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Genome-wide association mapping for cardiomyocyte ploidy identifies Shroom3 as responsible for hyperpolyploidy and ventricular dilation [bulkRNA-Seq]

ABSTRACT: Cardiomyocyte (CM) polyploidy is widely observed across the animal kingdom and various ploidy states are associated with cardiac injury responses, including regeneration and heart failure. However, our understanding of the comprehensive mechanisms governing CM ploidy and its relationship with heart physiology has been hindered by a lack of experimental tools. To address this issue and uncover novel genetic regulators, we surveyed CM ploidy across a new genetic resource known as the Hybrid Rat Diversity Panel and founnd significant variation in ploidy phenotypes across the panel. Using select rat strains with divergent displays of CM ploidy, we found that hyperpolyploidization (≥8N) positively correlates with various physiological parameters namely left ventricular dilation and reduced ejection fraction. Genome-wide association mapping identified several loci significantly associated with frequency of hyperpolyploid CMs. Investigation of genes harboring damaging protein coding variants within these loci identified enrichment of cytoarchitectural genes, of which the ACTIN-binding protein, Shroom3, was found to be strongly and specifically expressed in CMs and harbors 7 damaging protein coding variants. CM-specific deletion of Shroom3 resulted in increased hyperpolyploidization and promoted left ventricular dilation and reduced ejection fraction. Furthermore, functional characterization of single nucleotide variants resulting in amino acid changes within SHROOM3 confirmed two protein coding variants that disrupted SHROOM3-ACTIN interaction and led to altered expression of cell cycle genes. This study elucidates the genetic determinants of CM ploidy phenotypes and solidifies a correlative relationship between CM ploidy and left ventricular function. Importantly, CM intrinsic expression of at least one gene mapped in this study, Shroom3, is confirmed to regulate CM hyperpolyploidization and cardiac function.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE314057 | GEO | 2026/03/25

REPOSITORIES: GEO

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Project description:Background: Cardiac macrophages have been implicated in myocardial repair following myocardial infarction (MI), yet their therapeutic potential in ischemic cardiomyopathy (ICM) remains limited by an incomplete understanding of their molecular regulation. CD163 is highly expressed in these macrophages, yet its functional role in regulating post-MI cardiac repair remains unknown. Methods: A cross-sectional clinical study was conducted to assess the association between circulating soluble CD163 concentration and heart failure due to ICM. To investigate the functional contribution of CD163 in ICM, Wild-type (WT) and Cd163/ mice were subjected to permanent ligation of the left anterior descending coronary artery. Single-cell RNA sequencing was employed to analyze transcriptional changes in cardiac immune cells. Recombinant osteopontin (OPN) and CD163 were administered to assess their therapeutic effect in Cd163/ mice. Results: Circulating soluble CD163 levels were markedly elevated in patients with ICM-induced heart failure compared with individuals without heart failure (median difference 34.5 ng/mL, IQR 13.6–54.6 ng/mL, P = 0.002) and showed a positive correlation with the extent of systolic dysfunction and left ventricular dilation. Cd163/ mice displayed aggravated left ventricular systolic dysfunction, reduced ejection fraction and fractional shortening, impaired myocardial strain, and reduced relative wall thickness post-MI. Recombinant CD163 protein could reverse systolic dysfunction and left ventricular dilation in Cd163/ mice after MI. CD163 was predominantly expressed in CCR2⁻ resident cardiac macrophages, and CD163 deficiency altered transcriptional programs of macrophages without affecting their polarization status, with enrichment in cytokine signaling and extracellular matrix-related pathways. Spp1 (OPN) expression was significantly downregulated in Cd163/ hearts under both sham and MI conditions. Administration of recombinant OPN improved systolic function, reduced ventricular dilation, decreased fibrotic scar size, and restored the elastin-to-collagen ratio in Cd163/ mice. Conclusions: In cardiac macrophages, CD163 contributes to post-myocardial infarction repair by upregulating OPN expression, which in turn helps maintain systolic function.

Project description:Hypoplastic left heart syndrome (HLHS) is the most lethal congenital heart disease (CHD). The pathogenesis of HLHS is poorly understood and due to the likely oligogenic complexity of the disease, definitive HLHS-causing genes have not yet been identified. Postulating that impaired cardiomyocyte proliferation as a likely important contributing mechanism to HLHS pathogenesis, and we conducted a genome-wide siRNA screen to identify genes affecting proliferation of human iPSC-derived cardiomyocytes (hPSC-CMs). This yielded ribosomal protein (RP) genes as the most prominent class of effectors of CM proliferation. In parallel, whole genome sequencing and rare variant filtering of a cohort of 25 HLHS proband-parent trios with poor clinical outcome revealed enrichment of rare variants of RP genes. In addition, in another familial CHD case of HLHS proband we identified a rare, predicted-damaging promoter variant affecting RPS15A that was shared between the proband and a distant relative with CHD. Functional testing with an integrated multi-model system approach reinforced the idea that RP genes are major regulators of cardiac growth and proliferation, thus potentially contributing to hypoplastic phenotype observed in HLHS patients. Cardiac knockdown (KD) of RP genes with promoter or coding variants (RPS15A, RPS17, RPL26L1, RPL39, RPS15) reduced proliferation in generic hPSC-CMs and caused malformed hearts, heart-loss or even lethality in Drosophila. In zebrafish, diminished rps15a function caused reduced CM numbers, heart looping defects, or weakened contractility, while reduced rps17 or rpl39 function caused reduced ventricular size or systolic atrial dysfunction, respectively. Importantly, genetic interactions between RPS15A and core cardiac transcription factors TBX5 in CMs, Drosocross, pannier and tinman in flies, and tbx5 and nkx2-7 (nkx2-5 paralog) in fish, support a specific role for RP genes in heart development. Furthermore, RPS15A KD-induced heart/CM proliferation defects were significantly attenuated by p53 KD in both hPSC-CMs and zebrafish, and by Hippo activation (YAP/yorkie overexpression) in developing fly hearts. Based on these findings, we conclude that RP genes play critical roles in cardiogenesis and constitute an emerging novel class of gene candidates likely involved in HLHS and other CHDs.

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Genome-wide association mapping for cardiomyocyte ploidy identifies Shroom3 as responsible for hyperpolyploidy and ventricular dilation [bulkRNA-Seq]

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