Spatial multi-omic map of human myocardial infarction

Loss of LSD1 ameliorates myocardial infarction by regulating angiogenesis via transcriptional activation of Vegfa

AIMS

Our study aims to explore the regulatory role and underlying mechanisms of Lysine-specific demethylase 1 (LSD1) in angiogenesis following myocardial infarction (MI).

MATERIALS AND METHODS

We generated inducible cardiomyocyte-specific Lsd1 knockout (Lsd1-cKO) mice and established a MI model. The function of LSD1 in cardiac angiogenesis in MI mice was assessed through echocardiography, histopathological staining, and immunofluorescence analysis. In vitro, Lsd1 silencing in cardiomyocytes was achieved by transfecting small interfering RNA (siRNA), followed by hypoxic treatment to simulate the in vivo MI model. The above cardiomyocyte-conditioned medium was collected and used to treat endothelial cells to observe changes in endothelial function. Additionally, we employed Cleavage Under Targets and Tagmentation sequencing (CUT&Tag-seq) to investigate the potential mechanisms by which LSD1 exerts its effects.

KEY FINDINGS

We found that the absence of LSD1 protected against cardiac dysfunction and promoted angiogenesis in mice with MI. Lsd1-silenced cardiomyocytes enhance the migration and tube formation function of endothelial cells by releasing vascular endothelial growth factor A (VEGF-A) under hypoxic conditions. The combined analysis of CUT&Tag-seq data revealed that silencing of Lsd1 promoted the monomethylation of H3K4 at the Vegfa promoter and region, leading to the transcriptional activation of Vegfa mRNA in cardiomyocytes.

SIGNIFICANCE

Our research indicates that lowered level of LSD1 in cardiomyocytes enhances VEGF-A paracrine secretion and improves endothelial cell function through cross-talk, ultimately promoting angiogenesis. These findings suggest that targeting LSD1 might be an effective therapeutic approach to protect against MI.

Single-cell multi-omics reveals that FABP1 + renal cell carcinoma drive tumor angiogenesis through the PLG-PLAT axis under fatty acid reprogramming

Renal cell carcinoma is characterized by a poor prognosis. Recently, renal cell carcinoma has been recognized as a metabolic disease associated with fatty acid metabolic reprogramming, although in-depth studies on this topic are still lacking. We found that fatty acid metabolism reprogramming in renal cell carcinoma is primarily characterized by high expression of FABP1. FABP1 + tumors significantly impact survival and display distinct differentiation trajectories compared to other tumor subclusters. They show elevated expression of angiogenesis and cell migration signals, with PLG-PLAT-mediated interactions with endothelial cells notably enhanced. Spatial transcriptomics show a prominent co-localization of FABP1 + tumors with endothelial cells, and their spatial distribution closely aligns with that of PLAT + endothelial cells. FABP1 + tumors exhibit a unique pattern in spatial transcriptomics, enriched in Extracellular Matrix and angiogenesis-related pathways. Through receptor-ligand interaction analysis, a novel PLG-PLAT functional axis was found between tumor epithelial cells and endothelial cells. Based on results of experiments, we infer that FABP1 + tumors can promote plasmin-related tumor angiogenesis by triggering the PLG-PLAT signaling axis. Finally, utilizing preclinical models, we suggest that targeting the FABP1-PLG-PLAT axis may serve as promising strategy enhancing the sensitivity of Tyrosine Kinase Inhibitor therapy.

Identification of key proteins and pathways in myocardial infarction using machine learning approaches

Acute myocardial infarction (AMI) is a leading cause of global morbidity and mortality, requiring deeper insights into its molecular mechanisms for improved diagnosis and treatment. This study combines proteomics, transcriptomics and machine learning (ML) to identify key proteins and pathways associated with AMI. Plasma samples from 48 AMI patients and 50 healthy controls (HC) were used for proteomic sequencing. Differentially expressed proteins (DEPs) were identified and analyzed for pathway enrichment. Protein-protein interaction (PPI) networks were constructed, and we conducted a meta-analysis (GSE60993, GSE61144, GSE48060) using an inverse variance model to combine differentially expressed genes (DEGs) identified via LIMMA and FDR adjustment across three studies. Clustering and co-expression analysis were performed using K-Medoids and weighted gene co-expression network analysis (WGCNA). ML feature selection identified hub proteins, which were validated across bulk, single-cell, and spatial datasets for atherosclerosis (ATH) and MI. In this study, we identified 437 DEPs with 291 up-regulated and 146 down-regulated proteins. Functional enrichment analysis revealed key pathways involved in inflammation, immunity, metabolism, and cellular stress responses, among others. Using non-negative matrix factorization (NNMF) and K-Medoids clustering, AMI patients were divided into two clusters (C1 and C2), with distinct protein expression patterns and inflammatory responses. Differential analysis between clusters revealed 200 cluster-specific DEPs, with C1 associated with angiogenesis and vascular remodeling, and C2 linked to cellular stress and apoptosis. A meta-analysis identified 1383 DEGs, and their intersection with DEPs yielded 63 proteins, which were subsequently refined by logistic regression to 36 AMI-associated proteins. Furthermore, a protein co-expression network analysis identified 49 modules, with the turquoise module being strongly associated with AMI highlighting pathways in lipid metabolism, immune response, and tissue repair. From this module, 17 key proteins were selected, and ML further distilled these to nine core features (CAMP, CLTC, CTNNB1, FUBP3, IQGAP1, MANBA, ORM1, PSME1, and SPP1) that are closely linked to immune regulation, apoptosis, and metabolism. These proteins were validated across multiple datasets. Single-cell analysis revealed distinct expression patterns of these proteins across cell types and spatial regions in ATH and MI, emphasizing their roles in inflammation, vascular remodeling, and plaque instability. This study identifies critical proteins and pathways in AMI, offering potential biomarkers and therapeutic targets. The use of ML provides a robust framework for identifying AMI's key molecular.

Functional diversity of cardiac macrophages in health and disease

Macrophages make up a substantial portion of the stromal compartment of the heart in health and disease. In the past decade, the origins of these cardiac macrophages have been established as two broad populations derived from either embryonic or definitive haematopoiesis and that can be distinguished by the expression of CC-motif chemokine receptor 2 (CCR2). These cardiac macrophage populations are transcriptionally distinct and have differing cell surface markers and divergent roles in cardiac homeostasis and disease. Embryonic-derived CCR2- macrophages are a tissue-resident population that participates in tissue development, repair and maintenance, whereas CCR2+ macrophages are derived from definitive haematopoiesis and contribute to inflammation and tissue damage. Studies from the past 5 years have leveraged single-cell RNA sequencing technologies to expand our understanding of cardiac macrophage diversity, particularly of the monocyte-derived macrophage populations that reside in the injured and diseased heart. Emerging technologies in spatial transcriptomics have enabled the identification of distinct disease-associated cellular neighbourhoods consisting of macrophages, other immune cells and fibroblasts, highlighting the involvement of macrophages in cell-cell communication. Together, these discoveries lend new insights into the role of specific macrophage populations in the pathogenesis of cardiac disease, which can pave the way for the identification of new therapeutic targets and the development of diagnostic tools. In this Review, we discuss the developmental origin of cardiac macrophages and describe newly identified cell states and associated cellular neighbourhoods in the steady state and injury settings. We also discuss various contributions and effector functions of cardiac macrophages in homeostasis and disease.

Microenvironmental determinants of endothelial cell heterogeneity

During development, endothelial cells (ECs) undergo an extraordinary specialization by which generic capillary microcirculatory networks spanning from arteries to veins transform into patterned organotypic zonated blood vessels. These capillary ECs become specialized to support the cellular and metabolic demands of each specific organ, including supplying tissue-specific angiocrine factors that orchestrate organ development, maintenance of organ-specific functions and regeneration of injured adult organs. Here, we illustrate the mechanisms by which microenvironmental signals emanating from non-vascular niche cells induce generic ECs to acquire specific inter-organ and intra-organ functional attributes. We describe how perivascular, parenchymal and immune cells dictate vascular heterogeneity and capillary zonation, and how this system is maintained through tissue-specific signalling activated by vasculogenic and angiogenic factors and deposition of matrix components. We also discuss how perturbation of organotypic vascular niche cues lead to erasure of EC signatures, contributing to the pathogenesis of disease processes. We also describe approaches that use reconstitution of tissue-specific signatures of ECs to promote regeneration of damaged organs.

Perinatal Exposure to Lead or Diethylhexyl Phthalate in Mice: Sex-Specific Effects on Cardiac DNA Methylation and Gene Expression across Time

BACKGROUND

Global and site-specific changes in DNA methylation and gene expression are associated with cardiovascular development, aging, and disease, but how the transcriptome and epigenome of the heart change across the life course in males vs. females and how chemical exposures early in life influence this programming have not yet been investigated.

OBJECTIVES

We used an established mouse model of developmental exposures to investigate the effects of perinatal exposure to either lead (Pb) or diethylhexyl phthalate (DEHP), two ubiquitous environmental contaminants that are both strongly associated with cardiovascular diseases (CVDs), on DNA methylation and gene expression across the life course in whole hearts.

METHODS

Dams were randomly assigned to receive human physiologically relevant levels of Pb (32  ppm in water), DEHP (25 mg / kg chow), or control water and chow. Exposures started 2 weeks prior to mating and continued until weaning at postnatal day 21 (3 wk of age). Approximately 1 male and 1 female offspring per litter were followed to 3 wk, 5 months, or 10 months of age, at which time whole hearts were collected (n ≥ 5 per sex per exposure). Enhanced reduced representation bisulfite sequencing (ERRBS) was used to assess the cardiac DNA methylome at 3 wk and 10 months, and RNA-Seq was conducted at all three time points. MethylSig and edgeR were used to identify age-related differentially methylated regions (DMRs) and differentially expressed genes (DEGs), respectively, within each sex and exposure group. Cell type deconvolution of bulk RNA-Seq data was conducted using the MuSiC algorithm and publicly available single-cell RNA-Seq data.

RESULTS

Thousands of DMRs and hundreds of DEGs were identified in control, DEHP, and Pb-exposed hearts across time between 3 wk and 10 months of age. A closer look at the genes and pathways showing differential DNA methylation revealed that the majority were unique to each sex and exposure group. Overall, pathways governing development and differentiation changed across time in all conditions. A small number of genes in each group showed significant differences in DNA methylation and gene expression with life stage, including several that were different in toxicant-exposed but not control mice. We also observed subtle but significant differences in the proportion of several cell types that were associated with life stage, sex, or developmental exposure.

DISCUSSION

Together these data suggest that gene expression and DNA methylation programs, as well as cellular composition, may differ across the life course long after cessation of exposure in perinatal Pb- or DEHP-exposed mice compared to controls and highlight potential biomarkers of developmental toxicant exposures; however, additional studies are required for confirmation. Further studies are also needed to investigate how epigenetic and transcriptional differences impact cardiovascular health across the life course, particularly in old age when the risk of cardiovascular diseases is markedly increased. https://doi.org/10.1289/EHP15503.

Omics-based Approach Towards Macrophages: New Perspectives of Biology and Function in the Normal and Diseased Heart

Macrophages play a crucial role not only in maintaining homeostasis but also in initiating inflammatory responses to various forms of stress or injury, thereby contributing to tissue damage while concurrently promoting recovery. Furthermore, the diversity of macrophage subtypes, their spatial distribution, and distinct cellular functions are closely linked to the pathogenesis and severity of cardiovascular diseases such as myocardial infarction, atherosclerosis, heart failure, and myocarditis. This association underscores the importance of investigating macrophage heterogeneity in different pathological contexts. Recent advances in multi-omics technologies-including single-cell RNA sequencing, spatial transcriptomics, and metabolomics-have elucidated the heterogeneity of macrophages, their intercellular interactions, underlying functional mechanisms, and spatial organization. In this review, we systematically summarize the diverse phenotypes and functional plasticity of macrophages in the regulation of cardiovascular diseases, with particular emphasis on the novel insights afforded by multi-omics approaches. We focus on the characteristics of macrophages in both physiological and pathological states, thereby providing reference points for clinical macrophage-targeted strategies and their translational significance.

Panoramic spatial enhanced resolution proteomics (PSERP) reveals tumor architecture and heterogeneity in gliomas

The spatial proteomic profiling of complex tissues is essential for investigating cellular function in physiological and pathological states. However, the imbalance among resolution, protein coverage, and expense precludes their systematic application to analyze whole tissue sections in an unbiased manner and with high resolution. Here, we introduce panoramic spatial enhanced resolution proteomics (PSERP), a method that combines tissue expansion, automated sample segmentation, and tryptic digestion with high-throughput proteomic profiling. The PSERP approach facilitates rapid quantitative profiling of proteomic spatial variability in whole tissue sections at sub-millimeter resolution. We demonstrated the utility of this method for determining the streamlined large-scale spatial proteomic features of gliomas. Specifically, we profiled spatial proteomic features for nine glioma samples across three different mutation types (IDH1-WT/EGFR-mutant, IDH1-mutant, and IDH1/EGFR-double-WT gliomas) at sub-millimeter resolution (corresponding to a total of 2,230 voxels). The results revealed over 10,000 proteins identified in a single slide, which helps us to portray the diverse proteins and pathways with spatial abundance patterns in the context of tumor heterogeneity and cellular features. Our spatial proteomic data revealed distinctive proteomic features of malignant and non-malignant tumor regions and depicted the distribution of proteins from tumor centers to tumor borders and non-malignant tumor regions. Through integrative analysis with single-cell transcriptomic data, we elucidated the cellular composition and cell-cell communications in a spatial context. Our PSERP also includes a spatially resolved tumor-specific peptidome identification workflow that not only enables us to elucidate the spatial expression patterns of tumor-specific peptides in glioma samples with different genomic types but also provides us with opportunities to select combinations of tumor-specific mutational peptides whose expression could cover the maximum tumor regions for future immune therapies. We further demonstrated that combining tumor-specific peptides might enhance the efficacy of immunotherapy in both patient-derived cell (PDC) and patient-derived xenograft (PDX) models. PSERP efficiently retains precise spatial proteomic information within the tissue context and provides a deeper understanding of tissue biology and pathology at the molecular level.

Metabolic and Immune Crosstalk in Cardiovascular Disease

Cardiovascular diseases including atherosclerosis and heart failure, arise from the intricate interplay of metabolic, immune, and neural dysregulation within vascular and cardiac tissues: This review focuses on integrating recent advances in metabolic and immune crosstalk of the cardiac vasculature that affects cardiometabolic health and disease progression. Coronary and lymphatic endothelial cells regulate cardiac metabolism, and their dysfunction is linked to cardiovascular diseases. Lymphatics maintain tissue homeostasis, including clearing metabolic waste, lipids, and immune cells, and their maladaptation in metabolic diseases worsens outcomes. Altered vascular endothelial metabolism in heart failure drives immune-mediated inflammation, fibrosis, and adverse cardiac remodeling. Concurrently, artery tertiary lymphoid organs formed in the adventitia of advanced atherosclerotic arteries, serve as pivotal neuroimmune hubs, coordinating local immunity through T and B cell activation and neurovascular signaling via artery-brain circuits. T cells within plaques and artery tertiary lymphoid organs undergo clonal expansion as a result of peripheral tolerance breakdown, with proinflammatory CD4+ and CD8+ subsets amplifying atherosclerosis, effects further shaped by systemic immune activation. Therapeutic strategies targeting endothelial cell metabolism, lymphatic dysfunction, neuroimmune crosstalk, and T cell plasticity hold promise for integrated cardiovascular disease management.

The immune system in cardiovascular diseases: from basic mechanisms to therapeutic implications

Immune system plays a crucial role in the physiological and pathological regulation of the cardiovascular system. The exploration history and milestones of immune system in cardiovascular diseases (CVDs) have evolved from the initial discovery of chronic inflammation in atherosclerosis to large-scale clinical studies confirming the importance of anti-inflammatory therapy in treating CVDs. This progress has been facilitated by advancements in various technological approaches, including multi-omics analysis (single-cell sequencing, spatial transcriptome et al.) and significant improvements in immunotherapy techniques such as chimeric antigen receptor (CAR)-T cell therapy. Both innate and adaptive immunity holds a pivotal role in CVDs, involving Toll-like receptor (TLR) signaling pathway, nucleotide-binding oligomerization domain-containing proteins 1 and 2 (NOD1/2) signaling pathway, inflammasome signaling pathway, RNA and DNA sensing signaling pathway, as well as antibody-mediated and complement-dependent systems. Meanwhile, immune responses are simultaneously regulated by multi-level regulations in CVDs, including epigenetics (DNA, RNA, protein) and other key signaling pathways in CVDs, interactions among immune cells, and interactions between immune and cardiac or vascular cells. Remarkably, based on the progress in basic research on immune responses in the cardiovascular system, significant advancements have also been made in pre-clinical and clinical studies of immunotherapy. This review provides an overview of the role of immune system in the cardiovascular system, providing in-depth insights into the physiological and pathological regulation of immune responses in various CVDs, highlighting the impact of multi-level regulation of immune responses in CVDs. Finally, we also discuss pre-clinical and clinical strategies targeting the immune system and translational implications in CVDs.

Transcriptional signatures of endothelial cells shape immune responses in cardiopulmonary health and disease

The cardiopulmonary vasculature and its associated endothelial cells (ECs) play an essential role in sustaining life by ensuring the delivery of oxygen and nutrients. Beyond these foundational functions, ECs serve as key regulators of immune responses. Recent advances in single-cell RNA sequencing have revealed that the cardiopulmonary vasculature is composed of diverse EC subpopulations, some of which exhibit specialized immunomodulatory properties. Evidence for immunomodulation includes distinct expression profiles associated with antigen presentation, cytokine secretion, immune cell recruitment, translocation, and clearance - functions critical for maintaining homeostasis in the heart and lungs. In cardiopulmonary diseases, ECs undergo substantial transcriptional reprogramming, leading to a shift from homeostasis to an activated state marked by heightened immunomodulatory activity. This transformation has highlighted the critical role for ECs in disease pathogenesis and their potential as future therapy targets. This Review emphasizes the diverse functions of ECs in the heart and lungs, particularly adaptive and maladaptive immunoregulatory roles in cardiopulmonary health and disease.

Spatial multiomics decipher fibroblast-macrophage dynamics in systemic sclerosis

OBJECTIVES

Stromal-immune crosstalk shapes the pathogenic microenvironment of systemic sclerosis (SSc), but the spatial regulatory networks underlying fibrogenesis remain poorly defined. We aimed to explore tissue organisation and cell coordination in SSc skin, providing spatiotemporal insights into disease mechanisms and bridging the gap between omics discovery and precision medicine.

METHODS

We performed spatial transcriptomics on skin biopsies from 10 patients with diffuse cutaneous SSc and 4 healthy controls using the 10× Visium platform. These findings were confirmed using higher-resolution Stereo-seq transcriptomics, spatial proteomics, and single-cell RNA sequencing data from patients with SSc, SSc mouse models, and wound-healing reindeer models. In vivo and in vitro studies were conducted to validate the key regulatory pathways.

RESULTS

Fourteen skin biopsies were analysed, revealing significant expansion of fibrotic niches enriched with fibroblasts and macrophages in SSc, correlating with clinical severity. We revealed disease-specific cell states of fibroblasts and macrophages and evaluated their spatial dependency and cell-cell communication. Stratification based on signature genes enabled the identification of patients with SSc with progressive disease and treatment-nonresponsive phenotype. ACKR3 (a CXCL12 decoy receptor) was selectively expressed in myofibroblast progenitors, which diminished during differentiation towards mature myofibroblast, potentially serving to regulate CXCL12/CXCR4-mediated proinflammatory macrophage recruitment. Inhibition of CXCR4 attenuated skin and lung fibrosis in experimental fibrosis mouse models.

CONCLUSIONS

Our spatially resolved atlas uncovered dynamic fibroblast-macrophage interplay as a hallmark of fibrotic niche expansion. These findings offer spatiotemporal insights into disease mechanisms and pave the way for advanced mechanistic and therapeutic studies, bridging the gap between omics discovery and precision medicine.

Spatial Insights in Cardiovascular Aging

Spatial omics provides unprecedented insights into how the cardiovascular system is spatially organized and how cellular phenotypes are distributed. Researchers have been able to clarify the complex spatial architecture of the cardiovascular system and how cellular phenotypes are distributed during the aging process by integrating data from spatial omics. In addition, this new technology has revealed previously hidden patterns of gene expression and cellular communication that were not detected using traditional bulk omics approaches. In this review, we explore the contribution of spatial omics in clarifying the molecular mechanisms that influence cardiovascular aging, highlighting the importance and application of spatial omics in unraveling the spatial heterogeneity within the aging cardiovascular system. This will help us understand the molecular mechanisms implicated in age-related cardiovascular diseases.

CausalCCC: a web server to explore intracellular causal pathways enabling cell-cell communication

Understanding cell-cell communication (CCC) pathways from single-cell or spatial transcriptomic data is key to unraveling biological processes. Recently, multiple CCC methods have been developed but primarily focus on refining ligand-receptor (L-R) interaction scores. A critical gap for a more comprehensive picture of cellular crosstalks lies in the integration of upstream and downstream intracellular pathways in the sender and receiver cells. We report here CausalCCC, https://miic.curie.fr/causalCCC.php, an interactive web server, which addresses this need by reconstructing gene-gene interaction pathways across two or more interacting cell types from single-cell or spatial transcriptomic data. CausalCCC includes a graphical introduction and a demo dataset within the workbench page as well as a comprehensive tutorial. CausalCCC methodology integrates a robust and scalable causal network reconstruction method, multivariate information-based inductive causation, with internally computed L-R pairs using LIANA+ (including CellphoneDBv5, SingleCellSignalR, Connectome, NATMI, and Log2FC). Alternatively, user-defined L-R pairs from any CCC methods can also be uploaded. We showcase here CausalCCC on different single-cell and spatial transcriptomic datasets from three original CCC methods (NicheNet, CellChat, and Misty). CausalCCC web server offers unique interactive visualization tools dedicated to single-cell data practitioners seeking to go beyond L-R scores and explore extended CCC pathways across multiple interacting cell types.

Emerging Epigenetic Therapies for the Treatment of Cardiac Fibrosis

Fibrosis is a pathological process characterized by excessive extracellular matrix (ECM) deposition, leading to tissue stiffening and organ dysfunction. It is a major contributor to chronic diseases affecting various organs, with limited therapeutic options available. Among the different forms of fibrosis, cardiac fibrosis is particularly relevant due to its impact on cardiovascular diseases (CVDs), which remain the leading cause of morbidity and mortality worldwide. This process is driven by activated cardiac fibroblasts (CFs), which promote ECM accumulation in response to chronic stressors. Epigenetic mechanisms, including DNA methylation, histone modifications, and chromatin remodeling, are key regulators of fibroblast activation and fibrotic gene expression. Enzymes such as DNA methyltransferases (DNMTs), histone methyltransferases (HMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs) have emerged as potential therapeutic targets, and epigenetic inhibitors have shown promise in modulating these enzymes to attenuate fibrosis by controlling fibroblast function and ECM deposition. These small-molecule compounds offer advantages such as reversibility and precise temporal control, making them attractive candidates for therapeutic intervention. This review aims to provide a comprehensive overview of the mechanisms by which epigenetic regulators influence cardiac fibrosis and examines the latest advances in preclinical epigenetic therapies. By integrating recent data from functional studies, single-cell profiling, and drug development, it highlights key molecular targets, emerging therapeutic strategies, and current limitations, offering a critical framework to guide future research and clinical translation.

Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure

Heart failure is a leading cause of morbidity and mortality; yet gene regulatory mechanisms driving cell type-specific pathologic responses remain undefined. Here, we present the cell type-resolved transcriptomes, chromatin accessibility, histone modifications and chromatin organization of 36 non-failing and failing human hearts profiled from 776,479 cells spanning all cardiac chambers. Integrative analyses revealed dynamic changes in cell type composition, gene regulatory programs and chromatin organization, which expanded the annotation of cardiac cis-regulatory sequences by ten-fold and mapped cell type-specific enhancer-gene interactions. Cardiomyocytes and fibroblasts particularly exhibited complex disease-associated cellular states, gene regulatory programs and global chromatin reorganization. Mapping genetic association data onto cell type-specific regulatory programs revealed likely causal genetic contributors to heart failure. Together, these findings provide comprehensive, multimodal gene regulatory maps of the human heart in health and disease, offering a valuable framework for designing precise cell type-targeted therapies for treating heart failure.

Spatial transcriptional landscape of human heart failure

BACKGROUND AND AIMS

Heart failure (HF) remains a significant clinical challenge due to its diverse aetiologies and complex pathophysiology. The molecular alterations specific to distinct cell types and histological patterns during HF progression are still poorly characterized. This study aimed to explore cell-type- and histology-specific gene expression profiles in cardiomyopathies.

METHODS

Ninety tissue cores from 44 participants, encompassing various forms of cardiomyopathy and control samples with diverse histological features, were analysed using the GeoMx Whole Human Transcriptome Atlas. Data on cell types, clinical information, and histological features were integrated to examine gene expression profiles in cardiomyopathy.

RESULTS

The study characterized the cellular composition of ventricular myocardium and validated the GeoMx platform's efficiency in compartmentalizing specific cell types, demonstrating high accuracy for cardiomyocytes but limitations for endothelial cells and fibroblasts. Differentially expressed genes, including UCHL1 from cardiomyocytes, were associated with degeneration, while CCL14, ACKR1, and PLVAP from endothelial cells were linked to fibrosis. Multiplex immunohistochemistry and integrative analysis of prior sc/snRNA-seq data identified a PLVAP, ACKR1, and CCL14-positive pro-inflammatory endothelial cell subtype linked to fibrosis in HF. Downregulation of ribosomal proteins in cardiomyocytes was associated with myocyte disarray in hypertrophic cardiomyopathy. Additionally, pronounced inflammatory responses were observed in end-stage HF. Combined histological and clinical analysis identified CRIP3, PFKFB2, and TAX1BP3 as novel contributors to HF pathogenesis.

CONCLUSIONS

These findings highlight the critical role of cell-enriched and histology-specific transcriptome mapping in understanding the complex pathophysiological landscape of failing hearts, offering molecular insights and potential therapeutic targets for future interventions.

Klf9 promotes the repair of myocardial infarction by regulating macrophage recruitment and polarization

The inflammatory response after myocardial infarction (MI) is a precisely regulated process that greatly affects subsequent wound healing and remodeling. However, understanding about the process is still limited. Macrophages are critically involved in inflammation resolution after MI. Krüppel-like factor 9 (Klf9) is a C2H2 zinc finger-containing transcription factor that has been implicated in glucocorticoid regulation of macrophages. However, the contribution of Klf9 to macrophage phenotype and function in the context of MI remains unclear. Our study revealed that KLF9 deficiency resulted in higher mortality and cardiac rupture rate, as well as a considerable exacerbation in cardiac function. Single-cell RNA sequencing and flow cytometry analyses revealed that, compared with WT mice, Klf9-/- mice displayed excessive neutrophil infiltration, insufficient macrophage infiltration, and a reduced proportion of monocyte-derived CD206+ macrophages after MI. Moreover, the expression of IFN-γ/STAT1 pathway genes in Klf9-/- cardiac macrophages was dysregulated, characterized by insufficient expression at 1 day post-MI and excessive expression at day 3 post-MI. Mechanistically, Klf9 directly binds to the promoters of Stat1 gene, regulating its transcription. Overall, these findings indicate that Klf9 beneficially influences wound healing after MI by modulating macrophage recruitment and differentiation by regulating the IFN-γ/STAT1 signaling pathway.

Integrating single-cell data with biological variables

Constructing single-cell atlases requires preserving differences attributable to biological variables, such as cell types, tissue origins, and disease states, while eliminating batch effects. However, existing methods are inadequate in explicitly modeling these biological variables. Here, we introduce SIGNAL, a general framework that leverages biological variables to disentangle biological and technical effects, thereby linking these metadata to data integration. SIGNAL employs a variant of principal component analysis to align multiple batches, enabling the integration of 1 million cells in approximately 2 min. SIGNAL, despite its computational simplicity, surpasses state-of-the-art methods across multiple integration scenarios: 1) heterogeneous datasets, 2) cross-species datasets, 3) simulated datasets, 4) integration on low-quality cell annotations, and 5) reference-based integration. Furthermore, we demonstrate that SIGNAL accurately transfers knowledge from reference to query datasets. Notably, we propose a self-adjustment strategy to restore annotated cell labels potentially distorted during integration. Finally, we apply SIGNAL to multiple large-scale atlases, including a human heart cell atlas containing 2.7 million cells, identifying tissue- and developmental stage-specific subtypes, as well as condition-specific cell states. This underscores SIGNAL's exceptional capability in multiscale analysis.

scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis

MOTIVATION

Combining single-cell sequencing with ligand-receptor (LR) analysis paves the way for the characterization of cell communication events in complex tissues. In particular, directed weighted graphs naturally represent cell-cell communication events. However, current computational methods cannot yet analyze sample-specific cell-cell communication events, as measured in single-cell data produced in large patient cohorts. Cohort-based cell-cell communication analysis presents many challenges, such as the nonlinear nature of cell-cell communication and the high variability given by the patient-specific single-cell RNAseq datasets.

RESULTS

Here, we present scACCorDiON (single-cell Analysis of Cell-Cell Communication in Disease clusters using Optimal transport in Directed Networks), an optimal transport algorithm exploring node distances on the Markov Chain as the ground metric between directed weighted graphs. Benchmarking indicates that scACCorDiON performs a better clustering of samples according to their disease status than competing methods that use undirected graphs. We provide a case study of pancreas adenocarcinoma, where scACCorDion detects a sub-cluster of disease samples associated with changes in the tumor microenvironment. Our study case corroborates that clusters provide a robust and explainable representation of cell-cell communication events and that the expression of detected LR pairs is predictive of pancreatic cancer survival.

AVAILABILITY AND IMPLEMENTATION

The code of scACCorDiON is available at https://scaccordion.readthedocs.io/en/latest/. and https://doi.org/10.5281/zenodo.15267648. The survival analysis package can be found at https://github.com/CostaLab/scACCorDiON.su.

Single-cell and spatial transcriptomic analyses reveal transcriptional cell lineage heterogeneity in extracranial arteriovenous malformation

BACKGROUND

Extracranial arteriovenous malformations (eAVMs) are rare congenital vascular anomalies consisting of abnormal artery-vein bypass with no intervening capillary network, and can lead to disability and death. The critical genetic determination factors and key transcriptional pathways of the eAVMs genesis process are still unclear.

OBJECTIVE

To generate an overview of the molecular information within eAVMs at the single-cell level.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) on nine samples of eAVMs receiving a confirmatory histopathologic evaluation from a board-certified dermatopathologist and two nonlesional tissue sample controls. 10x Visium spatial transcriptomics (ST) was performed on one eAVM to spatially localize heterogeneous cells and profile the gene expression dynamics of the cells in their morphological context. The scRNA-seq and ST data were integrated and analyzed to further query for spatially restricted mapping of intrapopulation heterogeneous cells.

RESULTS

We identified different cell states of endothelial cells (ECs), perivascular cells and immune cells in eAVMs, uncovered the presence of MAFB+ nidus ECs, characterized mesenchymal activation in ECs, and identified transcriptional variation within perivascular cells and the presence of smooth muscle-like pericytes in eAVMs. Dysregulated cell to cell interactions among ECs, perivascular cells and immune cells that are associated with eAVMs, including those involving MDK, VEGF, ANGPT, SEMA3 and GALECTIN-9 were cataloged. Together, our results depicted the heterogeneity underlying cell function and interaction of eAVMs at a single-cell resolution.

CONCLUSION

We present a comprehensive picture of the cell-resolution atlas that describes the transcriptomic heterogeneity underlying cell function and interaction in eAVMs.

Cardiac Immunotherapy, Immuno-Cardiology, and the Future of Cardiovascular Pharmacology

ABSTRACT

Immuno-cardiology is an emerging field that explores the interplay between the immune system, inflammation, and cardiovascular health/disease, aiming to develop innovative therapies for preventing and treating cardiac diseases. Indeed, chronic inflammation and immune dysregulation play pivotal roles in most cardiovascular conditions, including arrhythmias, atherothrombosis, ischemic heart disease, heart failure, and valve disease. Recent advances in immune-based therapies, including chimeric antigen receptor-T and chimeric antigen receptor-macrophage technologies, have demonstrated potential in impacting on cardiac fibrosis and thus improving surrogate end points in preclinical studies. Immune checkpoint inhibitors, while already established as an effective intervention in oncology, present challenges in their cardiovascular applications because of cardiotoxic side effects, highlighting the need for dedicated cardioprotective strategies or further molecular refinements. Nanoparticle-based delivery systems and cytokine-targeted therapies may offer precise modulation of immune responses, while gut microbiota interventions could exploit the systemic impact of inflammation on cardiovascular health. Despite these quite promising advances, barriers such as safety, scalability, and patient-specific responses must be addressed, and thus precision and personalized approaches will be crucial to overcoming these challenges and ensuring safe and also equitable access. By leveraging interdisciplinary collaboration and technological innovations, immuno-cardiology holds the promise of transforming the prevention and treatment landscape for cardiac diseases, paving the way for improved outcomes and quality of life for patients worldwide.

scaLR: a low-resource deep neural network-based platform for single cell analysis and biomarker discovery

Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) produces vast amounts of individual cell profiling data. Its analysis presents a significant challenge in accurately annotating cell types and their associated biomarkers. Different pipelines based on deep neural network (DNN) methods have been employed to tackle these issues. These pipelines have arisen as a promising resource and can extract meaningful and concise features from noisy, diverse, and high-dimensional data to enhance annotations and subsequent analysis. Existing tools require high computational resources to execute large sample datasets. We have developed a cutting-edge platform known as scaLR (Single-cell analysis using low resource) that efficiently processes data into feature subsets, samples in batches to reduce the required memory for processing large datasets, and running DNN models in multiple central processing units. scaLR is equipped with data processing, feature extraction, training, evaluation, and downstream analysis. Its novel feature extraction algorithm first trains the model on a feature subset and stores the importance of the features for all the features in that subset. At the end of the training of all subsets, the top-K features are selected based on their importance. The final model is trained on top-K features; its performance evaluation and associated downstream analysis provide significant biomarkers for different cell types and diseases/traits. Our findings indicate that scaLR offers comparable prediction accuracy and requires less model training time and computational resources than existing Python-based pipelines. We present scaLR, a Python-based platform, engineered to utilize minimal computational resources while maintaining comparable execution times and analysis costs to existing frameworks.

Effects of embryonic origin, tissue cues and pathological signals on fibroblast diversity in humans

Fibroblasts, once perceived as a uniform cell type, are now recognized as a mosaic of distinct populations with specialized roles in tissue homeostasis and pathology. Here we provide a global overview of the expanding compendium of fibroblast cell types and states, their diverse lineage origins and multifaceted functions across various human organs. By integrating insights from developmental biology, lineage tracing and single-cell technologies, we highlight the complex nature of fibroblasts. We delve into their origination from embryonic mesenchyme and tissue-resident populations, elucidating lineage-specific behaviours in response to physiological cues. Furthermore, we highlight the pivotal role of fibroblasts in orchestrating tissue repair, connective tissue remodelling and immune modulation across diverse pathologies. This knowledge is essential to develop novel fibroblast-targeted therapies to restore steady-state fibroblast function and advance regenerative medicine strategies across multiple diseases.

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.

Learning Phenotype Associated Signature in Spatial Transcriptomics with PASSAGE

Spatially resolved transcriptomics (SRT) is poised to advance the understanding of cellular organization within complex tissues under various physiological and pathological conditions at unprecedented resolution. Despite the development of numerous computational tools that facilitate the automatic identification of statistically significant intra-/inter-slice patterns (like spatial domains), these methods typically operate in an unsupervised manner, without leveraging sample characteristics like physiological/pathological states. Here PASSAGE (Phenotype Associated Spatial Signature Analysis with Graph-based Embedding), a rationally-designed deep learning framework is presented for characterizing phenotype-associated signatures across multiple heterogeneous spatial slices effectively. In addition to its outstanding performance in systematic benchmarks, PASSAGE's unique capability in calling sophisticated signatures has been demonstrated in multiple real-world cases. The full package of PASSAGE is available at https://github.com/gao-lab/PASSAGE.

Immune-mediated cardiac development and regeneration

The complex interplay between the immune and cardiovascular systems during development, homeostasis and regeneration represents a rapidly evolving field in cardiac biology. Single cell technologies, spatial mapping and computational analysis have revolutionised our understanding of the diversity and functional specialisation of immune cells within the heart. From the earliest stages of cardiogenesis, where primitive macrophages guide heart tube formation, to the complex choreography of inflammation and its resolution during regeneration, immune cells emerge as central orchestrators of cardiac fate. Translating these fundamental insights into clinical applications represents a major challenge and opportunity for the field. In this Review, we decode the immunological blueprint of heart development and regeneration to transform cardiovascular disease treatment and unlock the regenerative capacity of the human heart.

Cardiac PDK4 promotes neutrophilic PFKL methylation and drives the innate immune response in diabetic myocardial infarction

NETosis plays a pivotal role in the innate immune response after diabetic myocardial infarction (MI), exerting a profound influence on the overall pathological process and potential recovery outcomes. The metabolism of diabetic cardiomyocyte actively creates a specialized micro environment for the innate immune response after MI. However, the mechanism by which cardiac metabolism drives NETosis remains unclear. Utilizing public databases of human MI sc-RNA datasets, we discovered that cardiomyocyte PDK4 expression mediates the intensification of glycolysis, which is strongly correlated with NETosis. Through mass spectrometry imaging and phenotype assessment, we ascertained that specific knockout of PDK4 in cardiomyocytes (PDK4fl/flMyh6Cre, male, 6 weeks) led to a reduction in NETosis by restraining micro environmental lactate (LA) production. In addition, the role of LA in promoting NETosis has been further corroborated by in vivo/in vitro experiments involving LA supplementation and its absence. Moreover, LA redirects neutrophil metabolic flux from glycolysis to the pentose-phosphate pathway (PPP). Mechanistically, LA triggers metabolic remodeling through the PRMT9-mediated methylation of PFKL at the R301 residue, resulting in PFKL inactivation and the consequent restriction of glycolysis. Our findings reveal the crucial role of cardiomyocyte metabolism in NETosis, shedding light on the role of LA as a vital signaling molecule in the crosstalk between cardiomyocytes and neutrophils. Importantly, we screened pitavastatin, a potential inhibitor of PDK4 among the FDA-approved drugs, and verified that it can alleviate NETosis in diabetic MI, which provides a rationale for drug selection in diabetic MI patients.

Learning tissue representation by identification of persistent local patterns in spatial omics data

Spatial omics data provide rich molecular and structural information on tissues. Their analysis provides insights into local heterogeneity of tissues and holds promise to improve patient stratification by associating clinical observations with refined tissue representations. We introduce Kasumi, a method for identifying spatially localized neighborhood patterns of intra- and intercellular relationships that are persistent across samples and conditions. The tissue representation based on these patterns can facilitate translational tasks, as we show for stratification of cancer patients for disease progression and response to treatment using data from different experimental platforms. On these tasks, Kasumi outperforms related approaches and offers explanations of spatial coordination and relationships at the cell-type or marker level. We show that persistent patterns comprise regions of different sizes, and that non-abundant, localized relationships in the tissue are strongly associated with unfavorable outcomes.

A secretome atlas of cardiac fibroblasts from healthy and infarcted mouse hearts

Cardiac fibroblasts (CF) are key players after myocardial infarction (MI), but their signaling is only incompletely understood. Here we report a first secretome atlas of CF in control (cCF) and post-MI mouse hearts (miCF), combining a rapid cell isolation technique with SILAC and click chemistry. In CF, numerous paracrine factors involved in immune homeostasis are identified. Comparing secretome, transcriptome (SLAMseq), and cellular proteome disclose protein turnover. In miCF at day 5 post-MI, significantly upregulated proteins include SLIT2, FN1, and CRLF1 in mouse and human samples. Comparing the miCF secretome at days 3 and 5 post-MI reveals the dynamic nature of protein secretion. Specific in-vivo labeling of miCF proteins via biotin ligase TurboID using the POSTN promotor mirrors the in-vitro data. In summary, we identify numerous paracrine factors specifically secreted from CF in mice and humans. This secretome atlas may lead to new biomarkers and/or therapeutic targets for the activated CF.

An organ-wide spatiotemporal transcriptomic and cellular atlas of the regenerating zebrafish heart

Adult zebrafish robustly regenerate injured hearts through a complex orchestration of molecular and cellular activities. However, this remarkable process, which is largely non-existent in humans, remains incompletely understood. Here, we utilize integrated spatial transcriptomics (Stereo-seq) and single-cell RNA-sequencing (scRNA-seq) to generate a spatially-resolved molecular and cellular atlas of regenerating zebrafish heart across eight stages. We characterize the cascade of cardiomyocyte cell states responsible for producing regenerated myocardium and explore a potential role for tpm4a in cardiomyocyte re-differentiation. Moreover, we uncover the activation of ifrd1 and atp6ap2 genes as a unique feature of regenerative hearts. Lastly, we reconstruct a 4D "virtual regenerating heart" comprising 569,896 cells/spots derived from 36 scRNA-seq libraries and 224 Stereo-seq slices. Our comprehensive atlas serves as a valuable resource to the cardiovascular and regeneration scientific communities and their ongoing efforts to understand the molecular and cellular mechanisms underlying vertebrate heart regeneration.

The single-cell atlas of short-chain fatty acid receptors in human and mice hearts

Introduction

The gut microbiota metabolite, short-chain fatty acids (SCFAs), can protect against multiple cardiovascular diseases, while the molecular targets and underlying mechanisms need to be elucidated. One of the primary mechanisms of SCFA benefits was the direct activation of a group of G-protein-coupled receptors (GPCRs), termed free fatty acid receptors (FFARs), the FFAR2 (GPR43), and FFAR3 (GPR41). At present, the distribution of FFAR2/3 in cardiac cells has not been entirely clarified.

Methods

Using 18 public single-cell RNA-seq and single-nuclear RNA-seq data of human and mouse hearts, we illustrate the entire atlas of FFAR2/3 distribution in different regions and cell types in normal and infarcted hearts.

Results and discussion

We present the atlas of FFAR2/3 in the whole human body, normal and infarcted hearts at single-cell resolution. We also illustrated the entire atlas of FFAR2/3 in normal/ischemic hearts of newborn and adult mice by combining public and newly built sc/snRNA-seq datasets. These findings provide valuable information on the possible effect of SCFAs via FFAR2/3 in the heart and valuable references for future studies.

miR-24-3p secreted as extracellular vesicle cargo by cardiomyocytes inhibits fibrosis in human cardiac microtissues

AIMS

Cardiac fibrosis in response to injury leads to myocardial stiffness and heart failure. At the cellular level, fibrosis is triggered by the conversion of cardiac fibroblasts (CF) into extracellular matrix-producing myofibroblasts. miR-24-3p regulates this process in animal models. Here, we investigated whether miR-24-3p plays similar roles in human models.

METHODS AND RESULTS

Gain- and loss-of-function experiments were performed using human induced pluripotent stem cell-derived cardiomyocytes (hCM) and primary hCF under normoxic or ischaemia-simulating conditions. hCM-derived extracellular vesicles (EVs) were added to hCF. Similar experiments were performed using three-dimensional human cardiac microtissues and ex vivo cultured human cardiac slices. hCF transfection with miR-24-3p mimic prevented TGFβ1-mediated induction of FURIN, CCND1, and SMAD4-miR-24-3p target genes participating in TGFβ1-dependent fibrogenesis-regulating hCF-to-myofibroblast conversion. hCM secreted miR-24-3p as EV cargo. hCM-derived EVs modulated hCF activation. Ischaemia-simulating conditions induced miR-24-3p depletion in hCM-EVs and microtissues. Similarly, hypoxia down-regulated miR-24-3p in cardiac slices. Analyses of clinical samples revealed decreased miR-24-3p levels in circulating EVs in patients with acute myocardial infarction (AMI), compared with healthy subjects. Post-mortem RNAScope analysis showed miR-24-3p down-regulation in myocardium from patients with AMI, compared with patients who died from non-cardiac diseases. Berberine, a plant-derived agent with miR-24-3p-stimulatory activity, increased miR-24-3p contents in hCM-EVs, down-regulated FURIN, CCND1, and SMAD4, and inhibited fibrosis in cardiac microtissues.

CONCLUSION

These findings suggest that hCM may control hCF activation through miR-24-3p secreted as EV cargo. Ischaemia impairs this mechanism, favouring fibrosis.

Spatial genomics: Mapping the landscape of fibrosis

Organ fibrosis causes major morbidity and mortality worldwide. Treatments for fibrosis are limited, with organ transplantation being the only cure. Here, we review how various state-of-the-art spatial genomics approaches are being deployed to interrogate fibrosis across multiple organs, providing exciting insights into fibrotic disease pathogenesis. These include the detailed topographical annotation of pathogenic cell populations and states, detection of transcriptomic perturbations in morphologically normal tissue, characterization of fibrotic and homeostatic niches and their cellular constituents, and in situ interrogation of ligand-receptor interactions within these microenvironments. Together, these powerful readouts enable detailed analysis of fibrosis evolution across time and space.

Nrf3-Mediated Mitochondrial Superoxide Promotes Cardiomyocyte Apoptosis and Impairs Cardiac Functions by Suppressing Pitx2

BACKGROUND

Myocardial infarction (MI) elicits mitochondria reactive oxygen species (ROS) production and cardiomyocyte (CM) apoptosis. Nrf3 (nuclear factor erythroid 2-related factor 3) has an established role in regulating redox signaling and tissue homeostasis. Here, we aimed to evaluate the role and mechanism of Nrf3 in injury-induced pathological cardiac remodeling.

METHODS

Global (Nrf3-KO) and CM-specific (Nrf3△CM) Nrf3 knockout mice were subjected to MI or ischemia/reperfusion injury, followed by functional and histopathological analysis. Primary neonatal mouse and rat ventricular myocytes and CMs derived from human induced pluripotent stem cells were used to evaluate the impact of Nrf3 on CM apoptosis and mitochondrial ROS production. Chromatin immunoprecipitation sequencing and immunoprecipitation-mass spectrometry analysis were used to uncover potential targets of Nrf3. MitoParaquat administration and CM-specific adeno-associated virus vectors were used to further confirm the in vivo relevance of the identified signal pathways.

RESULTS

Nrf3 was expressed mainly in CMs in healthy human hearts, and an increased level of Nrf3 was observed in CMs within the border zone of infarcted human hearts and murine cardiac tissues after MI. Both global and CM-specific Nrf3 knockout significantly decreased injury-induced mitochondrial ROS production, CM apoptosis, and pathological cardiac remodeling, consequently improving cardiac functions. In addition, cardiac-specific Nrf3 overexpression reversed the ameliorative cardiac phenotypes observed in Nrf3-KO mice. Functional studies showed that Nrf3 promoted neonatal mouse ventricular myocyte, neonatal rat ventricular myocyte, and CMs derived from human induced pluripotent stem cell apoptosis by increasing mitochondrial ROS production. Critically, augmenting mitochondrial ROS with MitoParaquat blunted the beneficial effects of Nrf3 deletion on cardiac function and remodeling. Mechanistically, a redox regulator Pitx2 (paired-like homeodomain transcription factor 2) was identified as one of the main target genes of Nrf3. Specifically, Nrf3 binds to Pitx2 promoter, where it increases DNA methylation through recruiting heterogeneous nuclear ribonucleoprotein K and DNA-methyltransferase 1 complex, thereby inhibiting Pitx2 expression. CM-specific knockdown of Pitx2 blunted the beneficial effects of Nrf3 deletion on cardiac function and remodeling, and cardiac-specific Pitx2 overexpression attenuated MI-induced mitochondrial ROS production and CM apoptosis, as well as preserved cardiac functions after MI.

CONCLUSIONS

Nrf3 promotes injury-induced CM apoptosis and deteriorates cardiac functions by increasing mitochondrial ROS production through suppressing Pitx2 expression. Targeting the Nrf3-Pitx2-mitochondrial ROS signal axis may therefore represent a novel therapeutic approach for MI treatment.

Molecular gatekeepers of endogenous adult mammalian cardiomyocyte proliferation

Irreversible cardiac fibrosis, cardiomyocyte death and chronic cardiac dysfunction after myocardial infarction pose a substantial global health-care challenge, with no curative treatments available. To regenerate the injured heart, cardiomyocytes must proliferate to replace lost myocardial tissue - a capability that adult mammals have largely forfeited to adapt to the demanding conditions of life. Using various preclinical models, our understanding of cardiomyocyte proliferation has progressed remarkably, leading to the successful reactivation of cell cycle induction in adult animals, with functional recovery after cardiac injury. Central to this success is the targeting of key pathways and structures that drive cardiomyocyte maturation after birth - nucleation and ploidy, sarcomere structure, developmental signalling, chromatin and epigenetic regulation, the microenvironment and metabolic maturation - forming a complex regulatory framework that allows efficient cellular contraction but restricts cardiomyocyte proliferation. In this Review, we explore the molecular pathways underlying these core mechanisms and how their manipulation can reactivate the cell cycle in cardiomyocytes, potentially contributing to cardiac repair.

A large-scale integrated transcriptomic atlas for soybean organ development

Soybean is one of the most important crops globally, and its production must be significantly increased to meet increasing demand. Elucidating the genetic regulatory networks underlying soybean organ development is essential for breeding elite and resilient varieties to ensure increased soybean production under climate change. An integrated transcriptomic atlas that leverages multiple types of transcriptomics data can facilitate the characterization of temporal-spatial expression patterns of most organ development-related genes and thereby help us to understand organ developmental processes. Here, we constructed a comprehensive, integrated transcriptomic atlas for soybeans, integrating bulk RNA sequencing (RNA-seq) datasets from 314 samples across the soybean life cycle, along with single-nucleus RNA-seq and spatially enhanced resolution omics sequencing datasets from five organs: root, nodule, shoot apex, leaf, and stem. Investigating genes related to organ specificity, blade development, and nodule formation, we demonstrate that the atlas has robust power for exploring key genes involved in organ formation. In addition, we developed a user-friendly panoramic database for the transcriptomic atlas, enabling easy access and queries, which will serve as a valuable resource to significantly advance future soybean functional studies.

Atf3 controls transitioning in female mitochondrial cardiomyopathy as identified by spatial and single-cell transcriptomics

Oxidative phosphorylation defects result in now intractable mitochondrial diseases (MD) with cardiac involvement markedly affecting prognosis. The mechanisms underlying the transition from compensation to dysfunction in response to metabolic deficiency remain unclear. Here, we used spatially resolved transcriptomics and single-nucleus RNA sequencing (snRNA-seq) on the heart of a patient with mitochondrial cardiomyopathy (MCM), combined with an MCM mouse model with cardiac-specific Ndufs6 knockdown (FS6KD). Cardiomyocytes demonstrated the most heterogeneous expression landscape among cell types caused by metabolic perturbation, and pseudotime trajectory analysis revealed dynamic cellular states transitioning from compensation to severe compromise. This progression coincided with the transient up-regulation of a transcription factor, ATF3. Genetic ablation of Atf3 in FS6KD corroborated its pivotal role, effectively delaying cardiomyopathy progression in a female-specific manner. Our findings highlight a fate-determining role of ATF3 in female MCM progression and that the latest transcriptomic analysis will help decipher the mechanisms underlying MD progression.

Cardiac fibroblast-derived mitochondria-enriched sEVs regulate tissue inflammation and ventricular remodeling post-myocardial infarction through NLRP3 pathway

Resident cardiac fibroblasts (CFs) play crucial roles in sensing injury signals and regulating inflammatory responses post-myocardial infarction (MI). Damaged mitochondria can be transferred extracellularly via various mechanisms, including extracellular vesicles (EVs). In this study, we aimed to investigate whether CFs could transfer damaged mitochondrial components via small EVs (sEVs) and elucidate their role in regulating inflammatory responses post-MI. Left anterior descending coronary artery ligation was performed in mice. Mitochondrial components in sEVs were detected using nanoflow cytometry. Differential protein expression in sEVs from normoxia and normoglycemia CFs (CFs-Nor-sEVs) and CFs post oxygen-glucose deprivation (CFs-OGD-sEVs) was identified using label-free proteomics. CFs-sEVs were co-cultured with mouse bone marrow-derived macrophages (BMDMs) to assess macrophage inflammatory responses. Effects of intramyocardial injection of CFs-sEVs were assessed in MI mice in the absence or presence of NLRP3 inhibitor CY-09. Results demonstrated that mitochondrial components were detected in CFs-derived sEVs post-MI. Damaged mitochondrial components were enriched in CFs-OGD-sEVs (CFs-mt-sEVs), which promoted pro-inflammatory phenotype activation of BMDMs in vitro. Myocardial injection of CFs-mt-sEVs enhanced tissue inflammation, aggravated cardiac dysfunction, and exacerbated maladaptive ventricular remodeling post-MI in vivo. Mechanistically, above effects were achieved via activation of NLRP3 and above effects could be reversed by NLRP3 inhibitor CY-09. This study indicates that CFs could transfer damaged mitochondrial components via the sEVs post-MI, promote macrophage inflammatory activation and exacerbate maladaptive ventricular remodeling post MI by activating NLRP3. Our findings highlight the potential therapeutic effects of inhibiting CFs-mt-sEVs and NLRP3 to improve cardiac function and attenuate ventricular remodeling post-MI.

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.

Dynamic molecular atlas of cardiac fibrosis at single-cell resolution shows CD248 in cardiac fibroblasts orchestrates interactions with immune cells

Post-injury remodeling is a complex process involving temporal specific cellular interactions in the injured tissue where the resident fibroblasts play multiple roles. Here, we performed single-cell and spatial transcriptome analysis in human and mouse infarcted hearts to dissect the molecular basis of these interactions. We identified a unique fibroblast subset with high CD248 expression, strongly associated with extracellular matrix remodeling. Genetic Cd248 deletion in fibroblasts mitigated cardiac fibrosis and dysfunction following ischemia/reperfusion. Mechanistically, CD248 stabilizes type I transforming growth factor beta receptor and thus upregulates fibroblast ACKR3 expression, leading to enhanced T cell retention. This CD248-mediated fibroblast-T cell interaction is required to sustain fibroblast activation and scar expansion. Disrupting this interaction using monoclonal antibody or chimeric antigen receptor T cell reduces T cell infiltration and consequently ameliorates cardiac fibrosis and dysfunction. Our findings reveal a CD248+ fibroblast subpopulation as a key regulator of immune-fibroblast cross-talk and a potential therapy to treat tissue fibrosis.

Programmed cardiomyocyte death in myocardial infarction

Cardiovascular disease (CVD) is a leading cause of human mortality worldwide, with patients often at high risk of heart failure (HF) in myocardial infarction (MI), a common form of CVD that results in cardiomyocyte death and myocardial necrosis due to inadequate myocardial perfusion. As terminally differentiated cells, cardiomyocytes possess a severely limited capacity for regeneration, and an excess of dead cardiomyocytes will further stress surviving cells, potentially exacerbating to more extensive heart disease. The article focuses on the relationship between programmed cell death (PCD) of cardiomyocytes, including different forms of apoptosis, necrosis, and autophagy, and MI, as well as the potential application of these mechanisms in the treatment of MI. By gaining a deeper understanding of the mechanisms of cardiomyocyte death, it aims to provide new insights into the prevention and treatment of MI.

Translation of pathophysiological mechanisms of atrial fibrosis into new diagnostic and therapeutic approaches

Atrial fibrosis is one of the main manifestations of atrial cardiomyopathy, an array of electrical, mechanical and structural alterations associated with atrial fibrillation (AF), stroke and heart failure. Atrial fibrosis can be both a cause and a consequence of AF and, once present, it accelerates the progression of AF. The pathophysiological mechanisms leading to atrial fibrosis are diverse and include stretch-induced activation of fibroblasts, systemic inflammatory processes, activation of coagulation factors and fibrofatty infiltrations. Importantly, atrial fibrosis can occur in different forms, such as reactive and replacement fibrosis. The diversity of atrial fibrosis mechanisms and patterns depends on sex, age and comorbidity profile, hampering the development of therapeutic strategies. In addition, the presence and severity of comorbidities often change over time, potentially causing temporal changes in the mechanisms underlying atrial fibrosis development. This Review summarizes the latest knowledge on the molecular and cellular mechanisms of atrial fibrosis, its association with comorbidities and the sex-related differences. We describe how the various patterns of atrial fibrosis translate into electrophysiological mechanisms that promote AF, and critically appraise the clinical applicability and limitations of diagnostic tools to quantify atrial fibrosis. Finally, we provide an overview of the newest therapeutic interventions under development and discuss relevant knowledge gaps related to the association between clinical manifestations and pathological mechanisms of atrial fibrosis and to the translation of this knowledge to a clinical setting.

Single-nucleus multi-omics implicates androgen receptor signaling in cardiomyocytes and NR4A1 regulation in fibroblasts during atrial fibrillation

The dysregulation of gene expression programs in the human atria during persistent atrial fibrillation (AF) is not completely understood. Here, we reanalyze bulk RNA-sequencing datasets from two studies (N = 242) and identified 755 differentially expressed genes in left atrial appendages of individuals with persistent AF and non-AF controls. We combined the bulk RNA-sequencing differentially expressed genes with a left atrial appendage single-nucleus multi-omics dataset to assign genes to specific atrial cell types. We found noncoding genes at the IFNG locus (LINC01479, IFNG-AS1) strongly dysregulated in cardiomyocytes. We defined a gene expression signature potentially driven by androgen receptor signaling in cardiomyocytes from individuals with AF. Cell-type-specific gene expression modules suggested an increase in T cell and a decrease in adipocyte and neuronal cell gene expression in AF. Lastly, we showed that reducing NR4A1 expression, a marker of a poorly characterized human atrial fibroblast subtype, fibroblast activation markers, extracellular matrix remodeling and cell proliferation decreased.

Alpha-actinin-1 stabilizes focal adhesions to facilitate sarcomere assembly in cardiac myocytes

Cardiac sarcomere assembly is a highly orchestrated process requiring integration between intracellular contractile components and extracellular adhesions. While α-actinin-2 (ACTN2) is well known for its structural role at Z-discs, the function of the "non-muscle" paralog α-actinin-1 (ACTN1) in cardiomyocytes remains unclear. Using human induced pluripotent stem cell-derived cardiac myocytes (hiCMs), we demonstrate that ACTN1 is essential for sarcomere assembly. siRNA-mediated depletion of ACTN1 disrupted Z-line formation and impaired sarcomere organization, defects that were rescued by exogenous ACTN1 but not ACTN2, revealing non-redundant functions. Unlike ACTN2, ACTN1 localized predominantly to focal adhesions and was required for adhesion maturation, as evidenced by reduced adhesion size and number following ACTN1 depletion. Live-cell imaging of vinculin dynamics showed decreased stability of adhesion-associated vinculin in ACTN1-deficient cells, whereas paxillin dynamics were unaffected. These results suggest that ACTN1 stabilizes focal adhesions to promote effective force transmission during sarcomere assembly.

Cardiac Fibrosis in the Multi-Omics Era: Implications for Heart Failure

Cardiac fibrosis, a hallmark of heart failure and various cardiomyopathies, represents a complex pathological process that has long challenged therapeutic intervention. High-throughput omics technologies have begun revolutionizing our understanding of the molecular mechanisms driving cardiac fibrosis and are providing unprecedented insights into its heterogeneity and progression. This review provides a comprehensive analysis of how techniques-encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics-are providing insight into our understanding of cardiac fibrosis. Genomic studies have identified novel genetic variants and regulatory networks associated with fibrosis susceptibility and progression, and single-cell transcriptomics has unveiled distinct cardiac fibroblast subpopulations with unique molecular signatures. Epigenomic profiling has revealed dynamic chromatin modifications controlling fibroblast activation states, and proteomic analyses have identified novel biomarkers and potential therapeutic targets. Metabolomic studies have uncovered important alterations in cardiac energetics and substrate utilization during fibrotic remodeling. The integration of these multi-omic data sets has led to the identification of previously unrecognized pathogenic mechanisms and potential therapeutic targets, including cell-type-specific interventions and metabolic modulators. We discuss how these advances are driving the development of precision medicine approaches for cardiac fibrosis while highlighting current challenges and future directions in translating multi-omic insights into effective therapeutic strategies. This review provides a systems-level perspective on cardiac fibrosis that may inform the development of more effective, personalized therapeutic approaches for heart failure and related cardiovascular diseases.

Hypoxia in myocardial infarction and natriuretic peptides

BACKGROUND

Mechanical stress on the heart is commonly considered the sole stimulus explaining the synthesis and release of circulating natriuretic peptides and their derivatives. While one of the most critical paradigms in cardiology is that mechanical load increases oxygen consumption, clinical studies on these peptides have neglected the relationship between mechanical stress and oxygen metabolism. At the cellular level, cardiac myocytes have a ubiquitous oxygen-sensing pathway mediated by a nuclear transcription factor, the hypoxia-inducible factor (HIF). Published studies indicate that the human myocardium starts expressing HIF during infarction. In myocardial cell cultures, natriuretic peptides are synthesised and released under hypoxic conditions through immediate and sufficient actions of HIF.

CONCLUSION

Myocardial oxygen metabolism directly regulates the plasma levels of natriuretic peptides in heart diseases. The function of oxygen gradients should be correlated with circulating natriuretic peptides to achieve better sensitivity in plasma measurements of natriuretic peptides in myocardial infarction.

Integrating -Omic Technologies across Modality, Space, and Time to Decipher Remodeling in Cardiac Disease

PURPOSE OF REVIEW

Despite significant efforts to understand pathophysiological processes underlying cardiac diseases, the molecular causes for the most part remain unresolved. Rapid advancements in -omics technologies, and their application in cardiac research, offer new insight into cardiac remodeling in disease states. This review aims to provide an accessible overview of recent advances in omics approaches for studying cardiac remodeling, catering to readers without extensive prior expertise.

RECENT FINDINGS

We provide a methodologically focused overview of current methods for performing transcriptomics and proteomics, including their extensions for single-cell and spatial measurements. We discuss approaches to integrate data across modalities, resolutions and time. Key recent applications within the cardiac field are highlighted. Each -omics modality can provide insight, yet each existing experimental method has technical or conceptual limitations. Integrating data across multiple modalities can leverage strengths and mitigate weaknesses, ultimately enhancing our understanding of cardiac pathophysiology.