Biology subjects

Lavine, K. J.

Publications and source records attributed to Lavine, K. J..

At least 19 recordsLinked to original sources

bioRxiv2026

CD14 Blockade Attenuates Arrhythmogenic Cardiomyopathy

Background: Arrhythmogenic cardiomyopathy (ACM) is a genetic and phenotypically heterogeneous myocardial disorder characterized by progressive cardiomyocyte loss, immune cell infiltration, and fibro-fatty replacement of the ventricular myocardium, with an increased risk of sudden cardiac death (SCD), predominantly caused by mutations in cardiac desmosomal genes including PKP2, DSP, and DSG2. We previously described the pivotal role of NF{kappa}B and CCR2+ cardiac macrophage-triggered inflammation in ACM pathogenesis. Methods: WT or Dsg2mut/mut mice were treated with either isotype control or anti-CD14 antibody once a week for the described treatment period (4 or 8 weeks). At the end of the treatment period, disease characteristics were assessed by echocardiography, electrocardiography, histology, immunofluorescence, positron emission tomography (PET) imaging and single-cell transcriptomics. Results: Here, we demonstrate the efficacy of neutralizing CD14 signaling, an important mediator of inflammatory macrophage activation, in attenuating ACM disease in vivo. Additionally, we elucidate shifts in the cellular and transcriptomic landscapes that occur following anti-CD14 antibody treatment in a well-established mouse model of ACM and identify substantial reductions in inflammatory macrophage and pro-fibrotic fibroblast populations. Conclusion: This study provides evidence that blockade of CD14 can attenuate the ACM disease phenotype. It may do so by inhibiting macrophage-based activation and inflammation, while also altering the transcriptional state of other important cell types. Collectively, these findings suggest that CD14 inhibition may be an effective option for ACM, which should be explored in early-phase clinical studies.

immunology↗

bioRxiv2026

Multicellular Programs Associated with Right Ventricular Adaptation in Pulmonary Arterial Hypertension

BackgroundRight ventricular (RV) adaptation determines outcomes in pulmonary arterial hypertension (PAH), yet multicellular molecular programs associated with adaptive versus maladaptive RV remodeling in living humans remain incompletely defined. MethodsWe collected 32 human RV tissue biopsies from patients with idiopathic PAH, systemic sclerosis-associated PAH (SSc-PAH), systemic sclerosis without pulmonary hypertension, with 24 nonfailing donor RVs serving as controls. We performed single-nucleus RNA sequencing and integrated cell-type specific transcriptional programs with contemporaneously obtained multi-beat pressure-volume loop measurements of RV contractility (Ees, end-systolic elastance) and RV-pulmonary arterial coupling (the ratio of Ees to Ea, the effective arterial load). SSc modification of PAH-associated biology was assessed using interaction terms. Bulk RV proteomic pathway enrichment was performed to assess an orthogonal molecular layer, and exploratory cell-cell communication analyses alongside independent spatial transcriptomic analyses were performed to contextualize key findings. ResultsPAH was associated with broad depletion of biosynthetic, trafficking, and mitochondrial programs across cell types. SSc modified the magnitude of many PAH-associated transcriptional programs while largely preserving pathway directionality. Significant multicellular pathway enrichments were associated with RV-pulmonary arterial coupling. Joint analysis of Ees, Ea, and Ees/Ea identified biologic programs associated with different RV responses to varying loading conditions. Preserved coupling was characterized by enriched extracellular matrix, laminin-integrin, receptor tyrosine kinase, mitochondrial, and translational programs involving fibroblast, endothelial, endocardial, and cardiomyocyte compartments. Cell- cell communication analyses predicted coordinated stromal-vascular signaling networks involving laminin-integrin and endothelial-to-mural signaling in preserved coupling. Proteomic and spatial analyses supported recurrent multicellular themes. ConclusionsRV adaptation in PAH is associated with distinct, coordinated multicellular programs that vary with load and contractile response. RV-PA coupling in PAH is associated with multicellular remodeling that extends beyond cardiomyocytes and reflects organized vascular-stromal support architecture. These findings identify extracellular matrix, laminin- integrin signaling, mitochondrial, and translational programs as associated with adaptive RV remodeling in PAH. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LICell type-resolved molecular profiling of living human RV tissue identifies PAH-associated depletion of biosynthetic, trafficking, mitochondrial, and repair-associated programs across multiple cardiac cell types. C_LIO_LIIntegration with contemporaneously obtained pressure-volume loop physiology demonstrates that preserved RV-pulmonary arterial coupling under lower load was associated predominantly with cardiomyocyte mitochondrial and metabolic competency, whereas preserved coupling under higher load was associated with extracellular matrix remodeling and vascular-stromal signaling. C_LIO_LIProteomic, cell-cell communication, and spatial analyses provided orthogonal support for coordinated extracellular matrix and vascular-stromal programs associated with preserved RV-pulmonary arterial coupling. C_LI What are the clinical implications?O_LIThese findings shift the biology of RV adaptation from a predominantly cardiomyocyte- centered model toward a multicellular tissue model in which metabolic, matrix, and vascular support programs vary according to loading conditions and contractile states. C_LIO_LIExtracellular matrix-integrin signaling, endothelial-mural communication, and mitochondrial competency represent candidate pathways for mechanistic investigation toward RV-directed therapies in PAH. C_LI

molecular biology↗

bioRxiv2026

Stress Granule Coarsening Is a Pathological Inflection Point for Cardiac Electrophysiological Dysfunction

Arrhythmia risk rises early in many forms of cardiac stress, often before contractile failure is evident. Stressed cardiomyocytes accumulate biomolecular condensates, known as stress granules (SGs), whose contribution to this electrical vulnerability has been unclear. We mapped where SGs reside and followed their life cycle under acute and chronic oxidative stress across complementary model systems and assessed electrophysiological consequences with pharmacological tools targeting granule assembly, microtubule integrity, and calcium channel function. Under both stress regimes, SGs localized preferentially to z-lines and intercalated discs, marking these mechanically critical sites as hubs of condensate assembly. Merging of granules, referred to as coarsening, rather than initial formation, emerged as a pathological connection. Early granules were broadly cytoprotective, whereas progressive coarsening was accompanied by disruption of alpha-actinin and L-type calcium channel (Cav1.2) nanodomains and by shortening of action potential (AP) duration. Coarsened granules disorganized Cav1.2 nanodomains through a microtubule-dependent mechanism, and arresting coarsening with nocodazole preserved nanodomain integrity and restored AP morphology. The transition from nascent to coarsened SGs therefore represents a targetable inflection point, and limiting coarsening may prevent proarrhythmic remodeling during cardiac oxidative stress.

bioengineering↗

bioRxiv2026

Integrative Clinical-Molecular Modeling Identifies LRRN4CL as a Determinant of Structural and Functional Myocardial Improvement

BackgroundMechanical ventricular unloading and systemic circulatory support with left ventricular assist devices (LVADs) enable myocardial recovery in a subset of advanced heart failure (HF) patients, but predictors and mechanisms of recovery are not well understood. Integrating clinical and molecular data may improve identification of patients most likely to recover and uncover biologically relevant targets in HF. MethodsWe collected and analyzed left ventricular apical myocardial tissue and clinical data from 208 patients undergoing LVAD implantation across five centers. Pre-implant transcriptomic profiles (22,373 mRNA transcripts) were integrated with 59 clinical variables using supervised machine learning with repeated cross-validation to identify and prioritize features associated with myocardial recovery, defined as a binary outcome based on improvement in left ventricular ejection fraction (LVEF [≥]40%) and left ventricular end-diastolic diameter (LVEDD [≤]5.9 cm). We also modeled functional (LVEF) and structural (LVEDD) improvement as a continuous outcome without any predefined LVEF and LVEDD pathological thresholds. Feature prioritization was followed by validation in human myocardial tissue and mechanistic interrogation in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). ResultsIntegrative models achieved modest discrimination for myocardial recovery as a binary categorical outcome (maximum mean cross-validated area under the curve 0.73{+/-}0.15), identifying clinical features such as HF duration, LVEDD, HF pharmacologic therapy, and device configuration. Leucine-rich repeat neuronal 4C-like (LRRN4CL), measured in human myocardium, consistently emerged as a top transcriptomic predictor across both binary and continuous metric models (functional and structural). Higher pre-LVAD LRRN4CL expression was associated with reduced likelihood of myocardial recovery and localized primarily to cardiomyocytes. In iPSC-CMs, LRRN4CL overexpression localized to the sarcoplasmic reticulum, induced transcriptional remodeling characterized by suppression of contractile pathways and activation of stress programs, impaired calcium handling, impaired contraction-relaxation kinetics, and diminished mitochondrial respiratory reserve capacity. ConclusionsIntegration of clinical and myocardial transcriptomic data identifies LRRN4CL as a novel marker associated with impaired myocardial recovery following LVAD-mediated ventricular unloading and systemic circulatory support. These findings move beyond predictive modeling, linking integrative computational discovery to cardiomyocyte dysfunction and providing a translational framework for biologically informed risk stratification and therapeutic targeting for myocardial recovery. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIIntegrative clinical and myocardial transcriptomic modeling identifies LRRN4CL as a novel molecular determinant of structural and functional changes after LVAD-mediated ventricular unloading and enhanced systemic circulatory support. C_LIO_LIElevated LRRN4CL expression is associated with adverse remodeling signatures, impaired calcium handling, and stress responses in human iPSC-derived cardiomyocytes. C_LIO_LIExperimental overexpression of LRRN4CL directly disrupts calcium cycling, contractile performance, and mitochondrial respiration linking molecular signature to functional phenotype. C_LI What Are the Clinical Implications?O_LIIdentification of LRRN4CL as a marker associated with impaired myocardial recovery supports future efforts toward biologically informed risk stratification for patients undergoing LVAD therapy. C_LIO_LILRRN4CL as a marker of cardiac improvement potential may extend beyond advanced HF to earlier stage disease patients and inform prognosis, risk stratification, and response to medical therapies. C_LIO_LIThese findings highlight LRRN4CL-associated pathways as potential therapeutic targets and demonstrate how integrative clinical-transcriptomic approaches can move beyond clinical prediction toward identification of new biologically precise therapeutic targets in HF following a bedside to bench and back approach. C_LI

bioinformatics↗

bioRxiv2026

The Muscle Tissue Environment Limits Muscle Stem Cells in Aged Mice

Frailty arising from loss of muscle function and mass is a significant health concern impacting quality of life and dramatically increasing health care costs as our population ages. Ameliorating frailty derived from reduced muscle function is thus a critical research priority to improve health span. Cell intrinsic defects in muscle stem cells (MuSC), or satellite cells, occur as skeletal muscle ages, reducing the capacity of MuSCs to maintain and repair skeletal muscle and are accompanied by cell nonautonomous changes. Although rejuvenating stem cells in aged tissues or organs has potential to improve muscle aging phenotypes, we found that the extracellular environment in aged mice abrogates rejuvenated muscle stem cell potential. MuSCs from young mice were unable to grow on extracellular matrix derived from aged mice that contains elevated collagen protein levels, establishing a critical role for the environment in contributing to muscle phenotypes in aging. Combining an inducible FGF receptor 1 (FGFR1) to rescue MuSC intrinsic aging defects with a drug to reduce fibrosis partially rescued muscle mass loss in aged mice. We conclude that aging affects tissues, and particularly skeletal muscle tissue, via complex multifactorial processes requiring multifaceted interventions to improve aging phenotypes.

cell biology↗

bioRxiv2026

Circulating miRNA-Protein Signatures Predict Outcomes in Pediatric Dilated Cardiomyopathy

BackgroundPediatric dilated cardiomyopathy (DCM) is a rare, progressive heart disease with variable outcomes that range from recovery to heart transplantation. To date, there are no prognostic biomarkers for children with DCM. Identifying circulating biomarkers that are associated with clinical outcomes is critical for personalized management. MethodsmiRNAs were identified by RNA-seq, whereas proteins were identified by SomaScan(R). Machine learning methodologies were used to explore the predictive ability of circulating factors identified from serum samples collected at the time of presentation with acute heart failure. ResultsThirty patients experienced poor outcomes (cardiac transplantation, mechanical circulatory support, or death) and 19 patients recovered left ventricular function. Distinct miRNA and protein signatures differentiated outcomes groups. Top candidate proteins (COL2A1, CXCL12, and ADGRF5) and miRNAs (miR-874-3p, miR-335-3p, miR-323a-3p) demonstrated strong discriminatory performance within the study cohort (recovered vs poor outcomes; Area Under the Curve of 0.92). Ingenuity Pathway Analysis implicates cardiac remodeling, fibrosis, and inflammatory signaling as central pathways differentiating patient outcomes. ConclusionsCirculating miRNA and protein signatures at presentation identify a circulating molecular signature associated with divergent clinical trajectories in pediatric DCM. These findings support the potential utility of multi-omic biomarkers for early risk stratification and provide insight into mechanisms underlying divergent outcomes. CLINICAL PERSPECTIVEWhat Is New? O_LICirculating miRNA and protein profiles measured at presentation distinguish children with pediatric DCM who recover from those who progress to advanced heart failure. C_LIO_LIA combined multi-omic biomarker demonstrated strong discriminatory performance in this cohort (AUC 0.92). C_LIO_LIPathway analysis implicates extracellular matrix remodeling, fibrosis, and inflammatory signaling in children with adverse clinical trajectories. C_LI What Are the Clinical Implications? O_LISerum-based molecular biomarkers may enable earlier risk stratification in children presenting with dilated cardiomyopathy. C_LIO_LIMulti-omic integration may improve identification of pediatric patients at risk for transplantation, mechanical circulatory support, or death. C_LIO_LIThese findings support further validation of circulating biomarker panels to guide personalized management in this rare disease. C_LI RESEARCH PERSPECTIVEWhat New Question Does This Study Raise? O_LICan integrated circulating miRNA-protein signatures identify biologically distinct trajectories of recovery versus progression in children with dilated cardiomyopathy? C_LIO_LIDo circulating molecular profiles reflect underlying disease mechanisms that determine divergent clinical outcomes in pediatric DCM? C_LI What Question Should Be Addressed Next? O_LIDo the pathways identified by integrated miRNA-protein analysis (fibrosis, remodeling, and inflammation) play causal roles in determining recovery versus progression? C_LIO_LICan multi-omic biomarkers be incorporated into prospective studies to improve early risk stratification and guide clinical management? C_LI

systems biology↗

bioRxiv2025

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Despite advances in disease treatment, our understanding of how damaged organs recover and the mechanisms governing this process remain poorly defined. Here, we mapped the transcriptional and regulatory landscape of human cardiac recovery using single cell multiomics. Macrophages emerged as the most reprogrammed cell type. Deep learning identified the transcription factor RUNX1 as a key regulator of this process. Macrophage-specific Runx1 deletion recapitulated the human cardiac recovery phenotype in a chronic heart failure model. Runx1 deletion reprogrammed macrophages to a reparative phenotype, reduced fibrosis, and promoted cardiomyocyte adaptation. RUNX1 chromatin profiling revealed a conserved regulon that diminished during recovery. Mechanistically, the epigenetic reader BRD4 controlled Runx1 expression in macrophages. Chromatin activity mapping, combined with CRISPR perturbations, identified the precise regulatory element governing Runx1 expression. Therapeutically, small molecule Runx1 inhibition was sufficient to promote cardiac recovery. Our findings uncover a druggable RUNX1 epigenetic mechanism that orchestrates recovery of heart function.

immunology↗

bioRxiv2025

Tissue transcriptomics of endomyocardial biopsies reveals widespread molecular perturbations independent of leukocyte-rich foci in human myocarditis

BackgroundMyocarditis is an inflammatory disease of the myocardium, classically defined and graded by histologic criteria that emphasize immune infiltrates and focal cardiomyocyte injury. The broader transcriptional landscape and intercellular signaling networks underlying human myocarditis, particularly among non-immune cells, remain poorly understood. MethodsWe performed integrated spatial transcriptomic profiling of 38 endomyocardial biopsy (EMBx) specimens using two complementary platforms: 10X Visium FFPE and GeoMx Digital Spatial Profiling (DSP). The cohort included cases of histologically confirmed myocarditis, borderline myocarditis, and controls. For 10X Visium, data was refined by excluding leukocyte-enriched spots and enriching for cardiomyocyte-specific regions based on canonical marker expression. For GeoMx, immunohistochemistry-guided segmentation enabled targeted transcriptomic analysis of disparate cardiac cellular compartments. Differential gene expression was analyzed independently for each platform and subsequently integrated. These results were further leveraged to infer molecular interaction networks and ligand-receptor relationships in myocarditis relative to controls. ResultsBoth platforms revealed widespread gene expression changes consistent with immune activation in myocarditis and borderline myocarditis, particularly within cardiomyocyte-enriched regions. These included upregulation of HLA-A, HLA-DQA1, B2M, and CD74 in myocarditis, consistent with activation of major histocompatibility complex (MHC) class I and II related pathways. Molecular interaction analysis identified STAT1 and ISG15 as likely central immune signaling nodes. Ligand-receptor inference highlighted HLA-A, HLA-E, and HLA-DQA1 as key receptor hubs interacting with immune ligands such as IFNG, CD8A, and several members of the (NK) killer-cell immunoglobulin-like receptor (KIR) family. ConclusionsOur findings demonstrate that human myocarditis is characterized by widespread transcriptional dysregulation beyond immune cell foci, including upregulation of genes typically associated with professional antigen-presenting cells in cardiomyocytes. These insights extend our current understanding of myocarditis pathophysiology and suggest new opportunities for its diagnosis and therapeutic targeting.

immunology↗

bioRxiv2025

Macrophage-like vascular smooth muscle cells dominate early atherosclerosis and are inhibited by targeting iron regulation

Vascular smooth muscle cells (VSMCs) contribute dynamically to atherosclerosis at all stages but the molecular drivers of their phenotypic switching, especially during early plaque development, and how they contribute to plaque progression remain unclear. We performed spatial transcriptomics on 12 human aortic tissues with and without atherosclerotic plaque. Macrophage-like SMCs were the predominant cell-type in the atheroma, displaying high iron storage and dysregulation, confirmed by spatial elemental mapping with nuclear microscopy. The combination of soluble iron and oxidized LDL promoted foamy macrophage-like VSMC cell state transition, while chelation inhibited this switching. In vivo, iron dysregulation induced neointimal thickening and macrophage-like switching in wire-injured Ldlr-/- mice, which was significantly reversed by ferrostatin-1, a ferroptosis inhibitor. These data show how targeting iron regulation modifies the macrophage-like VSMC cell state, and inhibits disease progression in atherogenesis.

genomics↗

bioRxiv2025

Tracing LYVE1+ peritoneal fluid macrophages unveils two paths to resident macrophage repopulation with differing reliance on monocytes

Mouse resident peritoneal macrophages, called large cavity macrophages (LCM), arise from embryonic progenitors that proliferate as mature, CD73+Gata6+ tissue-specialized macrophages. After injury from irradiation or inflammation, monocytes are thought to replenish CD73+Gata6+ LCMs through a CD73-LYVE1+ LCM intermediate. Here, we show that CD73-LYVE1+ LCMs indeed yield Gata6+CD73+ LCMs through integrin-mediated interactions with mesothelial surfaces. CD73-LYVE1+ LCM repopulation of the peritoneum was reliant upon and quantitatively proportional to recruited monocytes. Unexpectedly, fate mapping indicated that only [~]10% of Gata6-dependent LCMs that repopulated the peritoneum after injury depended on the LYVE1+ LCM stage. Further supporting nonoverlapping lifecycles of CD73-LYVE1+ and CD73+Gata6+ LCMs, in mice bearing a paucity of monocytes, Gata6+CD73+ LCMs rebounded after ablative irradiation substantially more efficiently than their presumed LYVE1+ or CD73- LCM upstream precursors. Thus, after inflammatory insult, two temporally parallel pathways, each generating distinct differentiation intermediates with varying dependencies on monocytes, contribute to the replenish hment of Gata6+ resident peritoneal macrophages.

immunology↗

bioRxiv2025

Targeting Modulated Vascular Smooth Muscle Cells in Atherosclerosis via FAP-Directed Immunotherapy

Vascular smooth muscle cell (VSMC) and immune cell diversification play a central role in driving atherosclerotic coronary artery disease (CAD)1-3. However, the molecular mechanisms governing cell state transitions within the neo-intima in human CAD remain poorly understood, and no lipid-independent therapies are currently approved for its treatment. Here, we performed multi-omic single-cell gene expression profiling, epitope mapping, and spatial transcriptomics from 27 human coronary arteries. Our analysis identified fibroblast activation protein (FAP) as a marker of modulated VSMCs within the neo-intima. Genetic lineage tracing in mice confirmed that FAP cells in the plaque originate from medial VSMCs. Additionally, non-invasive positron emission tomography (PET) imaging in patients with CAD revealed focal FAP uptake in atherosclerotic lesions. Spatial transcriptomics further delineated the distinct localization of VSMC and immune cell subsets within plaques, with FAP states enriched in the neo-intima. To explore the therapeutic potential of targeting de-differentiated VSMCs, we developed an anti-FAP bispecific T-cell engager (BiTE) and demonstrated that it significantly reduced the plaque burden in multiple mouse models of atherosclerosis. Collectively, our study provides the first single-cell and spatially resolved map of human CAD, establishes FAP as a marker of modulated smooth muscle cells, and demonstrates the broader potential of immunotherapeutics for lipid independent targets in atherosclerotic CAD.

genomics↗

bioRxiv2024

Defining the cardiac fibroblast secretome in the healthy and infarcted mouse heart

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 hearts (miCF), combining a rapid cell isolation technique with SILAC and click chemistry. In CF, numerous paracrine factors involved in immune homeostasis were identified. Comparing secretome, transcriptome (SLAMseq), and cellular proteome disclosed protein turnover. In miCF at day 5 post-MI, significantly upregulated proteins included SLIT2, FN1, and CRLF1 in mouse and human samples. Comparing the miCF secretome at day 3 and 5 post-MI showed the dynamic nature of protein secretion. Specific in-vivo labeling of miCF proteins via biotin ligase TurboID using the POSTN promotor mirrored the in-vitro data. In summary, we have identified 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.

physiology↗

bioRxiv2024

An Unbiased Proteomic Platform for Activity-based Arginylation Profiling

Protein arginylation is an essential posttranslational modification (PTM) catalyzed by arginyl-tRNA-protein transferase 1 (ATE1) in mammalian systems. Arginylation features a post-translational conjugation of an arginyl to a protein, making it extremely challenging to differentiate from translational arginine residues with the same mass in a protein sequence. Here we present a general ATE1-based arginylation profiling platform for the unbiased discovery of arginylation substrates and their precise modification sites. This method integrates isotopic arginine labeling into an ATE1 assay utilizing biological lysates (ex vivo) rather than live cells, thus eliminating translational bias derived from the ribosomal activity and enabling bona fide arginylation identification using isotopic features. The method has been successfully applied to an array of peptide, protein, cell, patient, and animal tissue samples using 20 {micro}g sample input, with 235 unique arginylation sites revealed from human proteomes. Representative sites were validated and followed up for their biological functions. The developed platform is globally applicable to the aforementioned sample types and therefore paves the way for functional studies of this difficult-to-characterize protein modification.

biochemistry↗

bioRxiv2024

Integrating molecular and clinical variables to predict myocardial recovery

Mechanical unloading and circulatory support with left ventricular assist devices (LVADs) mediate significant myocardial improvement in a subset of advanced heart failure (HF) patients. The clinical and biological phenomena associated with cardiac recovery are under intensive investigation. Left ventricular (LV) apical tissue, alongside clinical data, were collected from HF patients at the time of LVAD implantation (n=208). RNA was isolated and mRNA transcripts were identified through RNA sequencing and confirmed with RT-qPCR. To our knowledge this is the first study to combine transcriptomic and clinical data to derive predictors of myocardial recovery. We used a bioinformatic approach to integrate 59 clinical variables and 22,373 mRNA transcripts at the time of LVAD implantation for the prediction of post-LVAD myocardial recovery defined as LV ejection fraction (LVEF) [≥]40% and LV end-diastolic diameter (LVEDD) [≤]5.9cm, as well as functional and structural LV improvement independently by using LVEF and LVEDD as continuous variables, respectively. To substantiate the predicted variables, we used a multi-model approach with logistic and linear regressions. Combining RNA and clinical data resulted in a gradient boosted model with 80 features achieving an AUC of 0.731{+/-}0.15 for predicting myocardial recovery. Variables associated with myocardial recovery from a clinical standpoint included HF duration, pre-LVAD LVEF, LVEDD, and HF pharmacologic therapy, and LRRN4CL (ligand binding and programmed cell death) from a biological standpoint. Our findings could have diagnostic, prognostic, and therapeutic implications for advanced HF patients, and inform the care of the broader HF population. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/589326v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@17f0503org.highwire.dtl.DTLVardef@2231c1org.highwire.dtl.DTLVardef@f0ac56org.highwire.dtl.DTLVardef@c278f3_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

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 Ccr2crERT2Rosa26LSL-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-IIhi 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.

immunology↗

bioRxiv2022

Defining Cardiac Recovery at Single Cell Resolution

Recovery of cardiac function is the ultimate goal of heart failure therapy. Unfortunately, cardiac recovery remains a rare and poorly understood phemomenon. Herein, we performed single nucleus RNA-sequencing (snRNA-seq) from non-diseased donors and heart failure patients. By comparing patients who recovered LV systolic function following LV assist device implantation to those who did not recover and donors, we defined the cellular and transcriptional landscape and predictors of cardiac recovery. We sequenced 40 hearts and recovered 185,881 nuclei with 13 distinct cell types. Using pseudobulk differential expression analysis to explicate cell specific signatures of cardiac recovery, we observed that recovered cardiomyocytes do not revert to a normal state, and instead, retain transcriptional signatures observed in heart failure. Macrophages and fibroblasts displayed the strongest signatures of recovery. While some evidence of reversion to a normal state was observed, many heart failure associated genes remained elevated and recovery signatures were predominately indicative of a biological state that was unique from donor and heart failure conditions. Acquisition of recovery states was associated with improved LV systolic function. Pro-inflammatory macrophages and inflammatory signaling in fibroblasts were identified as negative predictors of recovery. We identified downregulation of RUNX1 transcriptional activity in macrophages and fibroblasts as a central event associated with and predictive of cardiac recovery. In silico perturbation of RUNX1 in macrophages and fibroblasts recapitulated the transcriptional state of cardiac recovery. This prediction was corroborated in a mouse model of cardiac recovery mediated by BRD4 inhibition where we observed a decrease in macrophage and fibroblast Runx1 expression, diminished chromatin accessibility within peaks linked to the Runx1 locus, and acquisition of recovery signatures. These findings suggest that cardiac recovery is a unique biological state and identify RUNX1 as a possible therapeutic target to facilitate cardiac recovery.

genomics↗

bioRxiv2022

Hypoxia Sensing in Resident Cardiac Macrophages Regulates Monocyte-Derived Macrophage Fate Specification following Myocardial Infarction

Myocardial infarction initiates cardiac remodeling and is central to heart failure pathogenesis. Following myocardial ischemia reperfusion injury, monocytes enter the heart and differentiate into diverse subpopulations of macrophages. The mechanisms and dynamics of monocyte differentiation within this context are unknown. We investigated the role of macrophage hypoxia sensing on monocyte differentiation following reperfused myocardial infarction. We show that deletion of Hif1, a hypoxia response transcription factor, in resident cardiac macrophages led to increased remodeling and overrepresentation of a macrophage subset marked by arginase 1 (Arg1) expression. Arg1+ macrophages displayed an inflammatory gene signature and were predicted to represent an intermediate state within the monocyte differentiation cascade. Lineage tracing of Arg1+ macrophages revealed the existence of a monocyte differentiation trajectory consisting of multiple transcriptionally distinct macrophage states. We further showed that deletion of Hif1 in resident cardiac macrophages resulted in arrested progression through this trajectory and accumulation of an inflammatory intermediate state marked by persistent Arg1 expression. Collectively, our findings unveil distinct trajectories of monocyte differentiation and identify hypoxia sensing as an important determinant of monocyte differentiation following myocardial infarction.

immunology↗

bioRxiv2021

Single Cell Transcriptomics Reveals Cell Type Specific Diversification in Human Heart Failure

Heart failure represents a major cause of morbidity and mortality worldwide. Single cell transcriptomics have revolutionized our understanding of cell composition and associated gene expression across human tissues. Through integrated analysis of single cell and single nucleus RNA sequencing data generated from 45 individuals, we define the cell composition of the healthy and failing human heart. We identify cell specific transcriptional signatures of heart failure and reveal the emergence of disease associated cell states. Intriguingly, cardiomyocytes converge towards a common disease associated cell state, while fibroblasts and myeloid cells undergo dramatic diversification. Endothelial cells and pericytes display global transcriptional shifts without changes in cell complexity. Collectively, our findings provide a comprehensive analysis of the cellular and transcriptomic landscape of human heart failure, identify cell type specific transcriptional programs and states associated with disease, and establish a valuable resource for the investigation of human heart failure.

genomics↗