A transcriptional switch governs fibroblast activation in heart disease

Michael Alexanian, Pawel F. Przytycki, Rudi Micheletti, Arun Padmanabhan, Lin Ye, Joshua G. Travers, Barbara Gonzalez-Teran, Ana Catarina Silva, Qiming Duan, Sanjeev S. Ranade, Franco Felix, Ricardo Linares-Saldana, Li Li, Clara Youngna Lee, Nandhini Sadagopan, Angelo Pelonero, Yu Huang, Gaia Andreoletti, Rajan Jain, Timothy A. McKinsey, Michael G. Rosenfeld, Casey A. Gifford, Katherine S. Pollard, Saptarsi M. Haldar () and Deepak Srivastava ()
Additional contact information
Michael Alexanian: Gladstone Institutes
Pawel F. Przytycki: Gladstone Institutes
Rudi Micheletti: University of California, San Diego
Arun Padmanabhan: Gladstone Institutes
Lin Ye: Gladstone Institutes
Joshua G. Travers: University of Colorado Anschutz Medical Campus
Barbara Gonzalez-Teran: Gladstone Institutes
Ana Catarina Silva: Gladstone Institutes
Qiming Duan: Gladstone Institutes
Sanjeev S. Ranade: Gladstone Institutes
Franco Felix: Gladstone Institutes
Ricardo Linares-Saldana: University of Pennsylvania
Li Li: University of Pennsylvania
Clara Youngna Lee: Gladstone Institutes
Nandhini Sadagopan: Gladstone Institutes
Angelo Pelonero: Gladstone Institutes
Yu Huang: Gladstone Institutes
Gaia Andreoletti: University of California
Rajan Jain: University of Pennsylvania
Timothy A. McKinsey: University of Colorado Anschutz Medical Campus
Michael G. Rosenfeld: University of California, San Diego
Casey A. Gifford: Gladstone Institutes
Katherine S. Pollard: Gladstone Institutes
Saptarsi M. Haldar: Gladstone Institutes
Deepak Srivastava: Gladstone Institutes

Nature, 2021, vol. 595, issue 7867, 438-443

Abstract: Abstract In diseased organs, stress-activated signalling cascades alter chromatin, thereby triggering maladaptive cell state transitions. Fibroblast activation is a common stress response in tissues that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains unclear1,2. Pharmacological inhibition of bromodomain and extra-terminal domain (BET) proteins alleviates cardiac dysfunction3–7, providing a tool to interrogate and modulate cardiac cell states as a potential therapeutic approach. Here we use single-cell epigenomic analyses of hearts dynamically exposed to BET inhibitors to reveal a reversible transcriptional switch that underlies the activation of fibroblasts. Resident cardiac fibroblasts demonstrated robust toggling between the quiescent and activated state in a manner directly correlating with BET inhibitor exposure and cardiac function. Single-cell chromatin accessibility revealed previously undescribed DNA elements, the accessibility of which dynamically correlated with cardiac performance. Among the most dynamic elements was an enhancer that regulated the transcription factor MEOX1, which was specifically expressed in activated fibroblasts, occupied putative regulatory elements of a broad fibrotic gene program and was required for TGFβ-induced fibroblast activation. Selective CRISPR inhibition of the single most dynamic cis-element within the enhancer blocked TGFβ-induced Meox1 activation. We identify MEOX1 as a central regulator of fibroblast activation associated with cardiac dysfunction and demonstrate its upregulation after activation of human lung, liver and kidney fibroblasts. The plasticity and specificity of BET-dependent regulation of MEOX1 in tissue fibroblasts provide previously unknown trans- and cis-targets for treating fibrotic disease.

Date: 2021
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DOI: 10.1038/s41586-021-03674-1

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