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Cited by 140Cardiac Fibrosis and RemodelingCongenital heart defects researchGenomics and Chromatin Dynamics

Chromatin remodelling drives immune cell–fibroblast communication in heart failure

Open access
Alexanian, Michael, Padmanabhan, Arun, Nishino, Tomohiro, Travers, Joshua G., Ye, Lin, Pelonero, Angelo, Lee, Clara Youngna, Sadagopan, Nandhini +22 more·2024·Nature
DOI 10.1038/s41586-024-08085-6PMC PMC11698514
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Abstract

Chronic inflammation and tissue fibrosis are common responses that worsen organ function, yet the molecular mechanisms governing their cross-talk are poorly understood. In diseased organs, stress-induced gene expression changes fuel maladaptive cell state transitions1 and pathological interaction between cellular compartments. Although chronic fibroblast activation worsens dysfunction in the lungs, liver, kidneys and heart, and exacerbates many cancers2, the stress-sensing mechanisms initiating transcriptional activation of fibroblasts are poorly understood. Here we show that conditional deletion of the transcriptional co-activator Brd4 in infiltrating Cx3cr1+ macrophages ameliorates heart failure in mice and significantly reduces fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancy in vivo in Cx3cr1+ cells identified a large enhancer proximal to interleukin-1β (IL-1β, encoded by Il1b), and a series of CRISPR-based deletions revealed the precise stress-dependent regulatory element that controls Il1b expression. Secreted IL-1β activated a fibroblast RELA-dependent (also known as p65) enhancer near the transcription factor MEOX1, resulting in a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL-1β neutralization improved cardiac function and tissue fibrosis in heart failure. Systemic IL-1β inhibition or targeted Il1b deletion in Cx3cr1+ cells prevented stress-induced Meox1 expression and fibroblast activation. The elucidation of BRD4-dependent cross-talk between a specific immune cell subset and fibroblasts through IL-1β reveals how inflammation drives profibrotic cell states and supports strategies that modulate this process in heart disease and other chronic inflammatory disorders featuring tissue remodelling. Conditional deletion of the transcriptional co-activator Brd4 in infiltrating Cx3cr1+ mouse macrophages ameliorates heart failure and substantially reduces fibroblast activation.

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Crossref · 10.1038/s41586-024-08085-6

Cites

55 of 55 references verified0 citation errors · 0 not checkable

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Nothing to recompute.

Claims the paper makes

42 of 45 cited sources checked · 28 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    JQ1-associated transcriptional changes in cardiomyocytes are modest compared with other cardiac cell populations.

    “Given our observation that transcriptional changes associated with JQ1 in the cardiomyocyte (CM) compartment are modest compared to other cardiac cell populations4,11”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [4] Alexanian, M. et al. A transcriptional switch governs fibroblast activation in heart disease. Nature 595, 438–443 (2021). source
    • cites [11] Padmanabhan, A. et al. BRD4 (bromodomain-containing protein 4) interacts with GATA4 (GATA binding protein 4) to govern mitochondrial homeostasis in adult cardiomyocytes. Circulation 142, 2338–2355 (2020). source

      The Results section reports that JQ1-treated sham-operated mouse hearts showed no dramatic transcriptional changes. The Discussion suggests that JQ1’s dominant targets in heart failure may be non-cardiomyocytes, but the paper does not directly compare JQ1-associated transcriptional changes in cardiomyocytes with those in other cardiac cell populations. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
  • Findingown data

    Flow cytometry at day 7 after TAC showed no significant change in infiltrated immune cell, monocyte or macrophage numbers after JQ1.

    “Flow cytometry analyses of cardiac tissue at day 7 post-TAC, a time point associated with immune cell expansion23,24, revealed no significant changes in the number of infiltrated immune cells, monocytes, or macrophages following JQ1 (Extended Data Fig. 1H,I).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [23] Patel, B. et al. CCR2+ monocyte-derived infiltrating macrophages are required for adverse cardiac remodeling during pressure overload. JACC Basic Transl. Sci. 3, 230–244 (2018). source
    • cites [24] Revelo, X. S. et al. Cardiac resident macrophages prevent fibrosis and stimulate angiogenesis. Circ. Res. 129, 1086–1101 (2021). source
  • Findingown data

    Myeloid clusters 1 and 5 highly expressed Ccr2, a marker of monocyte-derived macrophages that enter from the circulation.

    “Clusters 1 and 5 had high expression of Ccr2, a marker of monocyte-derived macrophages that infiltrate from the circulation17-19 (Fig. 1J and Extended Data Fig. 1C-E).”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [17] Nahrendorf, M. et al. The healing myocardium sequentially mobilizes two monocyte subsets with divergent and complementary functions. J. Exp. Med. 204, 3037–3047 (2007). source

      The Results section on chemokine-mediated recruitment (page unavailable) reports that circulating Ly-6Chi monocytes selectively express CCR2 and that their recruitment into infarcted myocardium depends on it. The paper distinguishes these monocytes from macrophages, however, and the cited passages do not establish CCR2 as a marker specifically of monocyte-derived macrophages. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [18] Epelman, S. et al. Embryonic and adult-derived resident cardiac macrophages are maintained through distinct mechanisms at steady state and during inflammation. Immunity 40, 91–104 (2014). source
    • cites [19] Bajpai, G. et al. Tissue resident CCR2− and CCR2+ cardiac macrophages differentially orchestrate monocyte recruitment and fate specification following myocardial injury. Circ. Res. 124, 263–278 (2019). source
  • Premisecitation

    BRD4 has specific importance in aspects of heart failure pathogenesis.

    “We previously showed the specific importance of BRD4 in aspects of heart failure pathogenesis4,25.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [4] Alexanian, M. et al. A transcriptional switch governs fibroblast activation in heart disease. Nature 595, 438–443 (2021). source
    • cites [25] Stratton, M. S. et al. Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation. Circ. Res. 125, 662–677 (2019). source
  • Findingown data

    Among cardiac cell clusters, fibroblasts showed the strongest enrichment for genes whose expression tracked cardiac function.

    “As expected4, fibroblasts had the highest enrichment of genes whose expression significantly correlated with cardiac function (Fig. 1E).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [4] Alexanian, M. et al. A transcriptional switch governs fibroblast activation in heart disease. Nature 595, 438–443 (2021). source

      The ‘Chromatin state and cardiac function’ section reports correlations between cardiac function and fibroblast enhancer accessibility, not gene expression. The ‘Transcriptional plasticity of fibroblasts’ section describes fibroblast transcriptomic changes, but our copy does not show that fibroblasts had the highest enrichment of genes whose expression significantly correlated with cardiac function. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 12
  • May combine two claims. 42

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    BET proteins act as transcriptional co-activators, and their inhibition is linked to protection in heart failure models.

    “As BET proteins are transcriptional co-activators and their inhibition is associated with protection in heart failure models6-8”
    Quote in the paperSubstantial claim3 of 3 sources checked
    • cites [6] Anand, P. et al. BET bromodomains mediate transcriptional pause release in heart failure. Cell 154, 569–582 (2013). source
    • cites [7] Spiltoir, J. I. et al. BET acetyl-lysine binding proteins control pathological cardiac hypertrophy. J. Mol. Cell. Cardiol. 63, 175–179 (2013). source
    • cites [8] Duan, Q. et al. BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aah5084 (2017). source

  • May combine two claims.

    Findingown data

    Resident macrophage markers Lyve1, Folr2 and Timd4 were enriched in myeloid clusters 4 and 6, with Lyve1 and Folr2 also marking clusters 0, 2 and 3.

    “Expression of the resident macrophage markers15,16 Lyve1, Folr2 and Timd4 were enriched in clusters 4 and 6, with Lyve1 and Folr2 also marking clusters 0, 2 and 3 (Fig. 1J and Extended Data Fig. 1C-E).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [15] Dick, S. A. et al. Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction. Nat. Immunol. 20, 29–39 (2019). source

      The Discussion identifies TIMD4 and LYVE1 as resident cardiac macrophage markers. The Results section on recruited cardiac macrophage plasticity lists Folr2 among genes associated with mature macrophages, but does not specifically establish it as a resident marker. The cluster-enrichment pattern is presented as the citing paper’s own figure result, not as a finding attributed to this source. (LLM, conf=0.83)

      Experimental — accuracy not yet measured
    • cites [16] Dick, S. A. et al. Three tissue resident macrophage subsets coexist across organs with conserved origins and life cycles. Sci. Immunol. 7, eabf7777 (2022). source

  • Classified as probably not a substantial claim.

    Premisecitation

    Myeloid cells can amplify the stress response in a non-cell autonomous manner through secreted factors.

    “Given the ability of myeloid cells to act as non-cell autonomous amplifiers of the stress-response through secreted factors12-14”
    Quote in the paperSubstantial claim1 of 3 sources checked
    • cites [12] Korf-Klingebiel, M. et al. Myeloid-derived growth factor protects against pressure overload-induced heart failure by preserving sarco/endoplasmic reticulum Ca2+-ATPase expression in cardiomyocytes. Circulation 144, 1227–1240 (2021). source
    • cites [13] Reboll, M. R. et al. EMC10 (endoplasmic reticulum membrane protein complex subunit 10) is a bone marrow-derived angiogenic growth factor promoting tissue repair after myocardial infarction. Circulation 136, 1809–1823 (2017). source
    • cites [14] Dobaczewski, M., Xia, Y., Bujak, M., Gonzalez-Quesada, C. & Frangogiannis, N. G. CCR5 signaling suppresses inflammation and reduces adverse remodeling of the infarcted heart, mediating recruitment of regulatory T cells. Am. J. Pathol. 176, 2177–2187 (2010). source

      The Discussion describes inflammatory monocytes secreting cytokines and explains how inflammatory mediators may affect cardiomyocytes and worsen remodeling after myocardial infarction. This supports an effect on other cells through secreted factors, but the paper does not establish that myeloid cells amplify a general stress response. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Interpretationcitation

    Because Cx3cr1 is not expressed in fibroblasts and Brd4 is not deleted in that population, the fibroblast gene expression changes reflect a non-cell autonomous effect.

    “As Cx3cr1 is not expressed in fibroblasts26 (Extended Data Fig. 1A), and therefore Brd4 is not deleted in this cell population (Extended Data Figs. 2B and 3B-D), the fibroblast gene expression changes reflect a non-cell autonomous effect.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [26] Heidt, T. et al. Differential contribution of monocytes to heart macrophages in steady-state and after myocardial infarction. Circ. Res. 115, 284–295 (2014). source

  • May combine two claims.

    Findingown data

    Motif analysis of these regions revealed enrichment for profibrotic TFs such as SMADs and MEOX1, and for RUNX1 and REL, regulators of proinflammatory responses.

    “Motif analysis of these regions revealed enrichment for TFs critical for profibrotic responses in heart failure, such as SMADs27 and MEOX14, as well as RUNX1 and REL, regulators of proinflammatory responses27 (Extended Data Fig. 4D).”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [27] Hanna, A., Humeres, C. & Frangogiannis, N. G. The role of Smad signaling cascades in cardiac fibrosis. Cell. Signal. 77, 109826 (2021). source

      The ‘Smad signaling cascades in fibroblasts’ section (page not provided) describes Smad3 as a central signal promoting cardiac myofibroblast conversion and extracellular-matrix production, supporting the profibrotic role attributed to SMADs. The passages retrieved for RUNX1 and REL do not establish their roles in proinflammatory responses. The motif enrichment is presented as the citing paper’s own analysis, and MEOX1 carries a different citation. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [4] Alexanian, M. et al. A transcriptional switch governs fibroblast activation in heart disease. Nature 595, 438–443 (2021). source

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    In human disease, stress-induced signaling converges in the nucleus, where chromatin receives, processes and amplifies upstream inputs, leading to altered gene expression, maladaptive cell state transitions and organ dysfunction.

    “In human disease, stress-induced signaling converges in the nucleus, where chromatin receives, processes, and amplifies upstream inputs, ultimately leading to altered gene expression, maladaptive cell state transitions and organ dysfunction1.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [1] Badeaux, A. I. & Shi, Y. Emerging roles for chromatin as a signal integration and storage platform. Nat. Rev. Mol. Cell Biol. 14, 211–224 (2013). source

      The Introduction (page not available) describes signaling reaching the nucleus and changing gene expression, while “Signal integration on histones” describes chromatin integrating multiple inputs into a transcriptional response. The Conclusion and perspectives links epigenetic signaling to disease and gives cancer-cell state changes as an example. It does not establish the full claimed chain from stress-induced signaling through chromatin amplification to organ dysfunction; its account of integration is partly speculative. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Meox1 transcription is sensitive to BET inhibition, confirmed in human cardiac fibroblasts treated with IL1B and TGFB.

    “As our previous work demonstrated that Meox1 transcription is sensitive to BET inhibition4, which we confirmed in human cardiac fibroblasts treated with IL1B and TGFB (Extended Data Fig. 9Q)”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [4] Alexanian, M. et al. A transcriptional switch governs fibroblast activation in heart disease. Nature 595, 438–443 (2021). source

  • May combine two claims.

    Findingown data

    Single-cell RNA sequencing of non-cardiomyocytes from mouse hearts captured 41,626 cells and resolved 20 transcriptional clusters, including fibroblasts, myeloid cells, endothelial cells and pericytes.

    “We captured 41,626 cells from Sham, TAC vehicle-treated (TAC), or TAC JQ1-treated (TAC JQ1) hearts, and identified 20 transcriptional clusters, including fibroblasts (Dcn+), myeloid cells (Lyz2+), endothelial cells (Fabp4+) and pericytes (Abcc9+) (Fig. 1C and Extended Data Fig. 1A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Il1b expression was enriched in cluster 4 and was sensitive to cardiac stress and Brd4 deletion in Cx3cr1-positive cells.

    “The expression of the proinflammatory cytokine Il1b (Interleukin-1β) was particularly interesting as it was enriched in cluster 4 (Fig. 2I,J) and sensitive to cardiac stress and Brd4 deletion in Cx3cr1-positive cells (Fig. 2K).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Top cluster 4 marker genes included MHC class 2 glycoproteins along with Il1b and Ccr2, both enriched in cluster 4 even relative to cluster 3.

    “Among the top cluster 4 marker genes were several encoding the major histocompatibility complex (MHC) class 2 glycoproteins (also present in cluster 3) along with Il1b and Ccr2, both of which were enriched in cluster 4, even when compared to cluster 3 (Fig. 2G).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the myeloid compartment, 22 genes were anti-correlated and 24 were positively correlated with cardiac function at a stringent threshold.

    “We ranked all genes expressed in the myeloid compartment by their correlation score using a stringent statistical threshold (p < 1e−6, corresponding to a correlation score < ± 5) and identified 22 anti-correlated (Fig. 1F) and 24 positively correlated (Fig. 1F and Extended Data Fig. 1B) with cardiac function.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cluster 4 expanded from Sham to TAC (9.3% to 14.9%) and was reduced after Brd4 deletion (14.9% to 2.5%).

    “We found that cluster 4 was expanded from Sham to TAC (9.3% to 14.9%) and reduced upon Brd4 deletion (14.9% to 2.5%) (Fig. 2E and Extended Data Fig. 2L).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Flow cytometry 7 days after TAC showed no significant effect of Brd4 deletion on immune cell, monocyte or macrophage numbers, but a trend toward fewer monocytes.

    “We assessed the impact of Brd4 deletion in Cx3cr1-positive cells on monocyte infiltration post-TAC by flow cytometry 7 days after surgery which showed no significant effect on immune cell, monocyte, or macrophage numbers, but a trend suggesting a potential reduction in monocytes (Extended Data Fig. 2M).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    By scRNA-seq, JQ1 reduced Ccr2-expressing infiltrating macrophages but did not affect Timd4-, Lyve1- and Folr2-expressing resident macrophages.

    “By scRNA-seq, JQ1 reduced cells expressing Ccr2 (infiltrating macrophages) but did not affect cells expressing Timd4, Lyve1, and Folr2 (resident macrophages) (Extended Data Fig. 1G).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cx3cr1 and Il1b were co-expressed in cluster 1, which was enriched in TAC and depleted in Sham and TAC JQ1 conditions.

    “Cx3cr1 and Il1b were co-expressed in cluster 1 (Fig. 1J), which was enriched in cells from TAC and depleted in Sham and TAC JQ1 conditions (Extended Data Fig. 1F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Single-cell RNA sequencing of sorted cardiac CD45-positive cells processed 10,450 immune cells and identified 16 transcriptomic clusters.

    “We processed 10,450 immune cells and identified 16 transcriptomic clusters.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cx3cr1 and Il1b increased in TAC compared with Sham and were downregulated by JQ1.

    “Consistent with Cx3cr1 and Il1b expression being negatively correlated with cardiac function (Fig. 1F), both genes were increased in TAC compared to Sham, and downregulated by JQ1 treatment (Fig. 1K).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Cx3cr1 accessibility was almost entirely in cluster 4, as was Il1b accessibility.

    “Interestingly, Cx3cr1 accessibility was almost entirely in cluster 4, as was accessibility of Il1b, one of the most dynamically regulated genes in the scRNA-seq analysis (Fig. 4D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Of the 15 super-enhancers with dynamic chromatin accessibility, 10 had greater BRD4 binding in TAC, including large enhancers proximal to Il1b, Mreg, Cdh26 and Cd83.

    “Of the 15 super-enhancers with dynamic chromatin accessibility across conditions (Fig. 4I, top right quadrant), 10 had greater BRD4 binding in TAC, including the large enhancers proximal to Il1b, Mreg, Cdh26, and Cd83 (Extended Data Fig. 6J).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Several p65/RELA motifs were present in this 2.7 kb distal region, and p65/RELA ChIP-seq on human cardiac fibroblasts showed direct binding at the human MEOX1 enhancer.

    “Several motifs for p65/RELA were present within this 2.7kb distal region (Extended Data Fig. 9P), and p65/RELA ChIP-seq on human cardiac fibroblasts revealed direct binding at the MEOX1 human enhancer (Fig. 5D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    IL1B significantly increased αSMA-positive fibers, and this increase was greater when IL1B was combined with TGFB than with TGFB alone.

    “IL1B led to a significant increase in α-smooth muscle (αSMA)-positive fibers, which was further increased when used in combination with TGFB compared to TGFB alone (Extended Data Fig. 9D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Genes significantly upregulated in TAC versus TAC-Brd4KO showed decreased accessibility in TAC-Brd4KO, indicating concordance between transcriptional and chromatin changes.

    “We then scored accessibility across the dysregulated fibroblast genes in our snRNA-seq analysis and found that genes significantly upregulated in TAC versus TAC-Brd4KO displayed decreased accessibility in TAC-Brd4KO, indicating concordance between transcriptional and chromatin changes (Fig. 3M,N).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    TAC cells were more numerous in the Cx3cr1/Il1b-accessible cluster 4 than Sham cells, and Brd4 deletion was associated with a decrease in its composition.

    “Cells from the TAC condition were greater in number in the Cx3cr1/Il1b accessible Cluster 4 relative to Sham, and Brd4 deletion was associated with a decrease in its composition (Extended Data Fig. 5C,D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Most CRISPR deletions did not significantly affect LPS-induced Il1b induction, but deletion of peaks 5 and 6 reduced stress-induced expression.

    “While most of the CRISPR deletions did not significantly affect LPS-induced Il1b induction, the deletion of peaks 5 and 6 reduced stress-induced expression (Fig. 4M).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Human myeloid cluster 3 had strong accessibility for CX3CR1, IL1B and CCR2, while clusters 5, 6 and 8 had high accessibility for TIMD4 and LYVE1.

    “with cluster 3 associated with strong accessibility for CX3CR1, IL1B and CCR2 (Fig. 4P and Extended Data Fig. 8A), while clusters 5, 6 and 8 were associated with high accessibility for the resident macrophage markers TIMD4 and LYVE1 (Extended Data Fig. 8A).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    IL1R1 knockdown impaired contractility triggered by IL1B and by TGFB+IL1B, but did not reduce contractility when TGFB was used alone.

    “Knockdown of IL1R1 impaired the contractility triggered by IL1B and TGFB+IL1B (Extended Data Fig. 9F-J), but had no effect in reducing contractility when TGFB was used alone (Extended Data Fig. 9I).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Single nuclei RNA-seq of hearts from TAC or TAC-Brd4KO animals processed 28,107 nuclei into 17 transcriptomic clusters covering major cardiac cell populations.

    “A group of 28,107 nuclei encompassing all the major cardiac cell populations was processed into 17 transcriptomic clusters (Fig. 3B, Extended Data Fig. 3A).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    In the merged analysis, cluster 0 was the largest and equally distributed between samples.

    “While cluster 0, the largest in number, was equally distributed between samples”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Within the fibroblast population, 7 transcriptional clusters encompassing 7,388 cells were identified, with TAC and TAC-Brd4KO fibroblasts clustering separately.

    “Within the fibroblast population, we identified 7 transcriptional clusters encompassing 7,388 cells (Fig. 3E), with TAC and TAC-Brd4KO fibroblasts clustering separately (Fig. 3F).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    scATAC-seq of sorted CD45-positive cells from Sham, TAC and TAC-Brd4KO identified 21 clusters, and C1qa, Cd163 and Cd14 gene scores identified the monocyte/macrophage population, which was also accessible for Cx3cr1.

    “We identified 21 clusters, and gene score signals of C1qa, Cd163, and Cd14 identified the monocyte/macrophage population, which was also accessible for Cx3cr1 (Extended Data Fig. 5A,B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In vivo, antibody-mediated IL1B neutralization improved cardiac function and tissue fibrosis in heart failure.

    “In vivo, antibody-mediated IL1B neutralization improved cardiac function and tissue fibrosis in heart failure.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Conditional deletion of Brd4 in infiltrating Cx3cr1-positive macrophages ameliorates heart failure and significantly reduces fibroblast activation.

    “Here, we show that conditional deletion of the transcriptional co-activator Brd4 in infiltrating Cx3cr1-positive macrophages ameliorates heart failure and significantly reduces fibroblast activation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Fibroblast cluster 6 specifically expressed activation genes such as Postn, Meox1, Comp, Cilp, Mfap4 and Thbs4, and was depleted of TAC-Brd4KO fibroblasts.

    “Cluster 6 was associated with specific expression of fibroblast activation genes such as Postn, Meox1, Comp, Cilp, Mfap4, and Thbs4 (Fig. 3G, Extended Data Fig. 3E-G), and was depleted of TAC-Brd4KO fibroblasts (Extended Data Fig. 3H).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    A second set of dynamic super-enhancers decreased with TAC and increased after Cx3cr1-specific Brd4 deletion.

    “ones that decrease with TAC and increase with the deletion”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Findingown data

    The analysis yielded 748 large enhancers.

    “This results in 748 large enhancers.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductown data

    Brd4 mRNA was significantly reduced in Cx3cr1CreERT2;Brd4flox/flox versus Brd4flox/flox animals only in CX3CR1-positive cells, with no effect in cardiomyocytes, fibroblasts or endothelial cells.

    “Brd4 mRNA levels were significantly reduced in Cx3cr1CreERT2;Brd4flox/flox versus Brd4flox/flox animals only in CX3CR1Pos cells, while Brd4 expression was not affected in CMs, fibroblasts or endothelial cells (Extended Data Fig. 2A,B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Neutralizing IL1B attenuated the increased fibroblast contractility caused by LPS-treated medium, demonstrating that myeloid-cell-derived IL1B modulates fibroblast contractile phenotype in a paracrine manner.

    “While the LPS-treated medium with IgG antibody increased fibroblast contractility, neutralizing IL1B significantly attenuated it, demonstrating that IL1B from myeloid cells modulates fibroblast contractile phenotype in a paracrine fashion (Fig. 5A).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: IL1B is a secreted factor that can influence other cell states through paracrine signaling.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    scATAC-seq annotated all major cell populations identified by snRNA-seq.

    “As expected, scATAC-seq annotated all major cell populations identified by snRNA-seq (Fig. 3I and Extended Data Fig. 4A).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    Il1b was one of the genes most sensitive to Brd4 deletion in Cx3cr1-expressing cells, suggesting direct regulation by BRD4.

    “Moreover, Il1b was one of the most sensitive genes to Brd4 deletion in Cx3cr1-expressing cells, suggesting direct regulation by BRD4 (Fig. 2H,K).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    siRNA-mediated downregulation of MEOX1 abolished the increased fibroblast contractility induced by IL1B plus TGFB, suggesting that fibroblast activation depends on MEOX1.

    “siRNA-mediated downregulation of MEOX1 abolished the increased fibroblast contractility induced by the combination of IL1B and TGFB (Fig. 5C and Extended Data Fig. 9L-O), suggesting dependency on MEOX1 for the activation of fibroblasts.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B reveals how inflammation drives profibrotic cell states and supports strategies to modulate this process in heart disease and other chronic inflammatory disorders with tissue remodeling.

    “The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B reveals how inflammation drives profibrotic cell states and supports strategies that modulate this process in heart disease and other chronic inflammatory disorders featuring tissue remodeling.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    One sample in one condition was excluded from fibrosis analysis because its fibrosis percentage was greater than two standard deviations above the mean across all data points.

    “One sample in one condition was excluded because the fibrosis percentage was greater than two standard deviations above the mean when considering all the data points across all conditions.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Echocardiography analyses were performed blinded, with mice assigned an alphanumeric code.

    “All echocardiography analyses were performed blinded (mice were assigned an alphanumeric code).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    To address variance from using few cells, the authors restricted coverage analysis to regions where at least two samples had at least one read and used a minimum coverage threshold of 4e−6.

    “To control for the large variance that can result from deriving coverage from a small number of cells, we only considered signal in regions in which at least two different samples had at least one read, and set a minimum threshold of 4e−6 for detectability of coverage”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Fibrosis analysis was performed blinded, with samples labeled by an alphanumeric code.

    “A blinded approach (labeling samples with an alphanumeric code) was implemented for analyzing fibrosis.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    All animal protocols were approved by the Institutional Animal Care and Use Committees at the University of California, San Francisco and conducted in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

    “All protocols concerning animal use were approved by the Institutional Animal Care and Use Committees at the University of California, San Francisco and conducted in strict accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    Luciferase constructs were tested in three technical replicates and at least three biological replicates.

    “Each construct was transfected in three technical replicates and at least 3 biological replicates were performed.”
    Quote in the paperNot a substantial claim
47 of 47

  • The paper relies on this without support.

    Before this study, the mechanism by which organ-level stress is sensed by cells to trigger downstream fibroblast activation was unknown.

    “However, the mechanism by which organ-level stress is sensed by cells to trigger downstream fibroblast activation remains unknown.”

  • The paper relies on this without support.

    IL1B is a secreted factor that can influence other cell states through paracrine signaling.

    “Importantly, Il1b encodes a secreted factor (IL1B) that can influence other cell states via paracrine signaling.”

  • The paper relies on this without support.

    In response to stress, chromatin remodeling can alter expression of secreted factors and thereby influence neighboring cells through non-cell autonomous mechanisms.

    “In response to stress, chromatin remodeling can alter the expression of secreted factors thus influencing neighboring cells through non-cell autonomous mechanisms and fueling pathological crosstalk between diverse cellular compartments.”

  • The paper relies on this without support.

    The molecular mechanisms governing crosstalk between chronic inflammation and tissue fibrosis are poorly understood.

    “Chronic inflammation and tissue fibrosis are common responses that worsen organ function, yet the molecular mechanisms governing their crosstalk are poorly understood.”

  • The paper relies on this without support.

    Systemic neutralizing antibody administration blocked IL1B from various possible cellular sources.

    “As systemic neutralizing antibody administration blocked IL1B from various possible cellular sources”

  • The paper relies on this without support.

    Little is known about how inflammatory signals can influence fibroblast cell states in disease.

    “little is known about how inflammatory signals can influence fibroblast cell states in disease.”

  • The paper relies on this without support.

    Findings from the mouse TAC model and anti-IL1B treatment translate to human heart disease.

    “IL1B antibody-mediated neutralization is sufficient to improve cardiac function in heart disease.”
7 of 7

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • JQ1 treatment can reversibly direct fibroblast activation away from the FAP/POSTN cell state, indicating therapeutic potential of targeting the differentiation and maturation of FAP-positive fibroblasts.

    “The possibility that JQ1 treatment can reversibly direct fibroblast activation away from the FAP/POSTN cell state indicates the therapeutic potential of targeting the differentiation and maturation of FAP+ fibroblasts28,30.”

    From Targeting immune–fibroblast cell communication in heart failure (2024) · cites this paper as [30]

    In “BRD4 in Cx3cr1+ cells activates fibroblasts” (page unavailable), the paper reports that JQ1 downregulated fibroblast genes including the profibrotic marker Postn. Its introduction describes a reversible fibroblast-activation switch under BET inhibition, but the paper does not establish that JQ1 reversibly redirects a FAP/POSTN-defined cell state or specifically targets the differentiation and maturation of FAP-positive fibroblasts. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • The Srivastava laboratory also showed that anti-IL-1β antibody treatment leads to fewer POSTN fibroblasts, improved cardiac function and decreased cardiac fibrosis.

    “They also show that anti-IL-1β mAb treatment leads to fewer POSTN fibroblasts, improved cardiac function and decreased cardiac fibrosis30.”

    From Targeting immune–fibroblast cell communication in heart failure (2024) · cites this paper as [30]

    The section ‘IL1B inhibition improves heart function’ reports that anti-IL1B treatment in mice reduced the representation of Postn-enriched fibroblast clusters, improved cardiac function and reduced fibrosis. The Methods identify the treatment as an anti-IL1B antibody but do not specify that it was monoclonal, so the ‘mAb’ detail is not established by our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • The Srivastava laboratory showed that Brd4 deletion in macrophages abrogates IL-1β signalling and suppresses fibroblast activation and fibrosis through a MEOX1-dependent regulatory mechanism in a pressure-overload model of heart failure.

    “Consistent with our findings, the Srivastava laboratory has shown that Brd4 deletion in macrophages abrogates IL-1β signalling and suppresses fibroblast activation and fibrosis through a MEOX1-dependent regulatory mechanism in a pressure-overload model of HF30.”

    From Targeting immune–fibroblast cell communication in heart failure (2024) · cites this paper as [30]

    In “BRD4 function in Cx3cr1+ cells during heart failure,” Brd4 deletion in Cx3cr1-positive cells reduced fibrosis after pressure overload; “BRD4 in Cx3cr1+ cells activates fibroblasts” reports reduced profibrotic fibroblast programs. The paper also links IL1B to MEOX1-dependent fibroblast activation, but “BRD4 drives proinflammatory transcription” reports decreased Il1b expression after Brd4 deletion, not that IL-1β signalling was abrogated. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Previous and concurrent work highlighted the functional role of this gene regulatory network in cardiac fibrosis.

    “Indeed, previous and concurrent work has highlighted the functional role of this gene regulatory network in cardiac fibrosis28–30.”

    From Targeting immune–fibroblast cell communication in heart failure (2024) · cites this paper as [30]

  • Concurrent work established a role for MEOX1 in the pathogenesis of cardiac fibrosis.

    “These findings are underscored by concurrent work establishing a role for MEOX1 in the pathogenesis of cardiac fibrosis30.”

    From Targeting immune–fibroblast cell communication in heart failure (2024) · cites this paper as [30]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Overlapping p-value reporting rules conflict

    Minor

    A p-value between 0.0001 and 0.001 satisfies both stated rules: one requires its exact value, while the other reports it as P<0.0001, which would be false.

1 of 1

Cites

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2 of the 57 references couldn’t be matched to a known paper.

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Related

Authors
Alexanian, M., Padmanabhan, A., Nishino, T., Travers, J. G., Ye, L., Pelonero, A., Lee, C. Y., Sadagopan, N., Huang, Y., Auclair, K., Zhu, A., An, Y., Ekstrand, C. A., Martinez, C., Teran, B. G., Flanigan, W. R., Kim, C. K.-S., Lumbao-Conradson, K., Gardner, Z., Li, L., Costa, M. W., Jain, R., Charo, I., Combes, A. J., Haldar, S. M., Pollard, K. S., Vagnozzi, R. J., McKinsey, T. A., Przytycki, P. F., & Srivastava, D.
Affiliations
  • Gladstone Institutes (US)
  • University of Colorado Anschutz (US)
  • University of California, San Francisco (US)
  • University of Pennsylvania (US)
  • Amgen (United States) (US)
  • Boston University (US)
Corresponding author
Alexanian, Michael
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2024-10-23
Volume
635
Issue
8038
Pages
434-443
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-024-08085-6
PMC
PMC11698514
OpenAlex
W4403680473
Semantic Scholar
4068b221dac01063659a124623f00bb7bc087cc7
Cited by
140
References
57
Citations by year
2026: 69 · 2025: 64 · 2024: 7
FWCI
41.90
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
Funders
  • National Science Foundation
  • American Heart Association
  • A.P. Giannini Foundation
  • Tobacco-Related Disease Research Program
  • Giannini Foundation of Agricultural Economics
  • Frank A. Campini Foundation
  • Sarnoff Cardiovascular Research Foundation
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (186704)
  • Italfarmaco
  • National Institutes of Health
  • Agency for Healthcare Research and Quality (R01HS015100)
  • Japan Society for the Promotion of Science
  • National Heart, Lung, and Blood Institute (R01HL147558, K99HL166708, R01HL116848, P01HL146366, R01HL150100, P01HL089707, R01HL127240, U01HL098179, R01HL150225, R01HL057181, K08HL157700, R01HL169578, R35HL166663)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK119594)
Topics
  • Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiac Fibrosis and Remodeling
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Congenital heart defects research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
heart failure, myocardial fibrosis, BRD4, chromatin remodeling, macrophages, CX3CR1+ macrophages, fibroblast activation, IL-1β, MEOX1, RelA/p65, chromatin accessibility, chronic inflammation, tissue remodeling
MeSH terms
CX3C Chemokine Receptor 1, Bromodomain Containing Proteins, Animals, Cell Communication, Chromatin, Enhancer Elements, Genetic, Female, Fibroblasts, Fibrosis, Heart Failure, Humans, Macrophages, Male, Mice, Inbred C57BL, Nuclear Proteins, Transcription Factors, Homeodomain Proteins, Cell Cycle Proteins, Chromatin Assembly and Disassembly, Mice, Transcription Factor RelA, Interleukin-1beta, Single-Cell Analysis

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read under definition version 3 (extract-v3) on 2026-09-28.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-09-28.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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