Transcriptional and Cellular Diversity of the Human Heart

MiR-1 alleviates chronic heart failure through HCN2/HCN4 axis in vitro

OBJECTIVE

Chronic heart failure (CHF) is a complex and progressive condition. This study aimed to investigate the potential regulatory effect of miR-1 on CHF through the hyperpolarization-activated cyclic nucleotide-gated channels 2 and 4 (HCN2/HCN4) axis.

METHOD

The expression of miR-1 was examined in individuals diagnosed with CHF. The patients' level of NT-proBNP was evaluated. A cellular model using H9c2 cells subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) was established. RT-qPCR and western blot were performed to determine the levels of miR-1, HCN2, or HCN4. Elisa was used to measure the levels of TNF-α and IL-6. The potential target of miR-1 on HCN2 and HCN4 was verified using the dual luciferase assay. Overexpression of miR-1 or HCN was employed to explore the specific mechanism of miR-1 and HCN on CHF. The MTT assay was used to evaluate cell viability, while apoptosis was quantified through flow cytometry.

RESULTS

In both patients with CHF and OGD/R-treated H9c2 cells, miR-1 levels were found to be reduced. The overexpression of miR-1 notably suppressed the secretion of TNF-α and IL-6 (P < 0.05). Overexpression of miR-1 also markedly increased cell viability (P < 0.01) and reduced apoptosis (P < 0.05) in OGD/R-treated H9c2 cells. Using miRNA-target prediction databases and luciferase reporter assays, we identified HCN2 and HCN4 as direct targets of miR-1. Moreover, overexpression of HCN2 and HCN4 counteracted the protective effects of miR-1, as evidenced by a significant reduction in cell viability (P < 0.01) and an increase in apoptosis (P < 0.05).

CONCLUSION

This study suggests that miR-1 regulates cell viability and apoptosis in CHF through the HCN2/HCN4 axis, highlighting its potential as a therapeutic target for CHF.

Transcriptomic signatures of atheroresistance in the human atrium and ventricle highlight potential candidates for targeted atherosclerosis therapeutics

Atherosclerosis risk is not uniform throughout the cardiovascular system. This study therefore aimed to compare the transcriptomes of atheroresistant human atrium and ventricle with atheroprone coronary arteries to identify transcriptomic signatures of atheroresistance and potential targets for atherosclerosis therapeutics. Using publicly available gene read counts, differentially expressed genes between the atrium, ventricle, and coronary artery were identified for each contrast and validated against the Swiss Institute of Bioinformatics' Bgee database. Over-representation analysis and active-subnetwork-oriented enrichment assessment then identified enriched terms, which were grouped into endothelial dysfunction-related processes. Potential biological significance was further explored with pathway analysis. Among 21474 features, 12656 differentially expressed genes were identified across the three contrasts and associated with 1215 enriched terms. There were 315 down-regulated and 133 up-regulated genes associated with endothelial dysfunction-related processes across the contrasts, including immune modulators, cell adhesion molecules, and lipid metabolism- and coagulation-related molecules. Differentially expressed genes were associated with six down-regulated Kyoto Encyclopedia of Genes and Genomes pathways, related to immune cell and associated endothelium functions. Review of regulated genes associated with endothelial dysfunction-related processes and included in these pathways, indicate immune cell-associated B cell scaffold protein with ankyrin repeats 1, as well as arterial endothelial cell-associated vascular cell adhesion molecule 1 and cadherin 5, as potential atherosclerosis targets.

Cardiac macrophage: Insights from murine models to translational potential for human studies

Macrophages are a cell type that are known to play dynamic roles in acute and progressive pathology. They are highly attuned to their microenvironments throughout maturation, tailoring their functional responses according to the specific tissues in which they reside and their developmental origin. Cardiac macrophages (cMacs) have emerged as focal points of interest for their interactions with the unique electrical and mechanical stimuli of the heart, as well as for their role in maintaining cardiac homeostasis. Through an in-depth analysis of their origin, lineage, and functional significance, this review aims to shed light on cMacs' distinct contributions to both normal physiological maintenance as well as disease progression. Central to our discussion is the comparison of cMac characteristics between mouse and human models, highlighting current challenges and proposing novel experimental tools for deciphering cMac function within the intricate human cardiac microenvironments based on current murine studies. Our review offers valuable insights for identifying novel therapeutic targets and interventions tailored to the distinct roles of these immune cells in cardiovascular diseases (CVDs).

Selective inhibition of stromal mechanosensing suppresses cardiac fibrosis

Matrix-derived biophysical cues are known to regulate the activation of fibroblasts and their subsequent transdifferentiation into myofibroblasts1-6, but whether modulation of these signals can suppress fibrosis in intact tissues remains unclear, particularly in the cardiovascular system7-10. Here we demonstrate across multiple scales that inhibition of matrix mechanosensing in persistently activated cardiac fibroblasts potentiates-in concert with soluble regulators of the TGFβ pathway-a robust transcriptomic, morphological and metabolic shift towards quiescence. By conducting a meta-analysis of public human and mouse single-cell sequencing datasets, we identify the focal-adhesion-associated tyrosine kinase SRC as a fibroblast-enriched mechanosensor that can be targeted selectively in stromal cells to mimic the effects of matrix softening in vivo. Pharmacological inhibition of SRC by saracatinib, coupled with TGFβ suppression, induces synergistic repression of key profibrotic gene programs in fibroblasts, characterized by a marked inhibition of the MRTF-SRF pathway, which is not seen after treatment with either drug alone. Importantly, the dual treatment alleviates contractile dysfunction in fibrotic engineered heart tissues and in a mouse model of heart failure. Our findings point to joint inhibition of SRC-mediated stromal mechanosensing and TGFβ signalling as a potential mechanotherapeutic strategy for treating cardiovascular fibrosis.

ARID5A orchestrates cardiac aging and inflammation through MAVS mRNA stabilization

Elucidating the regulatory mechanisms of human cardiac aging remains a great challenge. Here, using human heart tissues from 74 individuals ranging from young (≤35 years) to old (≥65 years), we provide an overview of the histological, cellular and molecular alterations underpinning the aging of human hearts. We decoded aging-related gene expression changes at single-cell resolution and identified increased inflammation as the key event, driven by upregulation of ARID5A, an RNA-binding protein. ARID5A epi-transcriptionally regulated Mitochondrial Antiviral Signaling Protein (MAVS) mRNA stability, leading to NF-κB and TBK1 activation, amplifying aging and inflammation phenotypes. The application of gene therapy using lentiviral vectors encoding shRNA targeting ARID5A into the myocardium not only mitigated the inflammatory and aging phenotypes but also bolstered cardiac function in aged mice. Altogether, our study provides a valuable resource and advances our understanding of cardiac aging mechanisms by deciphering the ARID5A-MAVS axis in post-transcriptional regulation.

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Understanding complex biological systems requires tracing cellular dynamic changes across conditions, time, and space. However, integrating multi-sample data in a unified way to explore cellular heterogeneity remains challenging. Here, we present Stereopy, a flexible framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this framework, we devise a universal container, a scope controller, and an integrative transformer tailored for multi-sample multimodal data storage, management, and processing. Stereopy showcases three representative applications: investigating specific cell communities and genes responsible for pathological changes, detecting spatiotemporal gene patterns by considering spatial and temporal features, and inferring three-dimensional niche-based cell-gene interaction network that bridges intercellular communications and intracellular regulations. Stereopy serves as both a comprehensive bioinformatics toolbox and an extensible framework that empowers researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

The future of cardiology: Integrating single-cell transcriptomics with multi-omics for enhanced cardiac disease insights

Recent advancements in single-cell transcriptome sequencing (scRNA-seq) have revolutionized our understanding of cellular heterogeneity in cardiovascular diseases, enabling the identification of novel therapeutic targets. This technology allows for high-resolution analysis of gene expression at the single-cell level, revealing the complex dynamics of human heart cell development and the diverse roles of cardiac cell types in health and disease. Despite its transformative potential, current applications of scRNA-seq face limitations, including challenges in data integration and the need for comprehensive multi-omic approaches to fully elucidate the mechanisms underlying cardiovascular pathologies. This review highlights the significant insights gained from scRNA-seq studies in the mammalian heart, emphasizing the importance of integrating spatial transcriptomics and other omics technologies to enhance our understanding of cardiac biology. Furthermore, it addresses the critical research gaps in the field, particularly in the context of personalized medicine and the need for improved methodologies to analyze rare cell populations. By exploring these challenges and opportunities, this review aims to pave the way for innovative diagnostic and therapeutic strategies that can ultimately improve outcomes for patients with cardiovascular diseases.

Genome-wide association study meta-analysis provides insights into the etiology of heart failure and its subtypes

Heart failure (HF) is a major contributor to global morbidity and mortality. While distinct clinical subtypes, defined by etiology and left ventricular ejection fraction, are well recognized, their genetic determinants remain inadequately understood. In this study, we report a genome-wide association study of HF and its subtypes in a sample of 1.9 million individuals. A total of 153,174 individuals had HF, of whom 44,012 had a nonischemic etiology (ni-HF). A subset of patients with ni-HF were stratified based on left ventricular systolic function, where data were available, identifying 5,406 individuals with reduced ejection fraction and 3,841 with preserved ejection fraction. We identify 66 genetic loci associated with HF and its subtypes, 37 of which have not previously been reported. Using functionally informed gene prioritization methods, we predict effector genes for each identified locus, and map these to etiologic disease clusters through phenome-wide association analysis, network analysis and colocalization. Through heritability enrichment analysis, we highlight the role of extracardiac tissues in disease etiology. We then examine the differential associations of upstream risk factors with HF subtypes using Mendelian randomization. These findings extend our understanding of the mechanisms underlying HF etiology and may inform future approaches to prevention and treatment.

Gain and loss of the centrosomal protein taxilin-beta influences cardiac proteostasis and stress

Centrosomes localize to perinuclear foci where they serve multifunctional roles, arranging the microtubule organizing center (MTOC) and anchoring ubiquitin proteasome system (UPS) machinery, as suggested by prior studies. In mature cardiomyocytes, centrosomal proteins redistribute into a specialized perinuclear cage-like structure, and a potential centrosomal-UPS interface has not been studied, despite established roles for UPS in cardiomyopathy. In addition, there have been no reports citing cardiomyocyte UPS dysfunction upon or after manipulation of centrosomal proteins. Taxilin-beta (Txlnb), a cardiomyocyte-enriched protein, belongs to a family of centrosome adapter proteins implicated in protein quality control. We hypothesize that Txlnb is part of the perinuclear centrosomal cage and regulates proteostasis in cardiomyocytes. Herein, we show that centrosome proteins, including Txlnb, have significantly broadly dysregulated RNA expressions in failing hearts; however, Txlnb protein levels appear to be unchanged. Reanalysis of Txlnb's interactome supports its involvement in cytoskeletal, microtubule, and UPS processes, particularly centrosome-related functions. Using gain and loss of function approaches, in cells and mice, we show that Txlnb is a novel regulator of cardiac proteostasis through its influence on UPS. Overexpressing Txlnb in cardiomyocytes reduces ubiquitinated protein accumulation and enhances proteasome activity during hypertrophy. Germline Txlnb knockout in mice increases ubiquitinated protein accumulation, decreases 26Sβ5 proteasome activity, and lowers cardiac mass with aging, indicating proteasomal insufficiency and altered cardiac growth. Loss of Txlnb worsens heart phenotypes in mouse models of cardiac proteotoxicity and pressure overload. Overall, our data implicate the centrosomal protein Txlnb as a novel regulator of cardiac proteostasis, highlighting the likely presence of an understudied and important centrosome-proteasome functional connection in cardiomyocytes.

Transcriptomic Landscape of Human Left and Right Atria Associated with Atrial Fibrillation

BACKGROUND

Atrial fibrillation (AF) is the most common acquired cardiac rhythm disorder and has become a notable public health concern. Investigating the left versus right atrium (RA) transcriptome in AF is crucial because it provides insights into the gene expression changes that drive the molecular mechanisms underlying AF, potentially leading to targeted therapies and better patient outcomes. In this study, it is proposed that variances in the transcriptomic profiles between the human left atrium (LA) and RA, as well as alterations in molecular pathways, could offer potential targets for the onset and persistence of AF.

METHODS

Here transcriptomes of LA and RA of patients (n = 31) undergoing mitral valve surgery were compared. Microarrays proceeded on the Affymetrix platform. Bioinformatic analyses were done on Partek Genomics Suite. Gene ontology, KEGG pathway, and functional enrichment analysis was conducted using differentially expressed genes on WebGestalt.

RESULTS

Notably, transforming growth factor-β (TGF-β) and peroxisome proliferator-activated receptors signaling pathways were enriched commonly. Claudin 18, which encodes a tight junction transmembrane protein, was one of the most upregulated genes in LA. PITX2 (paired like homeodomain 2) gene upregulation in LA is also involved in TGF-β signaling. Alongside the upregulation of TGF-β signaling, overexpression of extracellular matrix proteins like collagen, vitronectin, fibronectin, and thrombospondin also points out the cardiac fibrosis process preceded in LA, where AF originates.

CONCLUSIONS

In brief, comparisons of the AF-related transcriptomic landscapes of LA and RA propose targets for novel therapeutic and/or preventive strategies. This study highlights clinical evidence of genetic-based cardiac remodeling that could guide future therapeutic and preventive strategies.

Opportunities and challenges for the use of human samples in translational cardiovascular research: a scientific statement of the ESC Working Group on Cellular Biology of the Heart, the ESC Working Group on Cardiovascular Surgery, the ESC Council on Basic Cardiovascular Science, the ESC Scientists of Tomorrow, the European Association of Percutaneous Cardiovascular Interventions of the ESC, and the Heart Failure Association of the ESC

Animal models offer invaluable insights into disease mechanisms but cannot entirely mimic the variability and heterogeneity of human populations, nor the increasing prevalence of multi-morbidity. Consequently, employing human samples-such as whole blood or fractions, valvular and vascular tissues, myocardium, pericardium, or human-derived cells-is essential for enhancing the translational relevance of cardiovascular research. For instance, myocardial tissue slices, which preserve crucial structural and functional characteristics of the human heart, can be used in vitro to examine drug responses. Human blood serves as a rich source of biomarkers, including extracellular vesicles, various types of RNA (miRNA, lncRNA, and circRNAs), circulating inflammatory cells, and endothelial colony-forming cells, facilitating detailed studies of cardiovascular diseases. Primary cardiomyocytes and vascular cells isolated from human tissues are invaluable for mechanistic investigations in vitro. In cases where these are unavailable, human induced pluripotent stem cells serve as effective substitutes, albeit with specific limitations. However, the use of human samples presents challenges such as ethical approvals, tissue procurement and storage, variability in patient genetics and treatment regimens, and the selection of appropriate control samples. Biobanks are central to the efficient use of these scarce and valuable resources. This scientific statement discusses opportunities to implement the use of human samples for cardiovascular research within specific clinical contexts, offers a practical framework for acquiring and utilizing different human materials, and presents examples of human sample applications for specific cardiovascular diseases, providing a valuable resource for clinicians, translational and basic scientists engaged in cardiovascular research.

Decoding dengue's neurological assault: insights from single-cell CNS analysis in an immunocompromised mouse model

BACKGROUND

Dengue encephalitis, a severe neurological complication of dengue virus infection, is increasingly recognized for its rising incidence and significant public health burden. Despite its growing prevalence, the underlying mechanisms and effective therapeutic strategies remain poorly understood.

METHODS

Cellular atlas of dengue encephalitis was determined by single-nucleus RNA sequencing. Viral load of dengue virus and the level of cytokines expression was detected by RT-qPCR. The target cells of dengue virus were verified by immunofluorescence. The cytotoxic effect of CD8+ T cell was determined by flow cytometry, immunofluorescence, in vivo CD8+ T cell depletion, adoptive transfer and CCK-8-based cell viability assay. Axonal and synaptic reduction induced by dengue virus infection was demonstrated by RT-qPCR, Western blot, transmission electron microscope and immunofluorescence. Finally, motor and sensory functions of mice were detected by open field test and hot plate test, respectively.

RESULTS

In this study, we utilized single-nucleus RNA sequencing on brain tissues from a dengue-infected murine model to construct a comprehensive cellular atlas of dengue encephalitis. Our findings identify neurons, particularly inhibitory GABAergic subtypes, as the primary targets of dengue virus. Additionally, immune cell infiltration was observed, contributing to significant neurological damage. Comprehensive analyses of cell-cell communication, combined with CD8+ T cell depletion and transfer restoration experiments, have elucidated the critical role of CD8+ T cells in triggering encephalitis through their interaction with neurons. These cells infiltrate the brain from peripheral circulation, interact with neurons, and induce damage of synapse and axon, accompanied by neurological dysfunction.

CONCLUSION

We defined cellular atlas of dengue encephalitis in mouse model and identified the primary target neuron of dengue virus. In addition, we demonstrated the significant cytotoxic effect of CD8+ T cell, which leads to apoptosis of neuron and neurological dysfunction of mice. Our study provides a molecular and cellular framework for understanding dengue encephalitis through advanced sequencing technologies. The insights gained serve as a foundation for future investigations into its pathogenesis and the development of targeted therapeutic approaches.

From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.

Integration of single-nuclei and spatial transcriptomics to decipher tumor phenotype predictive of relapse-free survival in Wilms tumor

Background

Wilms tumor (WT) is the most common childhood renal malignancy, with recurrence linked to poor prognosis. Identifying the molecular features of tumor phenotypes that drive recurrence and discovering novel targets are crucial for improving treatment strategies and enhancing patient outcomes.

Methods

Single-nuclei RNA sequencing (snRNA-seq), spatial transcriptomics (ST), bulk RNA-seq, and mutation/copy number data were curated from public databases. The Seurat package was used to process snRNA-seq and ST data. Scissor analysis was applied to identify tumor subpopulations associated with poor relapse-free survival (RFS). Univariate Cox and LASSO analyses were utilized to reduce features. A prognostic ensemble machine learning model was developed. Immunohistochemistry was used to validate the expression of key features in tumor tissues. The CellChat and Commot package was utilized to infer cellular interactions. The PERCEPTION computational pipeline was used to predict the response of tumor cells to chemotherapy and targeted therapies.

Results

By integrating snRNA-seq and bulk RNA-seq data, we identified a subtype of Scissor+ tumor cells associated with poor RFS, predominantly derived from cap mesenchyme-like blastemal and fibroblast-like tumor subgroups. These cells displayed nephron progenitor signatures and cancer stem cell markers. A prognostic ensemble machine learning model was constructed based on the Scissor+ tumor signature to accurately predict patient RFS. TGFA was identified as the most significant feature in this model and validated by immunohistochemistry. Cellular communication analysis revealed strong associations between Scissor+ tumor cells and cancer-associated fibroblasts (CAFs) through IGF, SLIT, FGF, and PDGF pathways. ST data revealed that Scissor+ tumor cells were primarily located in immune-desert niche surrounded by CAFs. Despite reduced responsiveness to conventional chemotherapy, Scissor+ tumor cells were sensitive to EGFR inhibitors, providing insights into clinical intervention strategies for WT patients at high risk of recurrence.

Conclusion

This study identified a relapse-associated tumor subtype resembling nephron progenitor cells, residing in immune-desert niches through interactions with CAFs. The proposed prognostic model could accurately identify patients at high risk of relapse, offering a promising method for clinical risk stratification. Targeting these cells with EGFR inhibitors, in combination with conventional chemotherapy, may provide a potential therapeutic strategy for WT patients.

The role of mechanosignaling in the control of myocardial mass

Regulation of myocardial mass is key for maintaining cardiovascular health. This review highlights the complex and regulatory relationship between mechanosignaling and myocardial mass, influenced by many internal and external factors including hemodynamic and microgravity, respectively. The heart is a dynamic organ constantly adapting to changes in workload (preload and afterload) and mechanical stress exerted on the myocardium, influencing both physiological adaptations and pathological remodeling. Mechanosignaling pathways, such as the mitogen-activated protein kinases (MAPKs) and the phosphoinositide 3-kinases and serine/threonine kinase (PI3K/Akt) pathways, mediate downstream effects on gene expression and play key roles in transducing mechanical cues into biochemical signals, thereby modulating cellular processes, including control of myocardial mass. Dysregulation of these processes can lead to pathological cardiac remodeling, such as hypertrophic cardiomyopathy. Furthermore, recent studies have highlighted the importance of protein quality control mechanisms, such as the ubiquitin-proteasome system, in settings of extreme physiological conditions that alter the heart workload such as pregnancy and microgravity. Overall, this review provides a thorough insight into how mechanical signals are converted into chemical signals to regulate myocardial mass in both healthy and diseased conditions.

Homeostatic Role of Decorin in Right Ventricular Pressure Overload and Pulmonary Hypertension Induced Remodeling

Right ventricular (RV) pressure loading induces RV profibrotic signaling and fibrosis associated with RV dysfunction. RV decorin protein levels are decreased in patients with chronic RV pressure loading. RV decorin protein levels are also decreased in 4 animal models of mechanical RV pressure loading and pulmonary arterial hypertension. Human cardiac fibroblasts overexpressing decorin show diminished collagen-1 secretion in response to mechanical or chemical profibrotic stress while decorin knockout human cardiac fibroblasts show increased collagen-1 secretion in response to stress. Downregulation of decorin may play a key role in upregulating transforming growth factor-β1 profibrotic signaling and fibrosis that contribute to RV dysfunction in RV pressure loading.

The trabecular and compact myocardium of adult vertebrate ventricles are transcriptionally similar despite morphological differences

A poorly understood, major event in heart evolution is the convergent prioritization in mammals and birds of compact myocardium over trabecular myocardium. Compact myocardium is thought to facilitate the greater cardiac outputs that distinguish endothermic mammals and birds from ectotherms, but the underlying mechanism remains unclear. We used transcriptomics to investigate whether the compact layer myocardium is intrinsically different from that of the trabecular layer. In the embryonic mouse heart, spatial transcriptomics revealed that 3% of detected genes were differentially expressed between trabecular and compact myocardium. In the adult, this analysis yielded only 0.2% differentially expressed genes. Additionally, the transcriptomes of both embryonic trabecular and compact myocardium greatly differed from those of the adult myocardium. Reanalysis of available single-cell transcriptomes showed relationships between human embryonic and adult trabecular and compact myocardium similar to those in mice. Analysis of new and published transcriptomes from adult zebra finch, zebrafish, and tuna revealed few differentially expressed genes (<0.6%) and no conservation between species. We conclude that the transcriptional states of developing trabecular and compact myocardium do not persist into adulthood. In adult hearts, the compact layer myocardium is not intrinsically different from that of the trabecular layer despite the overt morphological differences.

Meta-analysis of genome-wide associations and polygenic risk prediction for atrial fibrillation in more than 180,000 cases

Atrial fibrillation (AF) is the most common heart rhythm abnormality and is a leading cause of heart failure and stroke. This large-scale meta-analysis of genome-wide association studies increased the power to detect single-nucleotide variant associations and found more than 350 AF-associated genetic loci. We identified candidate genes related to muscle contractility, cardiac muscle development and cell-cell communication at 139 loci. Furthermore, we assayed chromatin accessibility using assay for transposase-accessible chromatin with sequencing and histone H3 lysine 4 trimethylation in stem cell-derived atrial cardiomyocytes. We observed a marked increase in chromatin accessibility for our sentinel variants and prioritized genes in atrial cardiomyocytes. Finally, a polygenic risk score (PRS) based on our updated effect estimates improved AF risk prediction compared to the CHARGE-AF clinical risk score and a previously reported PRS for AF. The doubling of known risk loci will facilitate a greater understanding of the pathways underlying AF.

ADAMTS7, a target in atherosclerosis, cooperates with its homolog ADAMTS12 to protect against myxomatous valve degeneration

The physiological roles of the metalloprotease-proteoglycan ADAMTS7, a drug target in atherosclerosis and vascular restenosis, and its homolog ADAMTS12, are undefined in the cardiovascular system. The objective of the present work was to investigate their roles in mice with genetic inactivation of both proteases and in relation to the resulting valve defects, to define their proteolytic activities in the matrisome. Here, we demonstrate that Adamts7 and Adamts12 are co-expressed in heart valves and each buffers inactivation of the other by compensatory upregulation. Leaflets of Adamts7 -/-;Adamts12 -/- aortic valves, but not the respective single mutants, were abnormally shaped at birth, with progressively severe disorganization and enlargement occurring thereafter. Doppler echocardiography showed that Adamts7 -/-;Adamts12 -/- mice had stenotic and regurgitant aortic valves. We investigated ADAMTS7 and ADAMTS12 substrates relevant to the valve matrisome in secretome libraries from Adamts7 -/-;Adamts12 -/- cells using the N-terminomics technique Terminal Amine Isotopic Labeling of Substrates (TAILS). Although ADAMTS7 and ADAMTS12 shared several extracellular matrix (ECM) substrates, cleavage sites and sequence preference for each protease were distinct. Adamts7 -/-;Adamts12 -/- valve leaflets showed accumulation of several of the identified ECM substrates, including periostin, a matricellular protein crucial for cardiac valve homeostasis. We conclude that the myxomatous degeneration in Adamts7 -/-;Adamts12 -/- valve leaflets reflects a complex disturbance of ECM proteostasis with accumulation of multiple ADAMTS7 and ADAMTS12 ECM substrates, and perturbation of regulatory pathways with roots in ECM, such as TGFβ signaling, which was increased in the mutant valves.

Sequencing in over 50,000 cases identifies coding and structural variation underlying atrial fibrillation risk

Atrial fibrillation (AF) is a prevalent and morbid abnormality of the heart rhythm with a strong genetic component. Here, we meta-analyzed genome and exome sequencing data from 36 studies that included 52,416 AF cases and 277,762 controls. In burden tests of rare coding variation, we identified novel associations between AF and the genes MYBPC3, LMNA, PKP2, FAM189A2 and KDM5B. We further identified associations between AF and rare structural variants owing to deletions in CTNNA3 and duplications of GATA4. We broadly replicated our findings in independent samples from MyCode, deCODE and UK Biobank. Finally, we found that CRISPR knockout of KDM5B in stem-cell-derived atrial cardiomyocytes led to a shortening of the action potential duration and widespread transcriptomic dysregulation of genes relevant to atrial homeostasis and conduction. Our results highlight the contribution of rare coding and structural variants to AF, including genetic links between AF and cardiomyopathies, and expand our understanding of the rare variant architecture for this common arrhythmia.

Exploring transcriptomic signatures in sudden unexplained death (SUD) cases

BACKGROUND

Molecular autopsy in sudden unexplained death (SUD) has successfully identified pathogenic variants in cardiovascular genes in a substantial proportion of cases, contributing to prevention strategies in family members. However, many SUD cases remain genetically unresolved, prompting investigations into other omics technologies to better understand the pathogenic mechanisms leading to a sudden death event. In this study, whole transcriptome sequencing was performed on heart samples from 43 SUD cases and 17 heart-healthy controls, with the aim to identify disease-specific transcriptome signatures in sudden unexplained death.

RESULTS

PCA based on the top 500 genes with the highest variance among the samples showed no clear separation between SUD and controls or among the three SUD subgroups. DESeq2 identified 1,676 differentially expressed genes between SUD and controls with significantly upregulated genes involved in biological processes such as angiogenesis, blood vessel development, vasculogenesis and cell adhesion. Pathway analysis of the differentially expressed genes showed that most were downregulated and involved in amide/peptide biosynthesis and fatty acid metabolism. Additional analysis of SUD subgroups revealed unique gene expression patterns and highlighted differentially expressed genes within each subgroup.

CONCLUSION

Gene expression analysis of SUD heart tissue is a promising approach to identify cardiac disease-related pathways to further understand the pathological mechanisms leading to a sudden death event. However, due to the heterogeneity of the SUD cases and the unclear phenotype, further studies in larger cohorts are needed.

Unveiling the native architecture of adult cardiac tissue using the 3D-NaissI method

Accurately imaging adult cardiac tissue in its native state is essential for regenerative medicine and understanding heart disease. Current fluorescence methods encounter challenges with tissue fixation. Here, we introduce the 3D-NaissI (3D-Native Tissue Imaging) method, which enables rapid, cost-effective imaging of fresh cardiac tissue samples in their closest native state, and has been extended to other tissues. We validated the efficacy of 3D-NaissI in preserving cardiac tissue integrity using small biopsies under hypothermic conditions in phosphate-buffered saline, offering unparalleled resolution in confocal microscopy for imaging fluorescent small molecules and antibodies. Compared to conventional histology, 3D-NaissI preserves cardiac tissue architecture and native protein epitopes, facilitating the use of a wide range of commercial antibodies without unmasking strategies. We successfully identified specific cardiac protein expression patterns in cardiomyocytes (CMs) from rodents and humans, including for the first time ACE2 localization in the lateral membrane/T-Tubules and SGTL2 in the sarcoplasmic reticulum. These findings shed light on COVID-19-related cardiac complications and suggest novel explanations for therapeutic benefits of iSGLT2 in HFpEF patients. Additionally, we challenge the notion of "connexin-43 lateralization" in heart pathology, suggesting it may be an artifact of cardiac fixation, as 3D-NaissI clearly revealed native connexin-43 expression at the lateral membrane of healthy CMs. We also discovered previously undocumented periodic ring-like 3D structures formed by pericytes that cover the lateral surfaces of CMs. These structures, positive for laminin-2, delineate a specific spatial architecture of laminin-2 receptors on the CM surface, underscoring the pivotal role of pericytes in CM function. Lastly, 3D-NaissI facilitates the mapping of native human protein expression in fresh cardiac autopsies, offering insights into both pathological and non-pathological contexts. Therefore, 3D-NaissI provides unparalleled insights into native cardiac tissue biology and holds the promise of advancing our understanding of physiology and pathophysiology, surpassing standard histology in both resolution and accuracy.

Genetic Mapping of Monocyte Fate Decisions Following Myocardial Infarction

Inflammation contributes to the pathogenesis of myocardial infarction and heart failure and represents a viable therapeutic target. Monocytes and their progeny are highly abundant and display incredible functional diversity, serving as key determinants of myocardial inflammation and tissue repair. Much remains to be learned regarding mechanisms and signaling events that instruct monocyte fate decisions. We devised a genetic lineage tracing strategy using Ccr2 crERT2 Rosa26 LSL-tdTomato mice in combination with single cell RNA-sequencing to map the differentiation trajectories of monocytes that infiltrate the heart after reperfused myocardial infarction. Monocytes are recruited to the heart early after injury and give rise to transcriptionally distinct and spatially restricted macrophage and dendritic cell-like subsets that are specified prior to extravasation and chronically persist within the myocardium. Pseudotime analysis predicted two differentiation trajectories of monocyte-derived macrophages that are partitioned into the border and infarct zones, respectively. Among these trajectories, we show that macrophages expressing a type I IFN responsive signature are an intermediate population that gives rise to MHC-II hi macrophages, are localized within the border zone, and promote myocardial protection. Collectively, these data uncover new complexities of monocyte differentiation in the infarcted heart and suggest that modulating monocyte fate decisions may have clinical implications.

Pathophysiological insights into HFpEF from studies of human cardiac tissue

Heart failure with preserved ejection fraction (HFpEF) is a major, worldwide health-care problem. Few therapies for HFpEF exist because the pathophysiology of this condition is poorly defined and, increasingly, postulated to be diverse. Although perturbations in other organs contribute to the clinical profile in HFpEF, altered cardiac structure, function or both are the primary causes of this heart failure syndrome. Therefore, studying myocardial tissue is fundamental to improve pathophysiological insights and therapeutic discovery in HFpEF. Most studies of myocardial changes in HFpEF have relied on cardiac tissue from animal models without (or with limited) confirmatory studies in human cardiac tissue. Animal models of HFpEF have evolved based on theoretical HFpEF aetiologies, but these models might not reflect the complex pathophysiology of human HFpEF. The focus of this Review is the pathophysiological insights gained from studies of human HFpEF myocardium. We outline the rationale for these studies, the challenges and opportunities in obtaining myocardial tissue from patients with HFpEF and relevant comparator groups, the analytical approaches, the pathophysiological insights gained to date and the remaining knowledge gaps. Our objective is to provide a roadmap for future studies of cardiac tissue from diverse cohorts of patients with HFpEF, coupling discovery biology with measures to account for pathophysiological diversity.

BMP10 reflects pre-capillary pulmonary hemodynamics: association of biomarkers and hemodynamic parameters in pulmonary hypertension

BACKGROUND AND AIMS

The role of biomarkers in diagnosing pulmonary hypertension (PH) and distinguishing between pre- and post-capillary PH remains poorly understood. We aimed to identify biomarkers with a strong association with mean pulmonary arterial pressure, mPAP (PH diagnosis) and pulmonary vascular resistance, PVR (pre-capillary component), but not with pulmonary arterial wedge pressure, PAWP (post-capillary component).

METHODS

Blood samples were collected in patients undergoing right heart catheterization within a prospective cross-sectional study. Biomarkers measured included BMP10, NT-proBNP, ANG2, ESM1/endocan, FGF23, GDF15, IGFBP7, IL6, MyBPC3, proC3, and proC6/endotrophin. Primary outcomes were mPAP, PVR, and PAWP, while secondary outcomes included PH diagnosis (mPAP > 20 mmHg) and elevated PVR (> 2 Wood units). Multivariable linear and logistic regression models were used to assess the relationship between biomarkers and outcomes.

RESULTS

Of the 127 patients included (age 66 ± 13 years, 54% female), 73% were diagnosed with PH. BMP10, NT-proBNP, ANG2, MyBPC3, and FGF23 showed a strong association with mPAP (p < 0.001). BMP10 and NT-proBNP were strongly associated with PVR (p < 0.001), while NT-proBNP and ANG2 were strongly associated with PAWP (p < 0.001). NT-proBNP had the strongest association with the diagnosis of PH (area under the curve = 0.76). BMP10 was the only biomarker associated with elevated PVR (OR 1.60, 95%CI 1.01-2.54, p = 0.04) but not with PAWP (p = 0.86).

CONCLUSIONS

Several biomarkers were strongly associated with mPAP, PAWP, and PVR. BMP10 was the only biomarker strongly associated with mPAP and PVR, but not with PAWP, thus reflecting the pre-capillary PH component. Measurement of BMP10 along with NT-proBNP may aid in diagnosing PH.

Dysfunction of Endothelial Cell-Mediated Intercellular Communication and Metabolic Pathways in Age-Related Macular Degeneration

PURPOSE

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, but the therapies are not satisfactory. This study aimed to find AMD specific features through the analysis of high-throughput sequencing.

METHODS

In this study, we integrated six projects containing single-cell RNA sequencing (scRNA-seq) data to perform a comprehensive analysis for AMD samples in the tissues of retina and retinal pigment epithelium/choroid, and in the positions of macula and periphery. Differentially expressed genes (DEGs) were analyzed and crucial signaling pathways were identified across cell types and between the macula and periphery. The intercellular signaling transduction among cell types were inferred by "CellChat" to build cell-cell communication network under normal and AMD conditions, and verified at the transcriptional level. The CD31+ endothelial cells were obtained to evaluate the enrichment of KEGG pathways in atrophic and neovascular AMD, and GSVA was adopted to discover differential metabolic signals in each AMD type.

RESULTS

Thirteen major cell types were identified in the integrated scRNA-seq data. Although no disease-specific cell type or differential cell proportion was found, DEGs and enriched pathways were shown in cell-type- and position-dependent manners. Severe impairment of endothelial cell-mediated cell interactions was found in the signaling transduction network of the macula, and compromised cell interactions were observed in the periphery. Furthermore, distinct signaling pathways and metabolic states were uncovered in atrophic and neovascular AMD. Striking reduction in energy metabolism, lipid metabolism, and oxidative stress was indicated in the atrophic AMD.

CONCLUSION

Conclusively, we discover aberrant signals and metabolic pathways in AMD samples, providing insight into mechanisms and potential therapeutic targets for the AMD treatment.

Cardiomyocyte engineering: The meeting point of transcription factors, signaling networks, metabolism and function

Direct cardiac reprogramming or transdifferentiation is a relatively new and promising area in regenerative therapy, cardiovascular disease modeling, and drug discovery. Effective reprogramming of fibroblasts is limited by their plasticity, that is, their ability to reprogram, and depends on solving several levels of tasks: inducing cardiomyocyte-like cells and obtaining functionally and metabolically mature cardiomyocytes. Currently, in addition to the use of more classical approaches such as overexpression of exogenous transcription factors, activation of endogenous cardiac transcription factors via controlled nucleases, such as CRISPR, represents another interesting way to obtain cardiomyocytes. Therefore, special attention is given to the potential of synthetic biology, in particular the CRISPR system, for the targeted conversion of only certain subpopulations of fibroblasts into cardiomyocytes. However, obtaining functionally and metabolically mature cardiomyocytes remains a challenge despite the range of recently developed approaches. In this review, we summarized current knowledge on the function and diversity of human cardiac fibroblasts and alternative cell sources for in vitro human cardiomyocyte models. We examined in detail the transcription factors that initiate cardiomyogenic reprogramming and their interactions. Additionally, we critically analyzed the strategies used for the metabolic and physiological maturation of induced cardiomyocytes.

Transcriptional profile of the rat cardiovascular system at single-cell resolution

We sought to characterize cellular composition across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We performed single-nucleus RNA sequencing (snRNA-seq) in 78 samples in 10 distinct regions, including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins, which produced 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, with different cellular composition across cardiac regions and tissue-specific transcription for each cell type. Several cell subtypes were region specific, including a subtype of vascular smooth muscle cells enriched in the large vasculature. We observed tissue-enriched cellular communication networks, including heightened Nppa-Npr1/2/3 signaling in the sinoatrial node. The existence of tissue-restricted cell types suggests regional regulation of cardiovascular physiology. Our detailed transcriptional characterization of each cell type offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.

Utilizing sc-linker to integrate single-cell RNA sequencing and human genetics to identify cell types and driver genes associated with non-small cell lung cancer

BACKGROUND

Genome-wide association studies (GWAS) provide a powerful method for identifying the loci and genes that contribute to disease. However, in many cases, the specific cell types and states that confer disease risk through these genes remain unknown. Determining this relationship is crucial for identifying pathogenic processes and developing therapeutic strategies.

METHODS

In this study, we utilized the sc-linker framework developed by Jagadeesh, which is an integrated framework that combines single-cell RNA sequencing (scRNA-seq), epigenomic single nucleotide polymorphism (SNP)-to-gene mapping, and GWAS summary statistics to infer potential cell types and diseases affected by genetic variations.

RESULTS

Using normal cell type programs in the sc-linker, we identified type 2 alveolar cells in normal lung tissues that are closely associated with non-small cell lung cancer (NSCLC). Additionally, we identified cancer-associated fibroblasts (CAFs) associated with lung cancer using disease-dependent programs. By integrating extensive single-cell data from NSCLC, we discerned heterogeneity among CAFs subgroups. Finally, using MAGMA, we identified RAB31 as a driver gene in disease-related fibroblasts. Proteins from the RAB family are involved in the dynamic regulation of cell membrane compartments and are dysregulated in various tumor types, potentially altering biological properties such as the proliferation, migration, and invasion of cancer cells. We found that the Ras-related protein Rab-31 (RAB31) was significantly overexpressed in tumor-associated fibroblasts compared to that in normal fibroblasts and was closely associated with poor prognosis in patients with NSCLC.

CONCLUSIONS

By integrating scRNA-seq, epigenomic, and GWAS datasets, we found that ACT2 and CAFs have specific disease heritability in lung cancer and identified the driver gene RAB31 as a potential therapeutic target.

Glycoprotein 130 Antagonism Counteracts Metabolic and Inflammatory Alterations to Enhance Right Ventricle Function in Pulmonary Artery Banded Pigs

Background

Right ventricular dysfunction (RVD) is a risk factor for death in multiple cardiovascular diseases, but RV-enhancing therapies are lacking. Inhibition of glycoprotein-130 (GP130) signaling with the small molecule SC144 improves RV function in rodent RVD via anti-inflammatory and metabolic mechanisms. However, SC144's efficacy and molecular effects in a translational large animal model of RVD are unknown.

Methods

4-week-old castrated male pigs underwent pulmonary artery banding (PAB). After 3 weeks, PAB pigs were randomized into 2 groups (daily injections of SC144 [2.2 mg/kg, PAB-SC144, n=5] or vehicle [PAB-Veh, n=5] for 3 weeks). Five age-matched pigs served as controls. Cardiac MRI quantified RV size/function. Right heart catheterization evaluated hemodynamics. Single-nucleus RNA sequencing delineated cell-type specific changes between experimental groups. Electron microscopy evaluated RV mitochondrial morphology. Phosphoproteomics identified dysregulated RV kinases. Lipidomics and metabolomics quantified lipid species and metabolites in RV tissue. Quantitative proteomics examined RV mitochondrial protein regulation.

Results

SC144 significantly improved RV ejection fraction (Control: 60±4%, PAB-Veh: 22±10%, PAB-SC144: 37±6%) despite similar RV afterload. Single-nucleus RNA sequencing demonstrated PAB-Veh pigs had lower cardiomyocyte and higher macrophage/lymphocyte/pericyte/endothelial cell abundances as compared to control, and many of these changes were blunted by SC144. SC144 combatted the downregulation of cardiomyocyte metabolic genes induced by PAB. Kinome enrichment analysis suggested SC144 counteracted RV mTORC1 activation. Correspondingly, SC144 rebalanced RV autophagy pathway proteins and improved mitochondrial morphology. Integrated lipidomics, metabolomics, and proteomics analyses revealed SC144 restored fatty acid metabolism. Finally, CellChat analysis revealed SC144 restored pericyte-endothelial cell cross-talk.

Conclusion

GP130 antagonism blunts elevated immune cell abundance, reduces pro-inflammatory gene transcription in macrophages and lymphocytes, rebalances autophagy and preserves fatty acid metabolism in cardiomyocytes, and restores endothelial cell and pericyte communication to improve RV function.

Elucidating cardiomyocyte heterogeneity and maturation dynamics through integrated single-cell and spatial transcriptomics

The intricate development and functionality of the mammalian heart are influenced by the heterogeneous nature of cardiomyocytes (CMs). In this study, single-cell and spatial transcriptomics were utilized to analyze cells from neonatal mouse hearts, resulting in a comprehensive atlas delineating the transcriptional profiles of distinct CM subsets. A continuum of maturation states was elucidated, emphasizing a progressive developmental trajectory rather than discrete stages. This approach enabled the mapping of these states across various cardiac regions, illuminating the spatial organization of CM development and the influence of the cellular microenvironment. Notably, a subset of transitional CMs was identified, characterized by a transcriptional signature marking a pivotal maturation phase, presenting a promising target for therapeutic strategies aimed at enhancing cardiac regeneration. This atlas not only elucidates fundamental aspects of cardiac development but also serves as a valuable resource for advancing research into cardiac physiology and pathology, with significant implications for regenerative medicine.

Precision Medicine for Pulmonary Vascular Disease: The Future Is Now (2023 Grover Conference Series)

Pulmonary vascular disease is not a single condition; rather it can accompany a variety of pathologies that impact the pulmonary vasculature. Applying precision medicine strategies to better phenotype, diagnose, monitor, and treat pulmonary vascular disease is increasingly possible with the growing accessibility of powerful clinical and research tools. Nevertheless, challenges exist in implementing these tools to optimal effect. The 2023 Grover Conference Series reviewed the research landscape to summarize the current state of the art and provide a better understanding of the application of precision medicine to managing pulmonary vascular disease. In particular, the following aspects were discussed: (1) Clinical phenotypes, (2) genetics, (3) epigenetics, (4) biomarker discovery, (5) application of precision biology to clinical trials, (6) the right ventricle (RV), and (7) integrating precision medicine to clinical care. The present review summarizes the content of these discussions and the prospects for the future.

Next-Gen Therapeutics: Pioneering Drug Discovery with iPSCs, Genomics, AI, and Clinical Trials in a Dish

In the high-stakes arena of drug discovery, the journey from bench to bedside is hindered by a daunting 92% failure rate, primarily due to unpredicted toxicities and inadequate therapeutic efficacy in clinical trials. The FDA Modernization Act 2.0 heralds a transformative approach, advocating for the integration of alternative methods to conventional animal testing, including cell-based assays that employ human induced pluripotent stem cell (iPSC)-derived organoids, and organ-on-a-chip technologies, in conjunction with sophisticated artificial intelligence (AI) methodologies. Our review explores the innovative capacity of iPSC-derived clinical trial in a dish models designed for cardiovascular disease research. We also highlight how integrating iPSC technology with AI can accelerate the identification of viable therapeutic candidates, streamline drug screening, and pave the way toward more personalized medicine. Through this, we provide a comprehensive overview of the current landscape and future implications of iPSC and AI applications being navigated by the research community and pharmaceutical industry.

Molecular and physiological mechanisms of aging are distinct in the cardiac right and left ventricles

Aging is the primary risk factor for heart disease, the leading global cause of death. Right ventricular (RV) function predicts survival in several age-related clinical contexts, yet no therapies directly improve RV function, in large part due to a poor mechanistic understanding of RV aging and how it is distinct from the widely studied left ventricle (LV). To address this gap, we comprehensively quantified RV functional and morphological remodeling with age. We further aimed to identify molecular mechanisms of RV aging thus we performed RNAseq on RV and LV from male and female young (4 months) and aged (19-21 months) C57BL6 mice. Contrary to the concentric hypertrophic remodeling and diastolic dysfunction that occurs in the LV, the aging RV underwent eccentric remodeling with significant dilation and impaired systolic function. Transcriptomic data were also consistent with ventricle-specific aging, with few genes (13%) similarly shared between ventricles with aging. KEGG analysis identified shared aging genes in inflammatory and immune cell pathways that were confirmed by flow cytometry that demonstrated higher percent of GR1+ myeloid cells in both ventricles. Unique RV aging genes enriched in the biosynthesis of saturated fatty acids, PPAR signaling, and butanoate metabolism, and we identified putative novel RV-specific aging genes. Together, we suggest that the RV and LV are unique cardiac chambers that undergo distinct remodeling with age. These robust differences may explain why therapies designed from LV-based studies fail to improve RV function and suggest that future efforts emphasizing ventricular differences may elucidate new therapies for healthy cardiac aging.

The impact of common and rare genetic variants on bradyarrhythmia development

To broaden our understanding of bradyarrhythmias and conduction disease, we performed common variant genome-wide association analyses in up to 1.3 million individuals and rare variant burden testing in 460,000 individuals for sinus node dysfunction (SND), distal conduction disease (DCD) and pacemaker (PM) implantation. We identified 13, 31 and 21 common variant loci for SND, DCD and PM, respectively. Four well-known loci (SCN5A/SCN10A, CCDC141, TBX20 and CAMK2D) were shared for SND and DCD, while others were more specific for SND or DCD. SND and DCD showed a moderate genetic correlation (rg = 0.63). Cardiomyocyte-expressed genes were enriched for contributions to DCD heritability. Rare-variant analyses implicated LMNA for all bradyarrhythmia phenotypes, SMAD6 and SCN5A for DCD and TTN, MYBPC3 and SCN5A for PM. These results show that variation in multiple genetic pathways (for example, ion channel function, cardiac developmental programs, sarcomeric structure and cellular homeostasis) appear critical to the development of bradyarrhythmias.

Modeling the contribution of cardiac fibroblasts in dilated cardiomyopathy using induced pluripotent stem cells

Fibrosis is implicated in nearly all forms of cardiomyopathy and significantly influences disease severity and outcomes. The primary cell responsible for fibrosis is the cardiac fibroblast, which remains understudied relative to cardiomyocytes in the context of cardiomyopathy. The development of induced pluripotent stem cell-derived cardiac fibroblasts (iPSC-CFs) allows for the modeling of patient-specific disease characteristics and provides a scalable source of fibroblasts. iPSC-CFs are invaluable for understanding molecular pathways that affect disease progression and outcomes. This review explores various aspects of cardiomyopathy, with a focus on dilated cardiomyopathy, that can be modeled using iPSC-CFs and their application in drug discovery, given the current lack of approved therapies for cardiac fibrosis. We examine how iPSC-CFs can be utilized to study heart development, fibroblast heterogeneity, and activation, with the ultimate goal of developing better therapies for patients with cardiomyopathies. SIGNIFICANCE STATEMENT: We explore how induced pluripotent stem cell-derived cardiac fibroblasts (iPSC-CFs) are used to study the fibrotic component of dilated cardiomyopathy. Most research has focused on cardiomyocytes, but iPSC-CFs serve as a valuable tool to elucidate molecular pathways leading to fibrosis and paracrine interactions with cardiomyocytes. Gaining insights into these events could aid in the development of new therapies and enable the use of patient-derived iPSC-CFs for precision medicine, ultimately improving patient outcomes.

Single-cell RNA sequencing reveals the contribution of smooth muscle cells and endothelial cells to fibrosis in human atrial tissue with atrial fibrillation

AIMS

Atrial fibrillation (AF) has high mortality and morbidity rates. However, the intracellular molecular complexity of the atrial tissue of patients with AF has not been adequately assessed.

METHODS AND RESULTS

We investigated the cellular heterogeneity of human atrial tissue and changes in differentially expressed genes between cells using single-cell RNA sequencing, fluorescence in situ hybridization, intercellular communication, and cell trajectory analysis. Using genome-wide association studies (GWAS) and proteomics, we discovered cell types enriched for AF susceptibility genes. We discovered eight different cell types, which were further subdivided into 23 subpopulations. In AF, the communication strength between smooth muscle cells (SMCs) and fibroblast (FB) 3 cells increased and the relevant signaling pathways were quite similar. Subpopulations of endothelial cells (ECs) are mainly involved in fibrosis through TXNDC5 and POSTN. AF susceptibility genes revealed by GWAS were especially enriched in neuronal and epicardial cells, FB3, and lymphoid (Lys) cells, whereas proteomic sequencing differential proteins were concentrated in FB3 cells and SMCs.

CONCLUSIONS

This study provides a cellular landscape based on the atrial tissue of patients with AF and highlights intercellular changes and differentially expressed genes that occur during the disease process. A thorough description of the cellular populations involved in AF will facilitate the identification of new cell-based interventional targets with direct functional significance for the treatment of human disease.

Advancing Cardiac Organoid Engineering Through Application of Biophysical Forces

Cardiac organoids represent an important bioengineering opportunity in the development of models to study human heart pathophysiology. By incorporating multiple cardiac cell types in three-dimensional culture and developmentally-guided biochemical signaling, cardiac organoids recapitulate numerous features of heart tissue. However, cardiac tissue also experiences a variety of mechanical forces as the heart develops and over the course of each contraction cycle. It is now clear that these forces impact cellular specification, phenotype, and function, and should be incorporated into the engineering of cardiac organoids in order to generate better models. In this review, we discuss strategies for engineering cardiac organoids and report the effects of organoid design on the function of cardiac cells. We then discuss the mechanical environment of the heart, including forces arising from tissue elasticity, contraction, blood flow, and stretch, and report on efforts to mimic these biophysical cues in cardiac organoids. Finally, we review emerging areas of cardiac organoid research, for the study of cardiac development, the formation of multi-organ models, and the simulation of the effects of spaceflight on cardiac tissue and consider how these investigations might benefit from the inclusion of mechanical cues.

Integrated proteomics and transcriptomics analysis reveals insights into differences in premature mortality associated with disparate pathogenic RBM20 variants

Variants in RNA binding motif protein 20 (RBM20) are causative in a severe form of dilated cardiomyopathy referred to as RBM20 cardiomyopathy, yet the mechanisms are unclear. Moreover, the reason(s) for phenotypic heterogeneity in carriers with different pathogenic variants are similarly opaque. To gain insight, we carried out multi-omics analysis, including the first analysis of gene expression changes at the protein level, of mice carrying two different pathogenic variants in the RBM20 nuclear localization signal (NLS). Direct comparison of the phenotypes confirmed greater premature morality in S639G variant carrying mice compared to mice with the S637A variant despite similar cardiac remodeling and dysfunction. Analysis of differentially spliced genes uncovered alterations in the splicing of both RBM20 target genes and non-target genes, including several genes previously implicated in arrhythmia. Global proteomics analysis found that a greater number of proteins were differentially expressed in the hearts of Rbm20S639G mice relative to WT than in Rbm20S637A versus WT. Gene ontology analysis suggested greater mitochondrial dysfunction in Rbm20S639G mice, although direct comparison of protein expression in the hearts of Rbm20S639G versus Rbm20S637A mice failed to identify any significant differences. Similarly, few differences were found by direct comparison of gene expression at the transcript level in Rbm20S639G and Rbm20S637A despite greater coverage. Our data provide a comprehensive overview of gene splicing and expression differences associated with pathogenic variants in RBM20, as well as insights into the molecular underpinnings of phenotypic heterogeneity associated with different dilated cardiomyopathy-associated variants.

Myocardial fibrosis from the perspective of the extracellular matrix: Mechanisms to clinical impact

Fibrosis is defined by the excessive accumulation of extracellular matrix (ECM) and constitutes a central pathophysiological process that underlies tissue dysfunction, across organs, in multiple chronic diseases and during aging. Myocardial fibrosis is a key contributor to dysfunction and failure in numerous diseases of the heart and is a strong predictor of poor clinical outcome and mortality. The excess structural and matricellular ECM proteins deposited by cardiac fibroblasts, is found between cardiomyocytes (interstitial fibrosis), in focal areas where cardiomyocytes have died (replacement fibrosis), and around vessels (perivascular fibrosis). Although myocardial fibrosis has important clinical prognostic value, access to cardiac tissue biopsies for histological evaluation is limited. Despite challenges with sensitivity and specificity, cardiac magnetic resonance imaging (CMR) is the most applicable diagnostic tool in the clinic, and the scientific community is currently actively searching for blood biomarkers reflecting myocardial fibrosis, to complement the imaging techniques. The lack of mechanistic insights into specific pro- and anti-fibrotic molecular pathways has hampered the development of effective treatments to prevent or reverse myocardial fibrosis. Development and implementation of anti-fibrotic therapies is expected to improve patient outcomes and is an urgent medical need. Here, we discuss the importance of the ECM in the heart, the central role of fibrosis in heart disease, and mechanistic pathways likely to impact clinical practice with regards to diagnostics of myocardial fibrosis, risk stratification of patients, and anti-fibrotic therapy.

PRDM16 determines specification of ventricular cardiomyocytes by suppressing alternative cell fates

PRDM16 is a transcription factor with histone methyltransferase activity expressed at the earliest stages of cardiac development. Pathogenic mutations in humans lead to cardiomyopathy, conduction abnormalities, and heart failure. PRDM16 is specifically expressed in ventricular but not atrial cardiomyocytes, and its expression declines postnatally. Because in other tissues PRDM16 is best known for its role in binary cell fate decisions, we hypothesized a similar decision-making function in cardiomyocytes. Here, we demonstrated that cardiomyocyte-specific deletion of Prdm16 during cardiac development results in contractile dysfunction and abnormal electrophysiology of the postnatal heart, resulting in premature death. By combined RNA+ATAC single-cell sequencing, we found that PRDM16 favors ventricular working cardiomyocyte identity, by opposing the activity of master regulators of ventricular conduction and atrial fate. Myocardial loss of PRDM16 during development resulted in hyperplasia of the (distal) ventricular conduction system. Hence, PRDM16 plays an indispensable role during cardiac development by driving ventricular working cardiomyocyte identity.

Immune responses in checkpoint myocarditis across heart, blood and tumour

Immune checkpoint inhibitors are widely used anticancer therapies1 that can cause morbid and potentially fatal immune-related adverse events such as immune-related myocarditis (irMyocarditis)2-5. The pathogenesis of irMyocarditis and its relationship to antitumour immunity remain poorly understood. Here we sought to define immune responses in heart, tumour and blood in patients with irMyocarditis by leveraging single-cell RNA sequencing coupled with T cell receptor (TCR) sequencing, microscopy and proteomics analyses of samples from 28 patients with irMyocarditis and 41 unaffected individuals. Analyses of 84,576 cardiac cells by single-cell RNA sequencing combined with multiplexed microscopy demonstrated increased frequencies and co-localization of cytotoxic T cells, conventional dendritic cells and inflammatory fibroblasts in irMyocarditis heart tissue. Analyses of 366,066 blood cells revealed decreased frequencies of plasmacytoid dendritic cells, conventional dendritic cells and B lineage cells but an increased frequency of other mononuclear phagocytes in irMyocarditis. Fifty-two heart-expanded TCR clones from eight patients did not recognize the putative cardiac autoantigens α-myosin, troponin I or troponin T. Additionally, TCRs enriched in heart tissue were largely nonoverlapping with those enriched in paired tumour tissue. The presence of heart-expanded TCRs in a cycling blood CD8 T cell population was associated with fatal irMyocarditis case status. Collectively, these findings highlight crucial biology driving irMyocarditis and identify putative biomarkers.

Exercise training attenuates cardiac dysfunction induced by excessive sympathetic activation through an AMPK-KLF4-FMO2 axis

Cardiovascular diseases (CVDs) are a leading cause of mortality worldwide and are associated with an overactivated sympathetic system. Although exercise training has shown promise in mitigating sympathetic stress-induced cardiac remodeling, the precise mechanisms remain elusive. Here, we demonstrate that exercise significantly upregulates cardiac flavin-containing monooxygenase 2 (FMO2) expression. Notably, we find that exercise training effectively counteracts sympathetic overactivation-induced cardiac dysfunction and fibrosis by enhancing FMO2 expression via adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) activation. Functional investigations employing FMO2 knockdown with adeno-associated virus 9 (AAV9) underscore the necessity for FMO2 expression to protect the heart during exercise in vivo. Furthermore, we identify the krüppel-like factor 4 (KLF4) as a transcriptional mediator of FMO2 that is crucial for the mechanism through which AMPK activation protects against sympathetic overactivation-induced cardiac dysfunction and fibrosis. Taken together, our study reveals a cardioprotective mechanism for exercise training through an AMPK-KLF4-FMO2 signaling pathway that underscores how exercise alleviates cardiac dysfunction induced by excessive sympathetic activation.

Large-scale single-nuclei profiling identifies role for ATRNL1 in atrial fibrillation

Atrial fibrillation (AF) is the most common sustained arrhythmia in humans, yet the molecular basis of AF remains incompletely understood. To determine the cell type-specific transcriptional changes underlying AF, we perform single-nucleus RNA-seq (snRNA-seq) on left atrial (LA) samples from patients with AF and controls. From more than 175,000 nuclei we find that only cardiomyocytes (CMs) and macrophages (MΦs) have a significant number of differentially expressed genes in patients with AF. Attractin Like 1 (ATRNL1) was overexpressed in CMs among patients with AF and localized to the intercalated disks. Further, in both knockdown and overexpression experiments we identify a potent role for ATRNL1 in cell stress response, and in the modulation of the cardiac action potential. Finally, we detect an unexpected expression pattern for a leading AF candidate gene, KCNN3. In sum, we uncover a role for ATRNL1 which may serve as potential therapeutic target for this common arrhythmia.

Inhibition of the FOXO1-ROCK1 axis mitigates cardiomyocyte injury under chronic hypoxia in Tetralogy of Fallot by maintaining mitochondrial quality control

INTRODUCTION

Persistent chronic myocardial hypoxia causes disturbances in mitochondrial quality control (MQC), ultimately leading to increased cardiomyocyte injury in patients with Tetralogy of Fallot (TOF). The present study aimed to identify the key effector molecules of cardiomyocyte injury under chronic hypoxia in TOF.

METHODS

Clinical data from TOF patients were collected and whole transcriptome sequencing was performed on myocardial samples. Chronic hypoxia models were established in cardiac-specific knockout mice and cardiomyocytes, and a series of molecular experiments were used to determine the specific mechanisms involved.

RESULTS

Clinical cohort data and whole-transcriptome sequencing analysis of myocardial samples from TOF patients revealed that forkhead box O1 (FOXO1) plays an important role in chronic hypoxic cardiomyocyte injury. In a model of chronic hypoxia established in FOXO1 cardiac-specific knockout mice and FOXO1 gene-deficient cardiomyocytes, the AMPK signaling pathway regulates the expression of FOXO1, which in turn disrupts MQC by regulating the transcriptional activation of Rho-associated protein kinase 1 (ROCK1), and increasing the production of mitochondrial ROS, thereby exacerbating damage to cardiomyocytes. Excessive reactive oxygen species (ROS) production during MQC dysfunction further activates Cox7a2L to increase the assembly of the respiratory chain supercomplex. In addition, we found that miR-27b-3p partially binds to the 3' untranslated region of FOXO1 to exert a protective effect.

CONCLUSIONS

Maintenance of MQC under chronic hypoxia is achieved through a series of injury-protection mechanisms, suggesting that FOXO1 inhibition may be crucial for future mitigation of chronic hypoxic cardiomyocyte injury in TOF.

Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development

Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrate in vitro and in vivo human single-cell multi-omic studies with high-throughput functional genomic screening to reveal dynamic, cardiac-specific gene regulatory networks (GRNs) and transcriptional regulators during human cardiomyocyte development. Interrogating developmental trajectories reconstructed from single-cell data unexpectedly reveal divergent cardiomyocyte lineages with distinct gene programs based on developmental signaling pathways. High-throughput functional genomic screens identify key transcription factors from inferred GRNs that are functionally relevant for cardiomyocyte lineages derived from each pathway. Notably, we discover a critical heat shock transcription factor 1 (HSF1)-mediated cardiometabolic GRN controlling cardiac mitochondrial/metabolic function and cell survival, also observed in fetal human cardiomyocytes. Overall, these multi-modal genomic studies enable the systematic discovery and validation of coordinated GRNs and transcriptional regulators controlling the development of distinct human cardiomyocyte populations.

Single cell variant to enhancer to gene map for coronary artery disease

Although genome wide association studies (GWAS) in large populations have identified hundreds of variants associated with common diseases such as coronary artery disease (CAD), most disease-associated variants lie within non-coding regions of the genome, rendering it difficult to determine the downstream causal gene and cell type. Here, we performed paired single nucleus gene expression and chromatin accessibility profiling from 44 human coronary arteries. To link disease variants to molecular traits, we developed a meta-map of 88 samples and discovered 11,182 single-cell chromatin accessibility quantitative trait loci (caQTLs). Heritability enrichment analysis and disease variant mapping demonstrated that smooth muscle cells (SMCs) harbor the greatest genetic risk for CAD. To capture the continuum of SMC cell states in disease, we used dynamic single cell caQTL modeling for the first time in tissue to uncover QTLs whose effects are modified by cell state and expand our insight into genetic regulation of heterogenous cell populations. Notably, we identified a variant in the COL4A1/COL4A2 CAD GWAS locus which becomes a caQTL as SMCs de-differentiate by changing a transcription factor binding site for EGR1/2. To unbiasedly prioritize functional candidate genes, we built a genome-wide single cell variant to enhancer to gene (scV2E2G) map for human CAD to link disease variants to causal genes in cell types. Using this approach, we found several hundred genes predicted to be linked to disease variants in different cell types. Next, we performed genome-wide Hi-C in 16 human coronary arteries to build tissue specific maps of chromatin conformation and link disease variants to integrated chromatin hubs and distal target genes. Using this approach, we show that rs4887091 within the ADAMTS7 CAD GWAS locus modulates function of a super chromatin interactome through a change in a CTCF binding site. Finally, we used CRISPR interference to validate a distal gene, AMOTL2, liked to a CAD GWAS locus. Collectively we provide a disease-agnostic framework to translate human genetic findings to identify pathologic cell states and genes driving disease, producing a comprehensive scV2E2G map with genetic and tissue level convergence for future mechanistic and therapeutic studies.

Culturally responsive strategies and practical considerations for live tissue studies in Māori participant cohorts

Introduction

Indigenous communities globally are inequitably affected by non-communicable diseases such as cancer and coronary artery disease. Increased focus on personalized medicine approaches for the treatment of these diseases offers opportunities to improve the health of Indigenous people. Conversely, poorly implemented approaches pose increased risk of further exacerbating current inequities in health outcomes for Indigenous peoples. The advancement of modern biology techniques, such as three-dimensional (3D) in vitro models and next generation sequencing (NGS) technologies, have enhanced our understanding of disease mechanisms and individualized treatment responses. However, current representation of Indigenous peoples in these datasets is lacking. It is crucial that there is appropriate and ethical representation of Indigenous peoples in generated datasets to ensure these technologies can be used to maximize the benefit of personalized medicine for Indigenous peoples.

Methods

This project discusses the use of 3D tumor organoids and single cell/nucleus RNA sequencing to study cancer treatment responses and explore immune cell roles in coronary artery disease. Using key pillars from currently available Indigenous bioethics frameworks, strategies were developed for the use of Māori participant samples for live tissue and sequencing studies. These were based on extensive collaborations with local Māori community, scientific leaders, clinical experts, and international collaborators from the Broad Institute of MIT and Harvard. Issues surrounding the use of live tissue, genomic data, sending samples overseas and Indigenous data sovereignty were discussed.

Results

This paper illustrates a real-world example of how collaboration with community and the incorporation of Indigenous worldviews can be applied to molecular biology studies in a practical and culturally responsive manner, ensuring fair and equitable representation of Indigenous peoples in modern scientific data.

The Macrophage-Fibroblast Dipole in the Context of Cardiac Repair and Fibrosis

Stromal and immune cells and their interactions have gained the attention of cardiology researchers and clinicians in recent years as their contribution in cardiac repair is increasingly recognized. The repair process in the heart is a particularly critical constellation of complex molecular and cellular events and interactions that characteristically fail to ensure adequate recovery following injury, insult, or exposure to stress conditions in this regeneration-hostile organ. The tremendous consequence of this pronounced inability to maintain homeostatic states is being translated in numerous ways promoting progress into heart failure, a deadly, irreversible condition requiring organ transplantation. Fibrosis is in fact a repair response eventually promoting cardiac dysfunction and cardiac fibroblasts are the major cellular players in this process, overproducing collagens and other extracellular matrix components when activated. On the other hand, macrophages may differentially affect fibroblasts and cardiac repair depending on their status and subsets. The opposite interaction is also probable. We discuss here the multifaceted aspects and crosstalk of this cell dipole and the opportunities it may offer for beneficial manipulation approaches that will hopefully lead to progress in heart disease interventions.