult | IVS | Surgical Myectomy/Transplant | 10x Genomics | NF | Sequencing in 3/3 patients☨ 1. MYPBC3 |
| Drenckhahn et al.37 | 1 | Pediatric | IVS | Surgical Myectomy | 10x Genomics | DCM | Sequencing in 1/1 patient☨ 1. PTPN11 |
| Hill et al.38 | 1 | Pediatric | LV | Transplant | 10x Genomics | NF | Gene panel in 1/1 patient 1. TNNT2 |
| Tadros et al.41 | 3 | Pediatric | LV | Transplant | 10x Genomics | NF | Gene panel in 3/3 patient 1. TNNT2 2. MYH7 |
| Dilated Cardiomyopathy (DCM) | |||||||
| Koenig et al.45 | 18 | Adult | LV | VAD/Transplant | 10x Genomics | NF | Unknown |
| Chaffin et al.11 | 12 | Adult | LV | Transplant | 10x Genomics | HCM/NF | WGS in 10/12 patients 1. TTN 2. NEBL 3. A2ML1 |
| Rao et al.51 | 5 | Adult | LV/RV | Transplant | 10x Genomics |
NF | Unknown |
| Wang et al.44 | 4 | Adult | LA/LV | VAD/Transplant | Takara ICELL8 |
NF | Unknown |
| Kattih et al.50 | 1 | Adult | LV | VAD/Transplant | 10x Genomics |
NF | Unknown |
| Reichart et al.46 | 52 | Adult | LV | VAD/Transplant | 10x Genomics | NF | WGS/WES/Gene panel in 52/52 patients 1. TTN 2. LMNA 3. RBM20 |
| Amrute et al.52 | 6 | Adult | LV | VAD/Transplant | 10x Genomics | NF | Unknown |
| Nicin et al.40 | 6 | Pediatric | LV | Transplant | 10x Genomics | DCM | Sequencing in 1/6 patient☨ 1. TAZ |
| Mehdiabadi et al.39 | 4 | Pediatric | LV | Unknown | 10x Genomics | NF/Fetal | Unknown |
| Hill et al.38 | 2 | Pediatric | LV | Transplant | 10x Genomics | NF | WES panel in 2/2 patient 1. BAG3 2. TPO (unclear if related to phenotype) |
| Arrhythmogenic Cardiomyopathy (ACM) | |||||||
| Reichart et al.46 | 8 | Adult | LV | VAD/Transplant | 10x Genomics | NF | Gene panel in 8/8 patients 1. PKP2 2. LMNA 3. PLN |
| Fu et al.68 | 6 | Adult | LV/RV | Transplant | 10x Genomics | NF | Gene panel in 6/6 patients 1. DSG2 2. PKP2 3. DSC2 |
ACM, arrhythmogenic cardiomyopathy; DCM, dilated cardiomyopathy; HCM, hypertrophic cardiomyopathy; IVS, interventricular septum; LV, left ventricle; LVOTO, left ventricular outflow tract obstruction; NF, non-failing; VAD, ventricular assist device; WES, whole exome sequencing; WGS, whole genome sequencing.
Pertains to number of patients with single cell or nuclei sequencing
Adult patients indicates >18 years of age; pediatric patients indicate <18 years of age
Type of genetic test not specified
Unknown if free wall vs IVS
If Unknown, source data does not specific if genetic testing was performed.
Figure 1.

Cardiomyocyte-specific alterations identify maladaptive responses to stress
Earlier studies studying cardiomyocytes in pathologic hypertrophy identified genes associated with adaptive and maladaptive responses to stress.18 Adaptive responses include pathways associated with increased energy production, cell survival, and anti-oxidant production, while maladaptive include pathways associated with cell death, mitochondrial dysfunction, dysregulation of calcium handling proteins, and fibrosis.18
Similarly, scRNA-seq studies identify compensated (ie. adaptive) and stressed states in HCM. The latter are enriched in HCM and exhibit prototypical genes like MYH7, TPM3, and ACTN1 and genes associated with reactivation of the fetal gene program like NPPA, NPPB, and ACTA1.15–17 Although reactivation fetal genes is seen, contrasting findings in studies imply it is one aspect of response to stress. For instance, Liu et al. shows downregulation of MYH6, the fetal isoform in humans, in HCM and upregulation of the adult MYH7 isoform.15 Hence, the stress state represents a transcriptionally distinct remodeling phenotype. Pseudotime trajectory analysis, a predictive analysis used to order cells along a continuous trajectory, supports the conclusion that the stress state is a terminal state, implying that maladaptive responses are seen in late-stage disease.15 Genes that change along this trajectory include known markers like NPPB, as well as the lesser-known FGF12, an inhibitor of pathological remodeling, the former increasing and the latter decreasing over pseudotime (Figure 1B).15,19,20 Consistent with increased stress in HCM, functional enrichment analyses of over-represented genes derived from DEGs showed upregulation of sarcomere/muscle contraction, cell death, ribosomal assembly, protein translation, energy metabolism, and heart development pathways (Figure 1C).15–17 Conversely, compensated or homeostatic cell states are enriched in genes associated with adaptive responses like FGF12 and CORIN, the latter noted to be a positive prognostic marker if overexpressed in heart failure.21 Spatial transcriptomics, a method to assign spatially resolved gene expression in histological sections, support these findings with failing/maladaptive cardiomyocytes predicted to be located near fibrotic tissue and compensated cells near non-fibrotic regions.15,17 Overall, biological themes of cardiac stress, muscle contraction alterations, increased protein synthesis, reprogramming from adult to fetal genes, and increased energy utilization are seen in HCM.
Wehrens et al. focus on XIRP2, encoding Xin Actin Binding Repeat Containing 2, a protein associated with mechano-sensing and an early mediator of cardiac hypertrophy.17,22 XIRP2 is the highest expressed gene in HCM cluster 2, representing a cell state with heightened sarcomere remodeling, which positively correlates with genes like CMYA5 and MAP4, and negatively correlates with NPPA, ACTC1, and MYBPC3.17 The authors hypothesized that increased expression of XIRP2 relates to disease since correlations with other genes are strengthened in HCM compared to controls.17 Although there are associations of XIRP2 with mechanosensing regions at the Z-disc and costameres, the significance of this specific cluster to HCM pathogenesis requires further study.23,24
Fibroblast activation is a hallmark of HCM
Cardiac fibrosis is a hallmark of pathological remodeling in HCM and fibroblasts play a significant role in this process. Fibroblasts responding to stress or injury have been broadly termed as “activated”.25 Generally, this occurs when quiescent fibroblasts transition to cell states primed for fibrosis, proliferation, and cytokine and proteolytic enzyme release. Classically, upon acute stress, fibroblasts transition to myofibroblasts specialized in high ECM deposition and having contractile properties.26 As scar matures, they then transition to a more mature cell state that is less proliferative and contractile but is specialized in ECM maintenance termed a matrifibrocyte.26 Despite the availability of data, phenotypes and genes associated with fibroblast activation in HCM required further study to be fully understood, particularly in high-resolution fashion.
scRNA-seq studies have improved our understanding of fibroblast phenotypes and genes that drive fibroblast activation. In particular, these clusters have robust activation signatures that include genes like POSTN, FAP, and PALLD.11,15 Control cells are depleted in these clusters and conversely, HCM fibroblasts are depleted in clusters representing basal/quiescent states.15 Trajectory analyses implicated POSTN and THBS4 as genes upregulated from basal to activated states, but also newly implicated genes including RUNX1, a transcription factor and modulator of myofibroblast differentiation, and AEBP1, a transcriptional repressor that plays a protective role in attenuating TGF-β-induced activation (Figure 1B).11,15,27 Liu et al. identified AEBP1 as a candidate protective gene that was upregulated across the trajectory of fibroblast activation and confirmed AEBP1 protein upregulation via Western blot assays.15 In an in-vitro knockdown of AEBP1, fibroblasts had enhanced expression of activation markers ACTA2 and TAGLN as seen in their bulk-RNA-seq analysis.15 Conversely, in-vitro overexpression of AEBP1 attenuated TGF-β-induced activation of fibroblasts, revealing a protective role of AEBP1.15 Although AEBP1 may be protective, the fibrotic nature of these clusters was evident and further validated by spatial transcriptomics where activated fibroblasts were found in fibrotic regions and quiescent fibroblasts in non-fibrotic regions.15 Also, functional enrichment analyses implicated pathways such as ECM protein and TGF-β signaling pathways, all consistent with fibrosis (Figure 1C). Owing to the enhanced fibroblast activation noted in their study, Chaffin et al. validated their data by performing deconvolution and RNA in situ hybridization analyses to validate their presence in HCM patients.11 Using the Myocardial Applied Genomics Network, they found that none of the non-failing controls were predicted to have activated fibroblasts and that four of the seventeen HCM patients were predicted to have this population.11 When comparing patients with or without this population, no clinical or echocardiographic differences were found, including LV ejection fraction, end-systolic and diastolic dimensions, and history of concomitant diseases like atrial fibrillation.11 In an independent collection of patients with HCM undergoing surgical myectomy, a majority (~82%) were predicted to have activated fibroblasts, suggesting the prevalence of this cell subtype in earlier disease.11 Therefore, although not explicitly stated, these activated fibroblasts likely represent an aggressive, fibrotic cell state akin to the ECM-specialized matrifibrocytes enriched in HCM.
Cell-specific expression associated with vascular remodeling and inflammation
Vascular-related cell subtypes are expanded in HCM and comprise of endothelial cells, pericytes, and smooth muscle cells.11,15 This may represent vascular remodeling and other processes, such as lymphangiogenesis, as indicated by expansion of lymphatic endothelial cell expansion.28 Functional pathways enriched include pathways associated with energy utilization like oxidative phosphorylation.15 HCM endothelial cells are enriched in angiogenesis-associated genes such as KIT, NRP2, and NOTCH1 11,29–31. Enriched functional pathways include pathways associated with energy utilization like oxidative phosphorylation and NOTCH and vascular endothelial growth factor (VEGF) pathways implicated in angiogenesis, cell fate, and cell migration (Fig. 1C) 15,30. Importantly, VEGF and NOTCH cross-talk is vital for vascular endothelial cell maintenance and sprout formation 30.
Tissue-resident macrophages are depleted in HCM.11 These cells have reparative functions and are derived at the time of embryonic heart development, as opposed to recruited (ie. CCR2+) macrophages which are monocyte-derived and pro-inflammatory.32 Recruited macrophages are associated with persistent LV systolic dysfunction and LV remodeling.32 Macrophages with similar properties are enriched in HCM and are enriched in genes associated with neutrophil degranulation, antigen processing and presentation, toll-like receptor cascades, and immune response regulation (Figure 1C).11,15
Cell type and state composition changes
Analyzing relative proportions of cell types or cell states in scRNA-seq provides insights in disease cellular dynamics. Although some studies did not reveal global differences of cell type proportions in HCM13,14, others have shown that smooth muscle cells, endothelial cells, and pericytes are expanded while cardiomyocytes are decreased.11,15 Although the proportion of fibroblasts may be decreased, clusters representing activated states are greatly expanded.11,15 Expansion of inflammatory, monocyte-derived macrophages and depletion of reparative, tissue-resident macrophages have also been noted in HCM.11,15 Although proportional analyses are biased, as changes in one cell type can affect the relative proportions of others, using cell signatures seen previously may support compositional findings. For instance, lower cardiomyocyte proportions are supported by heightened signatures of cell death, while expansion of endothelial cells and activated fibroblasts reflect the underlying fibrosis and vascular remodeling.15
Cell-to-cell interactions are driven by fibroblasts in HCM
To delineate cell-to-cell communication, ligand to receptor prediction has become widely utilized and accepted as an indicator of intercellular interactions. Common characteristics of these analyses are that fibroblast clusters are the greatest contributors to outgoing interactions and express the most ligands.14,15 Further, HCM-enriched cardiomyocyte clusters display decreased autocrine and paracrine communication.14,15 In particular, signaling pathways enhanced in HCM include the TGF-β, ITGB2, and WNT pathways, which are important regulators of cardiac remodeling and fibrosis and in the case of ANGPTL, involve proteins that are associated with perturbation of LV contractility and decreased myocardial energy metabolism.15,33–35 In particular, Liu et al. showed that the TGF-β pathway is enhanced with ligands originating from T cells and natural killer cells, naïve T cells, and proinflammatory macrophages interacting with receptors on fibroblasts, cardiomyocytes, and endothelial cells.15 These pairings were validated in spatial transcriptomics.15 Despite their data revealing overall decreases in intercellular communication, Larson et al. showed increased communication in clusters attributable to ITGB1 expressed in HCM fibroblast and cardiomyocyte clusters.14 This highlights the enhancement of cardiac fibrosis in HCM, as ITGB1 is essential for myofibroblast proliferation, migration, and ECM production and is known to be upregulated in pro-fibrotic myofibroblasts.36 Although common themes are noted in these studies, the apparent discrepancy of some of the results likely reflect differences in methodologies. Larson et al. predicted networks from curated ligand-receptor pairings, evaluated expression of these pairings using gene counts above zero in over 20% of total cells, and then visualized network density, while Liu et al. used the CellChat framework that computes communication probabilities.14,15 These methodological differences highlight the difficulty of directly comparing predicted communication networks across studies and emphasize the importance of prioritizing validation at the spatial or protein level.
Pediatric-specific data in HCM
Owing to scarcity of pediatric samples, data on pediatric cardiomyopathy is limited.37–40 Data on 3 non-syndromic HCM patients and 1 patient with Noonan syndrome with multiple lentigines (NSML) is available.37,38 Including the sample from the study by Hill et al, we detailed 3 female patients with end-stage pediatric HCM in our recent study.41 We found prototypical signs of cardiac stress in cardiomyocytes, endothelial cell activation, and a modest enrichment of monocyte-derived macrophages.41 Importantly, pediatric HCM, similar to adults, were enriched in matrifibrocyte-like POSTN+ fibroblasts, but also a metabolically stressed myofibroblast-like cluster that drives ECM deposition and may resist apoptosis.41 Additionally, these clusters, through ligand-to-receptor analyses, exhibited the most enriched signaling.41 The NSML patient displayed a significant overlap with infant DCM and a predominance of effects on cardiomyocytes.37 There were high proportions of cardiomyocytes compared to endothelial cells and fibroblasts and NSML cardiomyocytes exhibited upregulation of muscle developmental pathways and fatty acid metabolism-related genes, akin to energy metabolism seen in proliferative and developmental cardiomyocytes.37 Similar to infant DCM, there were lower amounts of fibroblast activation genes like POSTN and COL4A3.37 HCM findings are summarized in Figure 2A and patient characteristics listed in Supplemental Table 1.
Figure 2.

IV. Dilated Cardiomyopathy
In contrast to the concentric hypertrophy and mainly diastolic dysfunction in HCM, DCM is a cardiomyopathy in which the LV, or in certain cases both ventricles, are dilated and have impaired systolic function.10 Patients with DCM develop progressive heart failure and in certain cases, necessitate mechanical support in the form of a ventricular assist device (VAD) and a heart transplant. This allows for ample scRNA-seq of DCM tissue (Table 1). An important observation is the significant overlap noted in end-stage HCM and DCM, supporting the idea of transcriptional convergence in end-stage cardiomyopathy. In this section, we detail the evidence on non-ischemic DCM transcriptomics, the overlap between end-stage HCM and DCM, and briefly comment on ACM (Figure 3).
Figure 3.

Cardiomyocyte gene expression in DCM overlaps with end-stage HCM
The molecular mechanisms underlying DCM are thought to differ significantly from those of HCM. In contrast, DCM cardiomyocytes have myocardial energy deficits, reduced force generation, calcium handling defects, and abnormal mechano-sensing, ultimately leading to impaired responses to cardiac stress.42 The genetic etiology is diverse, and includes genetic mutations in sarcomere, cytoskeletal, and ion channel proteins.42
Confirming previous studies, scRNA-seq reveal that cardiomyocyte signatures seen in DCM significantly overlap with end-stage HCM, with major differences noted in energy metabolism. Genes like NPPA, ACTA1, ANKRD1, and NPPB and those associated with muscle contraction/development, T-cell response, and NGF-stimulated transcription pathways are upregulated.43–45 These signatures are associated with cardiac stress, inflammatory responses, and cardiac regenerative processes seen in end-stage DCM. Conversely, MYH6 and MYL7, as well as energy metabolism pathways are downregulated.45 Moreover, apoptosis-associated genes are upregulated, consistent with cell death and lower cardiomyocyte proportions in DCM samples.46 Other genes like ROCK3, a protein kinase in the ROCK family implicated in endothelial dysfunction and immune cell recruitment, is significantly upregulated in DCM, in addition to DLL3 and ADGRL3; their role in the heart remains relatively unclear.44,45,47 Compared to left atrial cardiomyocytes, the LV myocardium is more affected in DCM, suggesting that DCM pathology is primarily an LV-specific disease.44 This overall exhibits similar themes of cardiac stress in end-stage cardiomyopathy.
Activated fibroblast states are enriched in DCM
As fibrillar collagen matrix and cardiac remodeling contributes significantly to LV geometry, the role of cardiac fibroblasts is of interest in DCM. Selective upregulation of certain matrix metalloproteinases (MMPs) vital in remodeling and tissue inhibitors of MMPs (TIMPs) has been reported in DCM and fibrosis is associated with poorer clinical outcomes.48,49 Nonetheless, our understanding of regulation of fibrosis and the role of fibroblasts in DCM remained poor prior to high-resolution sequencing.
In scRNA-seq, fibroblast signatures in DCM show significant overlap with HCM. In DCM hearts, fibroblast activation, myofibroblast abundance, and upregulation of fibrosis-associated processes have been observed. Clusters of fibroblasts enriched in DCM include those with activation genes (i.e., POSTN, FAP, MEOX1), and DCM-enriched pathways are involved in ECM organization, cellular response to TGF-β stimulus, and fibroblast regulation, akin to matrifibrocytes described above.11,45,46,50–52 Although shared amongst DCM and HCM, Chaffin et al.’s approach identified a smaller proportion of activated fibroblasts in DCM (~11% of total DCM patients) when compared to HCM (24% in HCM cohort; 82% in surgical myectomy patients).11 In cell-to-cell communication, fibroblast clusters, particularly those enriched with ECM receptors, proliferation, cell migration, and inflammatory pathways, are heavily involved.44 Supporting the importance of cell-to-cell interactions, Amrute et al. exhibited the importance of inflammatory, CCR2+ macrophages in driving FAP/POSTN+ fibroblasts through IL-1β signaling and that blocking this reduced fibrosis and improved cardiac function.52 As studied by Liu et al. in HCM, a common gene of interest noted by both Rao et al. and Kattih et al. is AEBP1-encoding AE Binding Protein 1.50,5115 Kattih et al. showed AEBP1 increased in murine cardiac fibroblasts following myocardial infarction and correlated to circulating levels of plasma AEBP1 with fibrosis on cardiac MRI, albeit in patients with hypertrophy secondary to aortic stenosis.50 They also silenced AEBP1 and found that deficient fibroblasts had less proliferation, contractility, and migration and that AEBP1 promotes fibrosis by modulating the TGF-β pathway.50 Consistently, Rao et al. observed that AEBP1 positively correlates with the activation genes POSTN, FAP, and THBS4 and ECM genes such as ELN, COL1A2, and VCAN.51 Overall, cardiac fibroblasts in DCM have similar signatures to HCM, although some evidence suggests less abundance.
Other cell-type specific genetic signatures
Other cell types of interest in DCM include immune and endothelial cells, which have important roles in remodeling and inflammation. Inflammation in DCM is significant in the clinical setting. Patients with increased immune cell activation noted on endomyocardial biopsies have poorer prognosis.53 scRNA-seq allows for better characterization of immune cells and exhibited a decrease in proliferating, tissue-resident macrophage clusters which have reparative functions.11,45,46 Conversely, expansion of monocytes, CD8+ and inflammatory CD4+ T cells, dendritic cells, and monocyte-derived macrophage clusters, as well as high HLA-DR, chemokine, and inflammatory mediator (ie. IL1A, IL-1β, TNG) expression, is seen in DCM.45,51,52 Hence, inflammation in DCM is multifaceted, and monocyte infiltration drives a large component of inflammation, while driving disease states in other cell types like fibroblasts.
In endothelial cells, specific populations noted in DCM express heightened angiogenic markers such as KIT, PCDH17, and NRP2, as well as genes associated with cell fate, ECM proteins and organization, and blood vessel development.11,45,46 Further, Koening et al. noted an increase of arterial endothelial cells in DCM and enrichment of pathways associated with inflammation like type I interferon and NTRK1 signaling.45 Endothelial cells also play a significant role in cell-to-cell interactions. A top interaction seen by Rao et al. was between macrophage CXCL8 and DARC in activated endothelial cells.51 This interaction is important for endothelial cell morphological changes and gene upregulation associated with leukocyte infiltration and cell adhesion.51 This exemplifies a macrophage-to-endothelial cell interaction that leads to heightened endothelial activation, again exhibiting the role of immune cells in driving disease in other cell types.
Variations in cell type and state composition and sex/age-related differences in DCM
Cellular composition in DCM samples is altered compared to their non-failing counterparts. Consistent with signatures of cell death, there are statistically lower proportions of DCM cardiomyocytes, similar to HCM.11,45 DCM tissues have increased proportions of fibroblasts, macrophages, and lymphocytes, consistent with increased inflammation, remodeling, and fibrosis.11,45 Moreover, DCM samples have lower tissue-resident macrophages and higher proportions of inflammatory, recruited macrophages, producing a non-reparative, inflammatory state.11,45 Although consistently higher than non-failing hearts, Reichart et al. uncovered a sex-specific difference in myeloid cells, where female DCM patients had higher proportions compared to males.46 In addition, immune cells are unchanged in RV while increased in LV samples.46 Comparing adult groups, age-related differences in cell proportions are not evident. However, gene level differences across ages are noted, like enrichment of pathways associated with protein synthesis and cardiac regeneration in young (i.e. ribosomal protein and DNA repair pathways) DCM samples.45 This exhibits consistent differences when compared to non-failing controls, but that factors like sex, age, and ventricular morphology affect gene expression and warrant further study.
Pediatric-specific data in DCM
Most pediatric data is available in the DCM phenotype. Nicin et al. identified age-dependent transcriptomic differences in six pediatric DCM patients.40 Compared to 12–13 year olds, they found that patients under one year had significantly higher proportions of cardiomyocytes (~57% vs ~18–22%), lower amounts of fibroblasts (~3% vs 18–23%), and trends of increased leukocytes and endothelial cells.40 In fibroblasts, older DCM patients exhibited upregulation of genes associated with fibrosis like LTBP1, POSTN, and FN1 and activity of pathways such as collagen fibril, fiber organization, and matrisome pathways, consistent with heightened fibroblast activation and fibrosis-related processes.40,54,55 This contrasts with the upregulation of genes in infant DCM like LIF, which is associated with cardiac repair and fibrosis reduction, and SULF1, which promotes VEGF bioavailability.56,57 Functional pathways enriched in this age group also included RNA splicing, regulation of mRNA metabolic processes, and FoxO signaling, indicative of protein synthesis. In cardiomyocytes, the number of DEGs was highest in infants and were associated with pathways like muscle development, heart growth, and muscle cell proliferation.40 Notably, cell cycle regulatory genes, such as the cell proliferation inducers CCND1, CCND2, and ERBB2, are upregulated in DCM cardiomyocytes.40,58 Importantly, decreased β-adrenergic Gs signaling and increased expression of maladaptive β2 Gi pathways in adolescent DCM patients suggests that treatments targeting these pathways may be limited in adolescents as opposed to infants.40 In another study, Hill et al. discovered trends in pediatric DCM similar to the adult population, including cardiac stress, fibroblast activation, elevated CRIM:CORIN expression ratios, and inflammatory infiltrates on histology.38
This reactivation of the fetal gene program, which is also seen in fibroblasts, has been shown by Mehdiabadi et. al.39 This group observed that 8% of the fetal gene program is reactivated in DCM fibroblasts and cardiomyocytes, with fibroblasts having upregulated muscle differentiation and downregulated oxidative, metabolic, and cell cycle processes and cardiomyocytes exhibiting upregulated muscle development pathway activity and downregulated innate immune response processes.39 They note that MEOX1, a regulator of fibroblast activation, is the most upregulated gene in DCM fibroblasts.39,59 A switch of expression of glycolytic genes in infants to fatty-acid oxidation pathways in older patients revealed differences in cardiac energy metabolism based on age. Differences between infants and adolescents with DCM are summarized in Figure 2B and patient characteristics listed in Supplemental Table 1.
Transcriptional Changes in DCM Cardiac Recovery
A growing field focuses on promoting regeneration in diseased myocardium and cardiac recovery. In response to injury, the fibrotic remodeling seen is dominated by activation of fibroblasts into ECM-depositing myofibroblasts and matrifibrocytes, TGF-β signaling, and ultimately mechanical stiffness, inflammation, and contractile decline.60 In regeneration, cardiomyocyte dedifferentiation, metabolic reprogramming towards glycolysis, and activation of developmental regulators to promote cell-cycle re-entry occur.61 Unfortunately, the adult mammalian heart has less than 1% renewal every year.62 Conversely, neonatal myocardium has the potential for more regeneration.61,63 The Hippo-YAP pathways have been a focus in cardiomyocyte regeneration; YAP pathway activation or Hippo pathway inactivation induces regeneration.64 snRNA-seq in YAP-activation in adult murine hearts reshapes the tissue microenvironment, but requires successful localization of multiple cell types to induce regeneration.65 This regenerative niche is made up of C3ar1+ macrophages, C3+ fibroblasts, and YAP+, fetal-like cardiomyocytes.65 These cell states are complimentary to each other, with C3+ fibroblasts providing anti-fibrotic signals, and C3ar1+ macrophages promoting cardiomyocyte proliferation through various signaling pathways.65 Additionally, high levels of Complement Factor H impede regeneration by interfering with complement signaling between C3+ fibroblasts and C3ar1+ macrophages.65 This provides insight that successful regeneration requires multiple cell types and is not solely a cardiomyocyte process.
In DCM, cardiac recovery has been observed in patients with VADs and is associated with transcriptional changes identified by scRNA-seq. Using a recovery index derived from a correlation coefficient comparing pre- and post-VAD samples to normal samples, Wang et al. exhibited significant changes in cardiomyocytes, fibroblasts, and endothelial cells in recovered patients.44 Recovered patient cardiomyocytes shifted closer to normal myocardium transcriptionally and had enrichment of pathways associated with metabolism and muscle development.44 Another study determined a set of recovery genes distinct from both normal and pathologic states and found that myeloid cells and fibroblasts had the greatest number of DEGs in recovered or reverse-remodeled patients.66 Some enrichment was noted in mechanically unloaded patients without ventricular recovery, suggesting that unloading alone leads to an intermediate state.66 Recovered hearts shifted to a less inflammatory state with downregulation of inflammatory transcription factors like STAT3 and JUND and pro-inflammatory macrophage cell states, and upregulation of CD163, a marker of resident macrophages.66 In addition, fibroblasts in recovered patients displayed normalization of genes like MEOX1 and TGFBR3 and downregulation of TNF-α/NF-κB and TGF-β signaling pathways.66 Nonetheless, some gene dysregulation remained in recovered hearts, including heart failure-related genes such as NPPA in cardiomyocytes and genes associated with activation in fibroblasts like FAP and POSTN.66 RUNX1 was also noted as the most downregulated transcription factor in recovery and was co-expressed with POSTN, FAP, MEOX1, and a macrophage inflammatory score, suggesting it’s involvement in fibroblast activation and its modulation by inflammation in macrophages.66 Perturbing the RUNX1 gene regulatory network by inhibiting bromodomain-containing proteins, which control transcription factors like RUNX1, led to recovery signatures in cardiac fibroblasts and macrophages; this may serve as a therapeutic option for cardiac recovery.66
Arrhythmogenic cardiomyopathy and DCM overlap
ACM is a rare cardiomyopathy that is thought to occur secondary to electromechanical uncoupling of cardiomyocytes and pathologic changes (ie. fibrofatty infiltration) that lead to arrhythmia and dysfunction.67 ACM classically affects the RV, but can also affect the LV in isolation or both the RV and LV together.67 Furthermore, a dilated phenotype may occur and lead to the need for transplantation.67 Reichert et al. attempts to characterize the transcriptome in a set of ACM patients with PKP2 variants. Notable PKP2 correlations included upregulation of an inflammatory macrophage cluster in LVs and significant dysregulation in neuronal cells, which may correlate with the “hot-phase” inflammatory presentation and heightened risk for sudden arrhythmic death in ACM, respectively.46,67 More recently, Fu et al. identified expansion of CCL3+ proinflammatory macrophages in RVs of ACM, where NLRP3, a mediator of inflammation, was identified as a key target.68 In a Dsg2 murine model, pharmacological inhibition of NLRP3 improved cardiac outcomes, with decreased fibrosis, reduced RV dilation, and lower infiltration of immune cells.68 In addition, ACM RVs interestingly share several features with DCM LVs. This included increased proportions of 1) a fibroblast cluster enriched with ECM and fibrosis pathways and 2) an endothelial cluster enriched with genes associated with myocardial stress adaptation and endocardial expansion following cardiac injury.46 This suggests, again, a common pathway in end-stage cardiomyopathy and the expected RV-focused disease in ACM.
V. Genotype Specific Signatures
Attempts to study specific gene-associated cardiomyopathy in transcriptomic studies are limited by low yield, but also by limitations in incorporating polygenic inheritance patterns, which have recently been shown to play a significant role in inheritance.69 Also, variants in different domains of a gene can have different functional effects, suggesting that specific variants should be grouped and studied.7 Nonetheless, studies have attempted to identify gene-specific transcriptomic signatures in cardiomyopathy. Chaffin et. al. performed whole genome sequencing in 40 of 42 patients and compared transcriptomic signatures amongst MYBPC3, TTN, and MYH7 genotyped samples.11 In comparing MYBPC3 and MYH7 variant-carrying HCM patients to other HCM patients and TTN variant-carrying DCM patients to other DCM patients, no significant transcriptional differences were noted.11 Reichart et. al., on the other hand, observed significant genotype-to-transcriptome and genotype-to-cell type proportion associations. Their cohort included patients with LMNA, RBM20, PKP2, and TTN variants.46 In cell type proportions, most genotypes had a depletion of cardiomyocytes except for TTN variants, and endothelial cells were increased in all genotypes except for PKP2 variants.46 Regarding the transcriptome, only LMNA and PKP2 genotypes showed an upregulation of FNIP2, encoding folliculin-interacting protein 2, in cardiomyocytes.46 FNIP2 encoding folliculin-interacting protein forms a complex with FNIP1 and folliculin (FLCN).70 Although the role of FNIP2 upregulation is unclear, it is known that AMP-activated protein kinase activity is significantly reduced and mTOR activity increased in Flcn-deficient murine hearts, exhibiting the role of this complex in energy metabolism regulation which may be dysregulated in LMNA and PKP2 genotypes.71 Additionally, DCM fibroblasts exhibited a genotype-specific collagen gene response: COL4A1/2 is upregulated in LMNA, TTN, and PKP2, and COL4A5 and COL24A1 are upregulated in pathogenic variant negative patients.46 These apparent discrepancies in these two studies like reflect study design differences rather fundamental contradiction. For instance, Chaffin et al. analyzed a mixed phenotype group with small per-genotype sample sizes (ie. TTN variants in 4 DCM patients) compared to Reichart et al. where they analyzed a population enriched with pathogenic variants (ie. TTN variants in 12 DCM patients).11,46 Arguably, Reichert et al. also approached the analysis to identify genotype-linked, cell-type and cell-state specific expression and employed pseudobulk approaches in both RV and LV samples and centered log ratio-based compositional models to sensitively detect these findings.46 This exhibits how differences in studies can stem from sample size and analytical approaches, underscoring the importance of large, well-powered datasets.
VI. Therapeutic insights of scRNA transcriptomics
With the introduction of precision medicine therapies, leveraging scRNA-seq data from a diagnostic, prognostic, and therapeutic perspective is paramount. Additionally, several common cell states are seen in different cardiomyopathy phenotypes, suggesting the applicability of these findings to a multitude of patients. Regardless, functional validation of scRNA-seq findings is essential. As discussed in “compensated” cardiomyocyte cell states, overexpression of CORIN and FGF12 is highlighted. As hypothesized from these studies, recent animal models with upregulated levels of FGF12 and CORIN exhibited reduced hypertrophy and fibrosis and improved cardiac function.72,73 Although CORIN’s association with heart failure is known, identifying lesser-known targets like FGF12 has future therapeutic potential. There is also a critical need for additional targets to inhibit cardiac fibrosis and inflammation, as many clinical trials using anti-fibrotic and inflammatory drugs have failed to achieve clinical endpoints.74–76 scRNA-seq has identified novel targets and validated important genes driving these processes. For instance, Kattih et al. reported that silencing AEBP1 in human cardiac fibroblasts has anti-fibrotic, proliferative, and migratory effects.50 Other targets like MEOX1, are druggable and targeted by available molecules like the BET inhibitor, JQ1.59 Amrute et al. leveraged this in a mouse model to validate the role of RUNX1 in human cardiac recovery.66 And finally, the use of anti-remodeling agents, termed goal-directed medical therapy, is not associated with improvements in transplantation-free survival outcomes or symptoms in children with DCM.77,78 Pediatric scRNA-seq suggest that this may be biological, as younger patients exhibited less cardiac remodeling compared to older patients, suggesting that cardiac regeneration therapies in the young as opposed to anti-remodeling agents in the old may be needed. All in all, scRNA-seq studies clarify that underlying processes in children with similar phenotypes are different compared to adults and identify novel therapeutic targets of interest.
VII. Future Perspectives
Despite this field continuing to grow significantly, several challenges remain including cost, time to process and analyze data, donor tissue quality and location, batch effects, and depth and coverage limitations remain. For instance, although integration approaches like Harmony and scVI attempt to address differences across datasets, cross-study comparisons are still complicated by batch effect introduced due to differences in sample processing, protocols, and sequencing platforms.79,80 In addition, donor tissue quality can vary depending on collection methodology and the anatomical location, which can affect cell composition and gene expression profiles. Protocolizing donor tissue harvesting and scRNA-seq pipelines are essential to enable reproducibility and comparisons across studies. We outline further limitations and challenges stratified by single cell approach and analytical approaches in Supplemental Table 2 and 3.
From a biological perspective, several factors rarely analyzed deserve future attention. For example, expression quantitative trait loci (eQTLs) may affect gene expression in cardiomyopathy. These loci may be cell-type specific, responsive to stimuli, and dynamic over time.81 One example of this is the dynamic process of cellular differentiation. Using single cell analyses, Elorbany et al. identified dynamic eQTLs that influence induced pluripotent stem cell differentiation to cardiomyocytes.82 Although efforts to describe and curate eQTLs are underway, data on eQTLs effects on gene expression in cardiomyopathy is relatively scarce. Another challenge includes the identification of expressed single nucleotide variants (eSNVs). Pathogenic, rare SNVs are known causes of cardiomyopathy. eSNVs are of interest as they may directly affect the cells they are expressed in. Strategies to identify eSNVs are hampered by a high number of false positives, given the error rates in reverse transcription, poor sensitivity in calling SNVs with low variant allele frequencies, and low read depths.83 As our ability to identify eSNVs improves, understanding how pathogenic variants affect cellular processes will improve.
Advancements in the field have also allowed for expansion beyond traditional scRNA-seq including spatial transcriptomics, single-cell metabolomics, and single-cell proteomics. Spatial transcriptomics preserves tissue while also capturing gene expression; this effectively allows for mapping of spatially resolved, high dimensional transcriptomics and the identification of transcriptomic niches, further characterizing disease microenvironments.84 Single cell metabolomics has the ability to characterize functional status of cells that can be masked when looked at in bulk.85 Nonetheless, significant challenges technically and involving the dynamic nature of the metabolome need to be addressed to ensure its accuracy and reproducibility.85 And finally, the integration of spatial proteomics further characterizes protein expression spatially, allowing for comprehensive understanding of relevant gene expression changes.86 As these modalities mature, it will allow for a well-rounded multi-omic approach to characterizing disease.
And finally, a clear gap in the field is the small number of studies focusing on children. From available data, there appear to be significant differences across the age continuum, suggesting that disease processes in children differ from adults.40,41 To address this, national and international collaborations are needed to build multi-omic databases of pediatric and adult samples to standardize sample collection and processing, enabling direct comparisons of different age groups. This will effectively address this underserved population. Additionally, restrictive cardiomyopathy (RCM) lacks available scRNA-seq datasets and represents a current gap in the field, limiting direct comparisons of cellular and molecular features between RCM and other cardiomyopathies. This highlights an important area for future research.
VIII. Conclusion
We provide a synopsis of scRNA-seq transcriptomic data in NICM. These technologies have paved the way for novel discoveries and development of therapeutics in this disease and exhibit common features across different phenotypes. Future studies should aim to continue to improve our knowledge of the underlying pathophysiology of cardiomyopathy, derive genotype-specific transcriptomic signatures, and apply novel therapeutics to clinical settings to advance patient care. Another important consideration is to focus on less accessible and understudied populations, particularly the pediatric population.
Supplementary Material
Highlights.
Single-cell RNA seq identifies underlying cellular processes in cardiomyopathy (CM).
These findings in CM phenotypes inform clinical treatment, course, or prognosis.
Further study on pediatrics and nucleotide variant effect on expression is needed.
Funding Statement
This work was supported by Graeme McDaniel Foundation (D.T.), Don McGill Gene Editing Laboratory of The Texas Heart Institute (X.L.), NIH R01 HL169511 (J.F.M), R01 HL171574 (J.F.M), R01 HL118761 (J.F.M), R01 HL177644 (J.F.M., X.L.), R01 HL173242 (J.F.M., X.L.), and R01 HL179012 (X.L.).
Abbreviations
- ACM
Arrhythmogenic cardiomyopathy
- DCM
dilated cardiomyopathy
- eSNVs
expressed single nucleotide variants
- eQTLs
expression quantitative trait loci
- HCM
hypertrophic cardiomyopathy
- LV
left ventricle
- NICM
non-ischemic cardiomyopathy
- RV
right ventricle
- scRNA
single-cell RNA
- VAD
ventricular assist device
Footnotes
Disclosure
JFM is cofounder and owns shares in Medley Therapeutics (formerly known as YAP Therapeutics). The other authors have no disclosures to make. Our central illustration was made with BioRender; Martin, L. (2025), https://BioRender.com/ b9clhoh.
AI Statement
The authors did not use generative AI or AI-assisted technologies in the development of this manuscript.
Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Data availability
There are no new data generated or associated with this article
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