Biology subjects

Lee, C. Y.

Publications and source records attributed to Lee, C. Y..

At least 19 recordsLinked to original sources

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

Cell-type targeted CRISPR/Cas9 Clock knockdown in mouse VTA dopamine neurons alter sleep, behavior, and cellular excitability

Bipolar disorder (BD) is a severe psychiatric disease characterized by recurrent mania, depression, and circadian rhythm disruption. Among circadian regulators implicated in mood-related dysfunction, Clock has emerged as a particularly strong mechanistic candidate. However, cell type-specific functions of Clock within mood-relevant circuits remain incompletely defined. Here, we developed and applied a Cre-dependent AAV-SaCas9 gene-editing strategy to disrupt Clock selectively in ventral tegmental area dopamine neurons. We first established a rapid in vitro screening pipeline for guide RNA selection that accurately predicted in vivo editing efficiency. We then targeted Clock in vivo using a single AAV-based editing strategy and observed robust titer-dependent reduction of Clock expression, by targeted sequencing, in situ hybridization, and immunohistochemistry. We assessed the functional consequences of Clock disruption across analysis levels, including a behavioral battery, circadian and sleep-wake measurements using EEG and EMG, and electrophysiological recordings. These results establish a practical framework for rapid, cell-type-specific disruption of candidate psychiatric risk genes and provide a mechanistically grounded model for investigating how loss of Clock function in mesolimbic dopaminergic circuits contributes to BD-relevant phenotypes.

neuroscience↗

bioRxiv2026

Landscape-scale navigation unlocks antibody CDR structural logic for AI-guided rescue and therapeutic optimization

While AI offers transformative potential for therapeutic antibody design, the lack of ground-truth data fundamentally constrains our ability to model the epistatic topology of fitness landscapes. Here, we establish a high-throughput workflow to characterize tens of thousands of antibody variants per week with gold-standard biophysical precision. By combinatorially assembling functional variants from deep mutational scanning, we charted antibody fitness landscapes comprising over 17,000 data points, which revealed an extremely rugged, non-navigable epistatic topology. Yet, navigating at this unprecedented scale enabled the discovery of rare peak clusters exhibiting simultaneous enhancements in affinity and productivity. Strikingly, ProteinMPNN predicted the CDR-dependent productivity landscape with remarkable accuracy, suggesting that sequence-structure compatibility within CDRs gates cellular productivity. This insight enabled a structure-guided rescue strategy combining AlphaFold3 and ProteinMPNN, which successfully restored the cellular productivity of high-affinity, low-productivity clones via single amino acid substitutions. Two elite variants drawn directly from peak clusters further demonstrated 20- to 100-fold in vivo efficacy gains in a murine psoriasis model. Our findings establish CDR structural fitness as a fundamental determinant of antibody cellular productivity and validate landscape-scale navigation as a powerful framework for therapeutic antibody optimization.

bioengineering↗

bioRxiv2026

Heterogeneous and specific localization of mRNAs at dendritic spine and its dependence on microtubule entry and kinesin motor

Local mRNA translation near neuronal synapses is crucial for structural plasticity during brain development and memory formation. Whereas mRNAs are transported from soma to dendrites as individual ribonucleoprotein (RNP) granules, how do they subsequently localize at synapses is unclear. In particular, whether different dendritic mRNAs might display differential synaptic localization and interact with specific postsynaptic proteins remains unexplored. Here we found that two well-known dendritic mRNAs, Actb and Camk2a, are targeted to different subdomains of dendritic spines and delivered to different spine populations after synaptic stimulation. Surprisingly, the induced mRNA localization to dendritic spines is associated with microtubule (MT) entry and specifically requires the MT-associated motor KIF5A. Proximity-labelling proteomics further identifies distinct postsynaptic proteins enriched by Actb and Camk2a, from which we uncover the cytoskeletal protein Septin7 to be co-localized with the two mRNAs at different subdomains of dendritic spines. Our study reveals an unexpectedly specific mRNA localization mechanism at synapses and demonstrates proximity-labelling as a useful approach to map their synaptic partners.

neuroscience↗

bioRxiv2026

Decoding Ethiopia's unique and structurally divergent Plasmodium falciparum populations using genomics

Previous genome-wide studies suggest that Ethiopian Plasmodium falciparum parasites are unique and structurally divergent from sub-Saharan African populations but were limited by small sample sizes. The emergence of molecular markers associated with reduced artemisinin susceptibility in northern Ethiopia, and the drug pressures created by sympatric P. falciparum and P. vivax, may have fostered a distinct and permissive genetic background for the emergence and spread of multidrug resistant parasites. To characterise parasite population structure and evolutionary dynamics in this setting, we generated whole-genome sequencing data for 163 P. falciparum isolates from southern Ethiopia (2017-2021) and integrated these with 854 isolates from across sub-Saharan Africa. Ethiopian parasites exhibited markedly reduced diversity, highly conserved genomes, and distinct admixture ancestry. Near-fixation of chloroquine and antifolate associated resistance markers, potentially driven by P. vivax co-circulation, suggests persistent drug-related selection pressures. We identified a previously undescribed deletion in the pfmdr1 5' UTR that is common in Ethiopia and potentially widespread across African populations. Although clinically relevant pfk13 variants have emerged in northern Ethiopia, these were not detected in southern Ethiopia. However, strong genetic connectivity between regions indicates the potential for rapid spread of resistance and is therefore important for public health policy and practice.

genomics↗

bioRxiv2025

Intestinal challenges shape the polarisation of protective dural memory CD4 T cells

The meninges house several innate and adaptive immune cell populations1-3. These predominantly localise within the dura mater and include gut-derived IgA-secreting plasma cells4. Whether T cell adaptive memory in the dura is similarly linked to the gut is currently unknown. Here we show that dural CD4 T cell polarisation to a T helper (Th) 1, Th2 and Th17 state is determined by the nature of the immunological challenge encountered in the gastrointestinal tract. We find that intestinally polarised CD4 T cells seed to the dura in a CXCR6-CXCL16-dependent manner, express tissue-residency markers and are long-lived. Functionally, these orally-primed dural CD4 T are capable of a rapid antigen-specific recall response that limits pathogen spread into the brain following intravenous re-challenge. Our work reveals how linked intestinal and dural immunity enables the central nervous system to accrue immunological memory of gut microbes, the most likely source of life-threatening bloodborne pathogens.

immunology↗

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

β-arrestin recruitment facilitates a direct association with G proteins

G protein-coupled receptors (GPCRs) are targets for almost a third of all FDA-approved drugs. GPCRs are known to signal through both heterotrimeric G proteins and {beta}-arrestins. Traditionally these pathways were viewed as largely separable, with G proteins primarily initiating downstream signaling while {beta}-arrestins modulate receptor trafficking and desensitization in addition to regulating their own signaling events. Recent studies suggest an integrated role of G proteins and {beta}-arrestins in GPCR signaling, however the cellular and biochemical requirements for G protein: {beta}-arrestin interactions remain unclear. Here we show that G proteins and {beta}-arrestins can directly interact. Through utilization of {beta}-arrestin-biased receptors and artificially enforced {beta}-arrestin relocalization, we demonstrate that recruitment of {beta}-arrestin to the plasma membrane is sufficient to interact with the G protein Gi. Using purified proteins, we show that Gi directly interacts with {beta}-arrestin. In addition, we find that Gi family members differ in their degree of association with {beta}-arrestin, and that a large degree of this selectivity resides within the alpha helical domain of Gi. These findings delineate the cellular and biochemical conditions that drive direct interactions between G proteins and {beta}-arrestins and illuminate the molecular basis for how they work together to effect GPCR signaling.

biochemistry↗

bioRxiv2025

Variant characterization in the intrinsically disordered human proteome

Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in the characterization of missense variants in folded protein regions. However, 37% of all annotated missense variants reside in 25% of the proteome that is intrinsically disordered, lacking positional sequence conservation and stable structures. To significantly advance variant effect prediction in disordered protein regions, we combined sequence pattern searches with AlphaFold and experiments to structurally annotate 1,300 protein-protein interactions with interfaces mediated by short disordered motifs binding to folded domains in partner proteins. These interfaces were selected based on their overlap with uncertain missense variants enabling reliable prediction of deleterious effects of 1,187 uncertain variants in disordered protein regions. Extensive experimental efforts validate predicted interfaces and deleterious variant effects that were predicted as benign by AlphaMissense. This study demonstrates how critical structural information on protein interaction interfaces is for variant effect prediction especially in disordered protein regions and provides a clear avenue towards its system-wide implementation.

systems biology↗

bioRxiv2024

Single-cell multi-omics reveals tumor microenvironment factors underlying poor immunotherapy responses in ALK-positive lung cancer

Anaplastic lymphoma kinase (ALK) rearrangement is a major oncogenic driver in non-small cell lung cancer (NSCLC). While ALK tyrosine kinase inhibitors have shown promising therapeutic effects, overcoming resistance with immunotherapy becomes necessary when resistance develops. However, various clinical trials have revealed that their efficacies remain limited. To investigate the tumor microenvironment (TME) factors contributing to poor immune checkpoint blockade responses in ALK-positive patients, we performed single-cell RNA and ATAC sequencing on lung adenocarcinoma (LUAD) tumors with and without ALK rearrangements. Integrative analysis with additional public LUAD cohorts revealed distinct immune landscapes in ALK-positive tumors, marked by enriched innate immunity and depleted adaptive immunity. ALK-positive malignant cells exhibit higher stemness and aggressive phenotype. Tumor-associated macrophages (TAMs) in these tumors predominantly maintain pro-tumoral M2-like states, reinforcing immune suppression. B cells show reduced immune reactivity and impaired tertiary lymphoid structure formation, while CD8+ T cells display bystander-like signatures and reduced tumor reactivity. Single-cell chromatin accessibility profiles combined with regulatory network analysis suggest that differences in transcription factor activities, rather than chromatin accessibility, may underlie T cell dysfunction. These findings provide insights into the immunosuppressive TME of ALK-positive LUAD, potentially explaining the failure of recent immunotherapy trials and highlighting targets for improving efficacy.

cancer biology↗

bioRxiv2024

Modeling epithelial homeostasis and perturbation in three-dimensional human esophageal organoids

BackgroundEsophageal organoids from a variety of pathologies including cancer are grown in Advanced Dulbeccos Modified Eagle Medium-Nutrient Mixture F12 (hereafter ADF). However, the currently available ADF-based formulations are suboptimal for normal human esophageal organoids, limiting the ability to compare normal esophageal organoids with those representing a given disease state. MethodsWe have utilized immortalized normal human esophageal epithelial cell (keratinocyte) lines EPC1 and EPC2 and endoscopic normal esophageal biopsies to generate three-dimensional (3D) organoids. To optimize ADF-based medium, we evaluated the requirement of exogenous epidermal growth factor (EGF) and inhibition of transforming growth factor-(TGF)-{beta} receptor-mediated signaling, both key regulators of proliferation of human esophageal keratinocytes. We have modeled human esophageal epithelial pathology by stimulating esophageal 3D organoids with interleukin (IL)-13, an inflammatory cytokine, or UAB30, a novel pharmacological activator of retinoic acid signaling. ResultsThe formation of normal human esophageal 3D organoids was limited by excessive EGF and intrinsic TGF{beta} receptor-mediated signaling. In optimized HOME0, normal human esophageal organoid formation was improved, whereas IL-13 and UAB30 induced epithelial changes reminiscent of basal cell hyperplasia, a common histopathologic feature in broad esophageal disease conditions including eosinophilic esophagitis. Conclusions: HOME0 allows modeling of the homeostatic differentiation gradient and perturbation of the human esophageal epithelium while permitting a comparison of organoids from mice and other organs grown in ADF-based media.

cell biology↗

bioRxiv2024

An in silico framework for the rational design of vaginal probiotic therapy

Bacterial vaginosis is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop an in silico framework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This framework highlighted the importance of resident microbial species on the efficacy of probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) and Lactobacillus spp. with candidate probiotic strains as a necessary selection criteria. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of the in silico platform. Results from the model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.

microbiology↗

bioRxiv2024

Single-cell genomics and regulatory networks for 388 human brains

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized [~]250 disease-risk genes and drug targets with associated cell types. Summary Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/585576v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@70b24org.highwire.dtl.DTLVardef@6c9eddorg.highwire.dtl.DTLVardef@131fae2org.highwire.dtl.DTLVardef@4e0f1e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

Rapid establishment of a tumor-retained state curtails the contribution of conventional NK cells to anti-tumor immunity in solid cancers

Immune cell dysfunction within the tumor microenvironment undermines the control of cancer progression. NK cells play critical roles in limiting early tumor growth and metastatic disease, however, established cancers contain a phenotypically distinct, tumor-specific NK cell compartment. The temporal dynamics, mechanistic underpinning and functional significance of this tumor NK pool remains incompletely understood. To address this, we exploited photo-labeling, combined with longitudinal transcriptomic and cellular analyses, to interrogate the fate of NK cells after tumor entry. In multiple murine cancer models we reveal that conventional NK cells are continuously recruited into tumors, but rapidly adopt a distinct phenotypic state with features associated with tissue-residency and complete loss of effector functions (including chemokine and cytokine production and cytotoxicity), within 48-72 hrs of entering the tumor. Depletion of NK cells from established tumors did not alter tumor growth, indicating that intratumoral NK cells cease to actively contribute to anti- tumor responses. Furthermore, comparable NK populations were identified in human colorectal cancers, confirming translational relevance and raising the possibility that interventions to reactivate NK cells within tissues may boost anti-tumor immunity in established cancers. Indeed, administration of IL-15:IL-15Ra complexes prevented the loss of NK cell function and improved tumor control, generating intratumoral NK cells with both enhanced tissue-residency characteristics and effector function. Collectively, our data reveals the fate of cNK cells after recruitment into tumors and provides insight into how intratumoral NK cell functions may be revived. SummaryConventional NK cells recruited from the circulation rapidly establish a tissue-resident phenotype defined by impaired cytotoxicity and chemokine production after tumor entry; administration of IL- 15:IL-15R complexes further promotes this tissue-residency programme but maintains core NK cell effector functions within the tumor.

immunology↗

bioRxiv2023

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation

Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. We thoroughly assessed AlphaFold-Multimer accuracy for structure prediction of interactions involving folded domains binding to short linear motifs from the ELM database. The structure predictions were highly sensitive but not very specific when using small protein fragments. Sensitivity decreased substantially when using long protein fragments or full length proteins with intrinsically disordered regions. We delineated a fragmentation strategy to optimize sensitivity and applied it to interactions between proteins associated with neurodevelopmental disorders. This enabled prediction of highly confident and likely disease-related novel interfaces, but also resulted in many high scoring false positive predictions. Experiments supported predicted interfaces between CREBZF-HCFC1, FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

systems biology↗

bioRxiv2023

Characterizing dysregulations via cell-cell communications in Alzheimer's brains using single-cell transcriptomes

Alzheimers disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing (snRNA-seq) in the human prefrontal cortex (PFC) from 23 AD samples and 13 controls to investigate cell-to-cell communication (C2C) in healthy brains and their perturbations in AD. Specifically, we first performed broad communication pattern analyses and discovered the inter-mixing of cell types and signaling pathways in AD brains. Secondly, we performed cell-type- centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGF{beta}, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type- specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, connecting signaling to genetic differences manifested in AD. Author SummaryAlzheimers is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The complex interplay of signaling genes suggests cells act in concert with other cells through cell-to-cell communication. Utilizing the recent advances in single-cell sequencing, we investigated dysregulated ligand-receptor gene pairs in the disease at the cell-type resolution. Specifically, our broad communication pattern analyses revealed the inter-mixing of cell types and signaling pathways in AD brains. Our cell-type-centric analysis found that excitatory neurons in AD have significantly increased their communications with inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. With a signaling-centric view, we show that CSF, TGF{beta}, and CX3C pathways are significantly dysregulated in their signaling to the cell type microglia/PVM while the WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, performing a cell-to-cell communication analysis better explains the genetic differences manifested in Alzheimers.

bioinformatics↗

bioRxiv2023

Time-, tissue- and treatment-associated heterogeneity in tumour-residing migratory DCs

Tumour dendritic cells (DCs) internalise antigen and upregulate CCR7, which directs their migration to tumour-draining lymph nodes (dLN). CCR7 expression is coupled to a maturation programme enriched in regulatory molecule expression, including PD-L1, termed mRegDC. However, the spatio- temporal dynamics and role of mRegDCs in anti-tumour immune responses remain unclear. Using photoconvertible mice to precisely track DC migration, we found that mRegDCs were the dominant DC population arriving in the dLN, but a subset remained tumour-resident despite CCR7 expression. These tumour-retained mRegDCs were phenotypically and transcriptionally distinct from their dLN counterparts and were heterogeneous. Specifically, they demonstrated a progressive reduction in the expression of antigen presentation and pro-inflammatory transcripts with more prolonged tumour dwell-time. Tumour mRegDCs spatially co-localised with PD-1+CD8+ T cells in human and murine solid tumours. Following anti-PD-L1 treatment, tumour-residing mRegDCs adopted a state enriched in lymphocyte stimulatory molecules, including OX40L, which was capable of augmenting anti- tumour cytolytic activity. Altogether, these data uncover previously unappreciated heterogeneity in mRegDCs that may underpin a variable capacity to support intratumoural cytotoxic T cells, and provide insights into their role in cancer immunotherapy.

immunology↗

bioRxiv2023

Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis

Chronic inflammation and tissue fibrosis are common stress responses that worsen organ function, yet the molecular mechanisms governing their crosstalk are poorly understood. In diseased organs, stress-induced changes in gene expression fuel maladaptive cell state transitions and pathological interaction between diverse cellular compartments. Although chronic fibroblast activation worsens dysfunction of lung, liver, kidney, and heart, and exacerbates many cancers, the stress-sensing mechanisms initiating the transcriptional activation of fibroblasts are not well understood. Here, we show that conditional deletion of the transcription co-activator Brd4 in Cx3cr1-positive myeloid cells ameliorates heart failure and is associated with a dramatic reduction in fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancy in vivo in Cx3cr1-positive cells identified a large enhancer proximal to Interleukin-1 beta (Il1b), and a series of CRISPR deletions revealed the precise stress-dependent regulatory element that controlled expression of Il1b in disease. Secreted IL1B functioned non-cell autonomously to activate a p65/RELA-dependent enhancer near the transcription factor MEOX1, resulting in a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL1B neutralization prevented stress-induced expression of MEOX1, inhibited fibroblast activation, and improved cardiac function in heart failure. The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B provides new therapeutic strategies for heart disease and other disorders of chronic inflammation and maladaptive tissue remodeling.

molecular biology↗