Franco Felix

All Publications

• GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience Collier, A. E., Piekos, S. N., Liu, A., Pattison, J. M., Felix, F., Bailetti, A. A., Sedov, E., Gaddam, S., Zhen, H., Oro, A. E. 2023; 26 (3): 106125

  Abstract

  Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.

  View details for DOI 10.1016/j.isci.2023.106125

  View details for PubMedID 36843855

• Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell Gonzalez-Teran, B., Pittman, M., Felix, F., Thomas, R., Richmond-Buccola, D., Hüttenhain, R., Choudhary, K., Moroni, E., Costa, M. W., Huang, Y., Padmanabhan, A., Alexanian, M., Lee, C. Y., Maven, B. E., Samse-Knapp, K., Morton, S. U., McGregor, M., Gifford, C. A., Seidman, J. G., Seidman, C. E., Gelb, B. D., Colombo, G., Conklin, B. R., Black, B. L., Bruneau, B. G., Krogan, N. J., Pollard, K. S., Srivastava, D. 2022

  Abstract

  Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains challenging. We hypothesized that genetic determinants for CHDs may lie in the protein interactomes of transcription factors whose mutations cause CHDs. Defining the interactomes of two transcription factors haplo-insufficient in CHD, GATA4 and TBX5, within human cardiac progenitors, and integrating the results with nearly 9,000 exomes from proband-parent trios revealed an enrichment of de novo missense variants associated with CHD within the interactomes. Scoring variants of interactome members based on residue, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied and co-activated cardiac developmental genes, and the identified GLYR1 missense variant disrupted interaction with GATA4, impairing in vitro and in vivo function in mice. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating genetic variants in heart disease.

  View details for DOI 10.1016/j.cell.2022.01.021

  View details for PubMedID 35182466

• A transcriptional switch governs fibroblast activation in heart disease. Nature Alexanian, M., Przytycki, P. F., Micheletti, R., Padmanabhan, A., Ye, L., Travers, J. G., Gonzalez-Teran, B., Silva, A. C., Duan, Q., Ranade, S. S., Felix, F., Linares-Saldana, R., Li, L., Lee, C. Y., Sadagopan, N., Pelonero, A., Huang, Y., Andreoletti, G., Jain, R., McKinsey, T. A., Rosenfeld, M. G., Gifford, C. A., Pollard, K. S., Haldar, S. M., Srivastava, D. 2021

  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.

  View details for DOI 10.1038/s41586-021-03674-1

  View details for PubMedID 34163071

• BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes CIRCULATION Padmanabhan, A., Alexanian, M., Linares-Saldana, R., Gonzalez-Teran, B., Andreoletti, G., Huang, Y., Connolly, A. J., Kim, W., Hsu, A., Duan, Q., Winchester, S. B., Felix, F., Perez-Bermejo, J. A., Wang, Q., Li, L., Shah, P. P., Haldar, S. M., Jain, R., Srivastava, D. 2020; 142 (24): 2338-2355

  Abstract

  Gene regulatory networks control tissue homeostasis and disease progression in a cell type-specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue specificity of their function is achieved are poorly understood. BRD4 (bromodomain-containing protein 4), a member of the BET (bromo- and extraterminal domain) family of ubiquitously expressed acetyl-lysine reader proteins, plays a pivotal role as a coactivator of enhancer signaling across diverse tissue types in both health and disease and has been implicated as a pharmacological target in heart failure. However, the cell-specific role of BRD4 in adult cardiomyocytes remains unknown.We combined conditional mouse genetics, unbiased transcriptomic and epigenomic analyses, and classic molecular biology and biochemical approaches to understand the mechanism by which BRD4 in adult cardiomyocyte homeostasis.Here, we show that cardiomyocyte-specific deletion of Brd4 in adult mice leads to acute deterioration of cardiac contractile function with mutant animals demonstrating a transcriptomic signature characterized by decreased expression of genes critical for mitochondrial energy production. Genome-wide occupancy data show that BRD4 enriches at many downregulated genes (including the master coactivators Ppargc1a, Ppargc1b, and their downstream targets) and preferentially colocalizes with GATA4 (GATA binding protein 4), a lineage-determining cardiac transcription factor not previously implicated in regulation of adult cardiac metabolism. BRD4 and GATA4 form an endogenous complex in cardiomyocytes and interact in a bromodomain-independent manner, revealing a new functional interaction partner for BRD4 that can direct its locus and tissue specificity.These results highlight a novel role for a BRD4-GATA4 module in cooperative regulation of a cardiomyocyte-specific gene program governing bioenergetic homeostasis in the adult heart.

  View details for DOI 10.1161/CIRCULATIONAHA.120.047753

  View details for Web of Science ID 000639226400010

  View details for PubMedID 33094644

  View details for PubMedCentralID PMC7736290