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Li S, Luo X, Sun M, Wang Y, Zhang Z, Jiang J, Hu D, Zhang J, Wu Z, Wang Y, Huang W, Xia L. Context-dependent T-BOX transcription factor family: from biology to targeted therapy. Cell Commun Signal 2024; 22:350. [PMID: 38965548 PMCID: PMC11225425 DOI: 10.1186/s12964-024-01719-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024] Open
Abstract
T-BOX factors belong to an evolutionarily conserved family of transcription factors. T-BOX factors not only play key roles in growth and development but are also involved in immunity, cancer initiation, and progression. Moreover, the same T-BOX molecule exhibits different or even opposite effects in various developmental processes and tumor microenvironments. Understanding the multiple roles of context-dependent T-BOX factors in malignancies is vital for uncovering the potential of T-BOX-targeted cancer therapy. We summarize the physiological roles of T-BOX factors in different developmental processes and their pathological roles observed when their expression is dysregulated. We also discuss their regulatory roles in tumor immune microenvironment (TIME) and the newly arising questions that remain unresolved. This review will help in systematically and comprehensively understanding the vital role of the T-BOX transcription factor family in tumor physiology, pathology, and immunity. The intention is to provide valuable information to support the development of T-BOX-targeted therapy.
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Affiliation(s)
- Siwen Li
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Zerui Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Junqing Jiang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Dian Hu
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Jiaqian Zhang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Zhangfan Wu
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China
| | - Wenjie Huang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Huazhong University of Science and Technology, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430030, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, China.
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2
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Giovou AE, Gladka MM, Christoffels VM. The Impact of Natriuretic Peptides on Heart Development, Homeostasis, and Disease. Cells 2024; 13:931. [PMID: 38891063 PMCID: PMC11172276 DOI: 10.3390/cells13110931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
During mammalian heart development, the clustered genes encoding peptide hormones, Natriuretic Peptide A (NPPA; ANP) and B (NPPB; BNP), are transcriptionally co-regulated and co-expressed predominately in the atrial and ventricular trabecular cardiomyocytes. After birth, expression of NPPA and a natural antisense transcript NPPA-AS1 becomes restricted to the atrial cardiomyocytes. Both NPPA and NPPB are induced by cardiac stress and serve as markers for cardiovascular dysfunction or injury. NPPB gene products are extensively used as diagnostic and prognostic biomarkers for various cardiovascular disorders. Membrane-localized guanylyl cyclase receptors on many cell types throughout the body mediate the signaling of the natriuretic peptide ligands through the generation of intracellular cGMP, which interacts with and modulates the activity of cGMP-activated kinase and other enzymes and ion channels. The natriuretic peptide system plays a fundamental role in cardio-renal homeostasis, and its potent diuretic and vasodilatory effects provide compensatory mechanisms in cardiac pathophysiological conditions and heart failure. In addition, both peptides, but also CNP, have important intracardiac actions during heart development and homeostasis independent of the systemic functions. Exploration of the intracardiac functions may provide new leads for the therapeutic utility of natriuretic peptide-mediated signaling in heart diseases and rhythm disorders. Here, we review recent insights into the regulation of expression and intracardiac functions of NPPA and NPPB during heart development, homeostasis, and disease.
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Affiliation(s)
- Alexandra E Giovou
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands
| | - Monika M Gladka
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, 1105AZ Amsterdam, The Netherlands
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3
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Charrier A, Ockunzzi J, Main L, Ghanta SV, Buchner DA. Molecular regulation of PPARγ/RXRα signaling by the novel cofactor ZFP407. PLoS One 2024; 19:e0294003. [PMID: 38781157 PMCID: PMC11115250 DOI: 10.1371/journal.pone.0294003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/20/2024] [Indexed: 05/25/2024] Open
Abstract
Cofactors interacting with PPARγ can regulate adipogenesis and adipocyte metabolism by modulating the transcriptional activity and selectivity of PPARγ signaling. ZFP407 was previously demonstrated to regulate PPARγ target genes such as GLUT4, and its overexpression improved glucose homeostasis in mice. Here, using a series of molecular assays, including protein-interaction studies, mutagenesis, and ChIP-seq, ZFP407 was found to interact with the PPARγ/RXRα protein complex in the nucleus of adipocytes. Consistent with this observation, ZFP407 ChIP-seq peaks significantly overlapped with PPARγ ChIP-seq peaks, with more than half of ZFP407 peaks overlapping with PPARγ peaks. Transcription factor binding motifs enriched in these overlapping sites included CTCF, RARα/RXRγ, TP73, and ELK1, which regulate cellular development and function within adipocytes. Site-directed mutagenesis of frequent PPARγ phosphorylation or SUMOylation sites did not prevent its regulation by ZFP407, while mutagenesis of ZFP407 domains potentially necessary for RXR and PPARγ binding abrogated any impact of ZFP407 on PPARγ activity. These data suggest that ZFP407 controls the activity of PPARγ, but does so independently of post-translational modifications, likely by direct binding, establishing ZFP407 as a newly identified PPARγ cofactor. In addition, ZFP407 ChIP-seq analyses identified regions that did not overlap with PPARγ peaks. These non-overlapping peaks were significantly enriched for the transcription factor binding motifs of TBX19, PAX8, HSF4, and ZKSCAN3, which may contribute to the PPARγ-independent functions of ZFP407 in adipocytes and other cell types.
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Affiliation(s)
- Alyssa Charrier
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jeremiah Ockunzzi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Leighanne Main
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Siddharth V. Ghanta
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - David A. Buchner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
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4
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Zhang Y, Guo J, Tang C, Xu K, Li Z, Wang C. Early life stage exposure to fenbuconazole causes multigenerational cardiac developmental defects in zebrafish and potential reasons. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123938. [PMID: 38588970 DOI: 10.1016/j.envpol.2024.123938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
With the increasing use of triazole fungicides in agriculture, triazole pesticides have aroused great concern about their toxicity and ecological risk. The current study investigated the impairments of embryonic exposure to fenbuconazole (FBZ) on cardiac transgenerational toxicity and related mechanisms. The fertilized eggs were exposed to 5, 50 and 500 ng/L FBZ for 72 h, and the larvae were then raised to adulthood in clean water. The adult fish were mated with unexposed fish to produce maternal and paternal F1 and F2 embryos, respectively. The results showed that increased arrhythmia were observed in F0, F1 and F2 larvae. Transcriptome sequencing indicated that the pathway of adrenergic signaling in cardiomyocytes was enriched in F0 and F2 larvae. In both F0 and F1 adult zebrafish hearts, ADRB2 protein expression decreased, and transcription of genes related to cardiac development and Ca2+ homeostasis was downregulated. These alterations might cause cardiac developmental defects. Significantly decreased protein levels of H3K9Ac and H3K14Ac might be linked with the downregulation in transcription of cardiac development genes. Protein‒protein interaction analysis exhibited that the pathway affecting the heart was well inherited in the paternal line. These results provide new ideas for the analysis and prevention of congenital heart disease.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Jiaojiao Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Chen Tang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Ke Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Zihui Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China
| | - Chonggang Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, PR China.
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5
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Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Nat Biotechnol 2024; 42:803-812. [PMID: 37592035 PMCID: PMC11098741 DOI: 10.1038/s41587-023-01873-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 06/21/2023] [Indexed: 08/19/2023]
Abstract
Single-cell omics technologies enable molecular characterization of diverse cell types and states, but how the resulting transcriptional and epigenetic profiles depend on the cell's genetic background remains understudied. We describe Monopogen, a computational tool to detect single-nucleotide variants (SNVs) from single-cell sequencing data. Monopogen leverages linkage disequilibrium from external reference panels to identify germline SNVs and detects putative somatic SNVs using allele cosegregating patterns at the cell population level. It can identify 100 K to 3 M germline SNVs achieving a genotyping accuracy of 95%, together with hundreds of putative somatic SNVs. Monopogen-derived genotypes enable global and local ancestry inference and identification of admixed samples. It identifies variants associated with cardiomyocyte metabolic levels and epigenomic programs. It also improves putative somatic SNV detection that enables clonal lineage tracing in primary human clonal hematopoiesis. Monopogen brings together population genetics, cell lineage tracing and single-cell omics to uncover genetic determinants of cellular processes.
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Affiliation(s)
- Jinzhuang Dou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yukun Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kian Hong Kock
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Jun Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xuesen Cheng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Le Min Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, RIKEN center for Integrative Medical Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Jay W Shin
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Laboratory for Advanced Genomics Circuit, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Haijing Jin
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yujia Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, USA
| | - Li Ding
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Shyam Prabhakar
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Nicholas Navin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Broman MT, Nadadur RD, Perez-Cervantes C, Burnicka-Turek O, Lazarevic S, Gams A, Laforest B, Steimle JD, Iddir S, Wang Z, Smith L, Mazurek SR, Olivey HE, Zhou P, Gadek M, Shen KM, Khan Z, Theisen JW, Yang XH, Ikegami K, Efimov IR, Pu WT, Weber CR, McNally EM, Svensson EC, Moskowitz IP. A Genomic Link From Heart Failure to Atrial Fibrillation Risk: FOG2 Modulates a TBX5/GATA4-Dependent Atrial Gene Regulatory Network. Circulation 2024; 149:1205-1230. [PMID: 38189150 PMCID: PMC11152454 DOI: 10.1161/circulationaha.123.066804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The relationship between heart failure (HF) and atrial fibrillation (AF) is clear, with up to half of patients with HF progressing to AF. The pathophysiological basis of AF in the context of HF is presumed to result from atrial remodeling. Upregulation of the transcription factor FOG2 (friend of GATA2; encoded by ZFPM2) is observed in human ventricles during HF and causes HF in mice. METHODS FOG2 expression was assessed in human atria. The effect of adult-specific FOG2 overexpression in the mouse heart was evaluated by whole animal electrophysiology, in vivo organ electrophysiology, cellular electrophysiology, calcium flux, mouse genetic interactions, gene expression, and genomic function, including a novel approach for defining functional transcription factor interactions based on overlapping effects on enhancer noncoding transcription. RESULTS FOG2 is significantly upregulated in the human atria during HF. Adult cardiomyocyte-specific FOG2 overexpression in mice caused primary spontaneous AF before the development of HF or atrial remodeling. FOG2 overexpression generated arrhythmia substrate and trigger in cardiomyocytes, including calcium cycling defects. We found that FOG2 repressed atrial gene expression promoted by TBX5. FOG2 bound a subset of GATA4 and TBX5 co-bound genomic locations, defining a shared atrial gene regulatory network. FOG2 repressed TBX5-dependent transcription from a subset of co-bound enhancers, including a conserved enhancer at the Atp2a2 locus. Atrial rhythm abnormalities in mice caused by Tbx5 haploinsufficiency were rescued by Zfpm2 haploinsufficiency. CONCLUSIONS Transcriptional changes in the atria observed in human HF directly antagonize the atrial rhythm gene regulatory network, providing a genomic link between HF and AF risk independent of atrial remodeling.
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Affiliation(s)
- Michael T. Broman
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Rangarajan D. Nadadur
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Carlos Perez-Cervantes
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sonja Lazarevic
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Anna Gams
- Department of Biomedical Engineering, George Washington University
| | - Brigitte Laforest
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Jeffrey D. Steimle
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Sabrina Iddir
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zhezhen Wang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Linsin Smith
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Stefan R. Mazurek
- Department of Medicine, Section of Cardiology, University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637
| | - Harold E. Olivey
- Department of Biology, Indiana University Northwest, Gary, IN 46408
| | | | - Margaret Gadek
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kaitlyn M. Shen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Zoheb Khan
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Joshua W.M. Theisen
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Xinan H. Yang
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Kohta Ikegami
- Division of Molecular and Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Igor R. Efimov
- Department of Biomedical Engineering, George Washington University
| | - William T. Pu
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, 02138
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, 02115
| | | | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University, 303 E. Superior, SQ5-516, Chicago, IL 60611
| | | | - Ivan P. Moskowitz
- Department of Pediatrics, University of Chicago, Chicago, IL 60637
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
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7
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Ang CE, Olmos VH, Vodehnal K, Zhou B, Lee QY, Sinha R, Narayanaswamy A, Mall M, Chesnov K, Dominicus CS, Südhof T, Wernig M. Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1. Proc Natl Acad Sci U S A 2024; 121:e2308401121. [PMID: 38446849 PMCID: PMC10945857 DOI: 10.1073/pnas.2308401121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
Generation of defined neuronal subtypes from human pluripotent stem cells remains a challenge. The proneural factor NGN2 has been shown to overcome experimental variability observed by morphogen-guided differentiation and directly converts pluripotent stem cells into neurons, but their cellular heterogeneity has not been investigated yet. Here, we found that NGN2 reproducibly produces three different kinds of excitatory neurons characterized by partial coactivation of other neurotransmitter programs. We explored two principle approaches to achieve more precise specification: prepatterning the chromatin landscape that NGN2 is exposed to and combining NGN2 with region-specific transcription factors. Unexpectedly, the chromatin context of regionalized neural progenitors only mildly altered genomic NGN2 binding and its transcriptional response and did not affect neurotransmitter specification. In contrast, coexpression of region-specific homeobox factors such as EMX1 resulted in drastic redistribution of NGN2 including recruitment to homeobox targets and resulted in glutamatergic neurons with silenced nonglutamatergic programs. These results provide the molecular basis for a blueprint for improved strategies for generating a plethora of defined neuronal subpopulations from pluripotent stem cells for therapeutic or disease-modeling purposes.
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Affiliation(s)
- Cheen Euong Ang
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Victor Hipolito Olmos
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kayla Vodehnal
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Bo Zhou
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Qian Yi Lee
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Rahul Sinha
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Aadit Narayanaswamy
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Moritz Mall
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kirill Chesnov
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Caia S. Dominicus
- Wellcome Sanger Institute, Hinxton, CambridgeshireCB10 1SA, United Kingdom
- OpenTargets, Hinxton, CambridgeshireCB10 1SA, United Kingdom
| | - Thomas Südhof
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Marius Wernig
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
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8
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Song S, Zhang X, Huang Z, Zhao Y, Lu S, Zeng L, Cai F, Wang T, Pei Z, Weng X, Luo W, Lu H, Wei Z, Wu J, Yu P, Shen L, Zhang X, Sun A, Ge J. TEA domain transcription factor 1(TEAD1) induces cardiac fibroblasts cells remodeling through BRD4/Wnt4 pathway. Signal Transduct Target Ther 2024; 9:45. [PMID: 38374140 PMCID: PMC10876703 DOI: 10.1038/s41392-023-01732-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 02/21/2024] Open
Abstract
Cardiac fibroblasts (CFs) are the primary cells tasked with depositing and remodeling collagen and significantly associated with heart failure (HF). TEAD1 has been shown to be essential for heart development and homeostasis. However, fibroblast endogenous TEAD1 in cardiac remodeling remains incompletely understood. Transcriptomic analyses revealed consistently upregulated cardiac TEAD1 expression in mice 4 weeks after transverse aortic constriction (TAC) and Ang-II infusion. Further investigation revealed that CFs were the primary cell type expressing elevated TEAD1 levels in response to pressure overload. Conditional TEAD1 knockout was achieved by crossing TEAD1-floxed mice with CFs- and myofibroblasts-specific Cre mice. Echocardiographic and histological analyses demonstrated that CFs- and myofibroblasts-specific TEAD1 deficiency and treatment with TEAD1 inhibitor, VT103, ameliorated TAC-induced cardiac remodeling. Mechanistically, RNA-seq and ChIP-seq analysis identified Wnt4 as a novel TEAD1 target. TEAD1 has been shown to promote the fibroblast-to-myofibroblast transition through the Wnt signalling pathway, and genetic Wnt4 knockdown inhibited the pro-transformation phenotype in CFs with TEAD1 overexpression. Furthermore, co-immunoprecipitation combined with mass spectrometry, chromatin immunoprecipitation, and luciferase assays demonstrated interaction between TEAD1 and BET protein BRD4, leading to the binding and activation of the Wnt4 promoter. In conclusion, TEAD1 is an essential regulator of the pro-fibrotic CFs phenotype associated with pathological cardiac remodeling via the BRD4/Wnt4 signalling pathway.
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Affiliation(s)
- Shuai Song
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Xiaokai Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Zihang Huang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Yongchao Zhao
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Shuyang Lu
- Department of cardiac surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Linqi Zeng
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Fengze Cai
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Tongyao Wang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Zhiqiang Pei
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Xinyu Weng
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Wei Luo
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Hao Lu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Zilun Wei
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Jian Wu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng Yu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Li Shen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Xiaochun Zhang
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China
- National Clinical Research Center for Interventional Medicine, Shanghai, China
| | - Aijun Sun
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, China.
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, China.
- State Key Laboratory of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China.
- Key Laboratory of Viral Heart Diseases, National Health Commission, Shanghai, China.
- Key Laboratory of Viral Heart Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
- National Clinical Research Center for Interventional Medicine, Shanghai, China.
- Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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9
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Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 2024; 187:692-711.e26. [PMID: 38262408 PMCID: PMC10872279 DOI: 10.1016/j.cell.2023.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
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Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Seppe Goovaerts
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Peter Claes
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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10
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Friedman CE, Cheetham SW, Negi S, Mills RJ, Ogawa M, Redd MA, Chiu HS, Shen S, Sun Y, Mizikovsky D, Bouveret R, Chen X, Voges HK, Paterson S, De Angelis JE, Andersen SB, Cao Y, Wu Y, Jafrani YMA, Yoon S, Faulkner GJ, Smith KA, Porrello E, Harvey RP, Hogan BM, Nguyen Q, Zeng J, Kikuchi K, Hudson JE, Palpant NJ. HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Dev Cell 2024; 59:91-107.e6. [PMID: 38091997 DOI: 10.1016/j.devcel.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
Genomic regulation of cardiomyocyte differentiation is central to heart development and function. This study uses genetic loss-of-function human-induced pluripotent stem cell-derived cardiomyocytes to evaluate the genomic regulatory basis of the non-DNA-binding homeodomain protein HOPX. We show that HOPX interacts with and controls cardiac genes and enhancer networks associated with diverse aspects of heart development. Using perturbation studies in vitro, we define how upstream cell growth and proliferation control HOPX transcription to regulate cardiac gene programs. We then use cell, organoid, and zebrafish regeneration models to demonstrate that HOPX-regulated gene programs control cardiomyocyte function in development and disease. Collectively, this study mechanistically links cell signaling pathways as upstream regulators of HOPX transcription to control gene programs underpinning cardiomyocyte identity and function.
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Affiliation(s)
- Clayton E Friedman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sumedha Negi
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Richard J Mills
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Masahito Ogawa
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuliangzi Sun
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Dalia Mizikovsky
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Romaric Bouveret
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Holly K Voges
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Scott Paterson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jessica E De Angelis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Stacey B Andersen
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuanzhao Cao
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yohaann M A Jafrani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sohye Yoon
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia; Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kelly A Smith
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Enzo Porrello
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Melbourne, VIC 3052, Australia; Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - Benjamin M Hogan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jian Zeng
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kazu Kikuchi
- Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia; School of Clinical Medicine and School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, Sydney, NSW 2052, Australia
| | - James E Hudson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia; School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
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11
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de Boer CG, Taipale J. Hold out the genome: a roadmap to solving the cis-regulatory code. Nature 2024; 625:41-50. [PMID: 38093018 DOI: 10.1038/s41586-023-06661-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/20/2023] [Indexed: 01/05/2024]
Abstract
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven to be exceedingly complex. Recently, advances in the scale and resolution of functional genomics assays and machine learning have enabled substantial progress towards deciphering this code. However, the cis-regulatory code will probably never be solved if models are trained only on genomic sequences; regions of homology can easily lead to overestimation of predictive performance, and our genome is too short and has insufficient sequence diversity to learn all relevant parameters. Fortunately, randomly synthesized DNA sequences enable testing a far larger sequence space than exists in our genomes, and designed DNA sequences enable targeted queries to maximally improve the models. As the same biochemical principles are used to interpret DNA regardless of its source, models trained on these synthetic data can predict genomic activity, often better than genome-trained models. Here we provide an outlook on the field, and propose a roadmap towards solving the cis-regulatory code by a combination of machine learning and massively parallel assays using synthetic DNA.
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Affiliation(s)
- Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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12
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Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler DM, Kueh HY. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. Proc Natl Acad Sci U S A 2023; 120:e2308366120. [PMID: 38113261 PMCID: PMC10756264 DOI: 10.1073/pnas.2308366120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023] Open
Abstract
Immune system threat detection hinges on T cells' ability to perceive varying peptide-major histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs but diverge only over longer (9+ h) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception and establish a framework for understanding T cell responses under diverse contexts.
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Affiliation(s)
- Matthew J. Wither
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - William L. White
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Sriram Pendyala
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Paul J. Leanza
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Douglas M. Fowler
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Hao Yuan Kueh
- University of Washington, Department of Bioengineering, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98109
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13
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Peña-Martínez EG, Pomales-Matos DA, Rivera-Madera A, Messon-Bird JL, Medina-Feliciano JG, Sanabria-Alberto L, Barreiro-Rosario AC, Rivera-Del Valle J, Rodríguez-Ríos JM, Rodríguez-Martínez JA. Prioritizing cardiovascular disease-associated variants altering NKX2-5 and TBX5 binding through an integrative computational approach. J Biol Chem 2023; 299:105423. [PMID: 37926287 PMCID: PMC10750078 DOI: 10.1016/j.jbc.2023.105423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies have mapped >90% of CVD-associated variants within the noncoding genome, which can alter the function of regulatory proteins, such as transcription factors (TFs). However, due to the overwhelming number of single-nucleotide polymorphisms (SNPs) (>500,000) in genome-wide association studies, prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1535 CVD-associated SNPs within TF footprints and putative cardiac enhancers plus 14,218 variants in linkage disequilibrium with genotype-dependent gene expression in cardiac tissues. Using ChIP-seq data from two cardiac TFs (NKX2-5 and TBX5) in human-induced pluripotent stem cell-derived cardiomyocytes, we trained a large-scale gapped k-mer SVM model to identify CVD-associated SNPs that altered NKX2-5 and TBX5 binding. The model was tested by scoring human heart TF genomic footprints within putative enhancers and measuring in vitro binding through electrophoretic mobility shift assay. Five variants predicted to alter NKX2-5 (rs59310144, rs6715570, and rs61872084) and TBX5 (rs7612445 and rs7790964) binding were prioritized for in vitro validation based on the magnitude of the predicted change in binding and are in cardiac tissue eQTLs. All five variants altered NKX2-5 and TBX5 DNA binding. We present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro analysis.
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Affiliation(s)
- Edwin G Peña-Martínez
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | - Diego A Pomales-Matos
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
| | | | - Jean L Messon-Bird
- Department of Biology, University of Puerto Rico Río Piedras Campus, San Juan, Puerto Rico
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14
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Kim ED, Torii KU. Stomatal cell fate commitment via transcriptional and epigenetic control: Timing is crucial. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37996970 DOI: 10.1111/pce.14761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023]
Abstract
The formation of stomata presents a compelling model system for comprehending the initiation, proliferation, commitment and differentiation of de novo lineage-specific stem cells. Precise, timely and robust cell fate and identity decisions are crucial for the proper progression and differentiation of functional stomata. Deviations from this precise specification result in developmental abnormalities and nonfunctional stomata. However, the molecular underpinnings of timely cell fate commitment have just begun to be unravelled. In this review, we explore the key regulatory strategies governing cell fate commitment, emphasizing the distinctions between embryonic and postembryonic stomatal development. Furthermore, the interplay of transcription factors and cell cycle machineries is pivotal in specifying the transition into differentiation. We aim to synthesize recent studies utilizing single-cell as well as cell-type-specific transcriptomics, epigenomics and chromatin accessibility profiling to shed light on how master-regulatory transcription factors and epigenetic machineries mutually influence each other to drive fate commitment and maintenance.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute and Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Keiko U Torii
- Howard Hughes Medical Institute and Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute of Transformative Biomolecules, Nagoya University, Nagoya, Japan
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15
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Zhong H, Zhang R, Li G, Huang P, Zhang Y, Zhu J, Kuang J, Hutchins AP, Qin D, Zhu P, Pei D, Li D. c-JUN is a barrier in hESC to cardiomyocyte transition. Life Sci Alliance 2023; 6:e202302121. [PMID: 37604584 PMCID: PMC10442936 DOI: 10.26508/lsa.202302121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
Loss of c-JUN leads to early mouse embryonic death, possibly because of a failure to develop a normal cardiac system. How c-JUN regulates human cardiomyocyte cell fate remains unknown. Here, we used the in vitro differentiation of human pluripotent stem cells into cardiomyocytes to study the role of c-JUN. Surprisingly, the knockout of c-JUN improved cardiomyocyte generation, as determined by the number of TNNT2+ cells. ATAC-seq data showed that the c-JUN defect led to increased chromatin accessibility on critical regulatory elements related to cardiomyocyte development. ChIP-seq data showed that the knockout c-JUN increased RBBP5 and SETD1B expression, leading to improved H3K4me3 deposition on key genes that regulate cardiogenesis. The c-JUN KO phenotype could be copied using the histone demethylase inhibitor CPI-455, which also up-regulated H3K4me3 levels and increased cardiomyocyte generation. Single-cell RNA-seq data defined three cell branches, and knockout c-JUN activated more regulons that are related to cardiogenesis. In summary, our data demonstrated that c-JUN could regulate cardiomyocyte cell fate by modulating H3K4me3 modification and chromatin accessibility and shed light on how c-JUN regulates heart development in humans.
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Affiliation(s)
- Hui Zhong
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ran Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Guihuan Li
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Yudan Zhang
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jieying Zhu
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Dajiang Qin
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences; Hong Kong, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease and Guangzhou Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Dongwei Li
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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16
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Peña-Martínez EG, Pomales-Matos DA, Rivera-Madera A, Messon-Bird JL, Medina-Feliciano JG, Sanabria-Alberto L, Barreiro-Rosario AC, Rodriguez-Rios JM, Rodríguez-Martínez JA. Prioritizing Cardiovascular Disease-Associated Variants Altering NKX2-5 Binding through an Integrative Computational Approach. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.01.23294951. [PMID: 37693486 PMCID: PMC10491373 DOI: 10.1101/2023.09.01.23294951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are heavily influenced by genetic factors. Genome-wide association studies (GWAS) have mapped > 90% of CVD-associated variants within the non-coding genome, which can alter the function of regulatory proteins, like transcription factors (TFs). However, due to the overwhelming number of GWAS single nucleotide polymorphisms (SNPs) (>500,000), prioritizing variants for in vitro analysis remains challenging. In this work, we implemented a computational approach that considers support vector machine (SVM)-based TF binding site classification and cardiac expression quantitative trait loci (eQTL) analysis to identify and prioritize potential CVD-causing SNPs. We identified 1,535 CVD-associated SNPs that occur within human heart footprints/enhancers and 9,309 variants in linkage disequilibrium (LD) with differential gene expression profiles in cardiac tissue. Using hiPSC-CM ChIP-seq data from NKX2-5 and TBX5, two cardiac TFs essential for proper heart development, we trained a large-scale gapped k-mer SVM (LS-GKM-SVM) predictive model that can identify binding sites altered by CVD-associated SNPs. The computational predictive model was tested by scoring human heart footprints and enhancers in vitro through electrophoretic mobility shift assay (EMSA). Three variants (rs59310144, rs6715570, and rs61872084) were prioritized for in vitro validation based on their eQTL in cardiac tissue and LS-GKM-SVM prediction to alter NKX2-5 DNA binding. All three variants altered NKX2-5 DNA binding. In summary, we present a bioinformatic approach that considers tissue-specific eQTL analysis and SVM-based TF binding site classification to prioritize CVD-associated variants for in vitro experimental analysis.
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17
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Lovato TL, Blotz B, Bileckyj C, Johnston CA, Cripps RM. Modeling a variant of unknown significance in the Drosophila ortholog of the human cardiogenic gene NKX2.5. Dis Model Mech 2023; 16:dmm050059. [PMID: 37691628 PMCID: PMC10548113 DOI: 10.1242/dmm.050059] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
Sequencing of human genome samples has unearthed genetic variants for which functional testing is necessary to validate their clinical significance. We used the Drosophila system to analyze a variant of unknown significance in the human congenital heart disease gene NKX2.5 (also known as NKX2-5). We generated an R321N allele of the NKX2.5 ortholog tinman (tin) to model a human K158N variant and tested its function in vitro and in vivo. The R321N Tin isoform bound poorly to DNA in vitro and was deficient in activating a Tin-dependent enhancer in tissue culture. Mutant Tin also showed a significantly reduced interaction with a Drosophila T-box cardiac factor named Dorsocross1. We generated a tinR321N allele using CRISPR/Cas9, for which homozygotes were viable and had normal heart specification, but showed defects in the differentiation of the adult heart that were exacerbated by further loss of tin function. We propose that the human K158N variant is pathogenic through causing a deficiency in DNA binding and a reduced ability to interact with a cardiac co-factor, and that cardiac defects might arise later in development or adult life.
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Affiliation(s)
- TyAnna L. Lovato
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Brenna Blotz
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Cayleen Bileckyj
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | | | - Richard M. Cripps
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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18
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Alzamrooni A, Mendes Vieira P, Murciano N, Wolton M, Schubert FR, Robson SC, Dietrich S. Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme. Dev Biol 2023; 501:39-59. [PMID: 37301464 DOI: 10.1016/j.ydbio.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
The vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm has generic cardiac competence, how long this may last, and what happens as cardiac competence fades, is not clear. Bone morphogenetic proteins (Bmps) are known to promote cardiogenesis. Using 41 different marker genes in the chicken embryo, we show that the paraxial head mesoderm that normally does not engage in cardiogenesis has the ability to respond to Bmp for a long time. However, Bmp signals are interpreted differently at different time points. Up to early head fold stages, the paraxial head mesoderm is able to read Bmps as signal to engage in the cardiac programme; the ability to upregulate smooth muscle markers is retained slightly longer. Notably, as cardiac competence fades, Bmp promotes the head skeletal muscle programme instead. The switch from cardiac to skeletal muscle competence is Wnt-independent as Wnt caudalises the head mesoderm and also suppresses Msc-inducing Bmp provided by the prechordal plate, thus suppressing both the cardiac and the head skeletal muscle programmes. Our study for the first time suggests a specific transition state in the embryo when cardiac competence is replaced by skeletal muscle competence. It sets the stage to unravel the cardiac-skeletal muscle antagonism that is known to partially collapse in heart failure.
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Affiliation(s)
- Afnan Alzamrooni
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Petra Mendes Vieira
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Nicoletta Murciano
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK; Nanion Technologies GmbH, Ganghoferstr. 70A, DE - 80339, München, Germany; Saarland University, Theoretical Medicine and Biosciences, Kirrbergerstr. 100, DE - 66424, Homburg, Germany
| | - Matthew Wolton
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Frank R Schubert
- Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Samuel C Robson
- Institute of Biological and Biomedical Sciences, Faculty of Science & Health, University of Portsmouth, Portsmouth, UK
| | - Susanne Dietrich
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK.
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19
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Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler D, Kueh HY. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543260. [PMID: 37333368 PMCID: PMC10274683 DOI: 10.1101/2023.06.01.543260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Immune system threat detection hinges on T cells' ability to perceive varying peptide major-histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs, but diverge only over longer (9+ hrs) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception, and establish a framework for understanding T cell responses under diverse contexts. SIGNIFICANCE STATEMENT To counter diverse pathogens, T cells mount distinct responses to varying peptide-major histocompatibility complex ligands (pMHCs). They perceive the affinity of pMHCs for the T cell receptor (TCR), which reflects its foreignness, as well as pMHC abundance. By tracking signaling responses in single living cells to different pMHCs, we find that T cells can independently perceive pMHC affinity vs dose, and encode this information through the dynamics of Erk and NFAT signaling pathways downstream of the TCR. These dynamics are jointly decoded by gene regulatory mechanisms to produce pMHC-specific activation responses. Our work reveals how T cells can elicit tailored functional responses to diverse threats and how dysregulation of these responses may lead to immune pathologies.
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20
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Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC. CHD-associated enhancers shape human cardiomyocyte lineage commitment. eLife 2023; 12:e86206. [PMID: 37096669 PMCID: PMC10156167 DOI: 10.7554/elife.86206] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/10/2023] [Indexed: 04/26/2023] Open
Abstract
Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We perform a single-cell CRISPRi screen to assess the endogenous roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHDs). We identify 16 enhancers whose repression leads to deficient differentiation of human cardiomyocytes (CMs). A focused CRISPRi validation screen shows that repression of TBX5 enhancers delays the transcriptional switch from mid- to late-stage CM states. Endogenous genetic deletions of two TBX5 enhancers phenocopy epigenetic perturbations. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients.
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Affiliation(s)
- Daniel A Armendariz
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sean C Goetsch
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Anjana Sundarrajan
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Sushama Sivakumar
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Yihan Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Shiqi Xie
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Nikhil V Munshi
- Department of Internal Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Cardiology, Department of Molecular Biology, McDermott Center for Human Growth and Development, University of Texas Southwestern Medical CenterDallasUnited States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical CenterDallasUnited States
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical CenterDallasUnited States
- Lyda Hill Department of Bioinformatics, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
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21
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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Song MK, Trembley MA, Wang P, Lu F, Gianeselli M, Prondzynski M, Bortolin RH, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity by regulating an atrial enhancer network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537535. [PMID: 37131696 PMCID: PMC10153240 DOI: 10.1101/2023.04.21.537535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa , and conversely, increased the expression of ventricular identity genes including Myl2 . Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining atrial genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. We tested this hypothesis by analyzing enhancer chromatin looping using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Together, these data demonstrate a genomic role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers and preserving tissue-specific chromatin architecture of atrial enhancers.
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22
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Taliani V, Buonaiuto G, Desideri F, Setti A, Santini T, Galfrè S, Schirone L, Mariani D, Frati G, Valenti V, Sciarretta S, Perlas E, Nicoletti C, Musarò A, Ballarino M. The long noncoding RNA Charme supervises cardiomyocyte maturation by controlling cell differentiation programs in the developing heart. eLife 2023; 12:81360. [PMID: 36877136 PMCID: PMC10023161 DOI: 10.7554/elife.81360] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/03/2023] [Indexed: 03/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are emerging as critical regulators of heart physiology and disease, although the studies unveiling their modes of action are still limited to few examples. We recently identified pCharme, a chromatin-associated lncRNA whose functional knockout in mice results in defective myogenesis and morphological remodeling of the cardiac muscle. Here, we combined Cap-Analysis of Gene Expression (CAGE), single-cell (sc)RNA sequencing, and whole-mount in situ hybridization analyses to study pCharme cardiac expression. Since the early steps of cardiomyogenesis, we found the lncRNA being specifically restricted to cardiomyocytes, where it assists the formation of specific nuclear condensates containing MATR3, as well as important RNAs for cardiac development. In line with the functional significance of these activities, pCharme ablation in mice results in a delayed maturation of cardiomyocytes, which ultimately leads to morphological alterations of the ventricular myocardium. Since congenital anomalies in myocardium are clinically relevant in humans and predispose patients to major complications, the identification of novel genes controlling cardiac morphology becomes crucial. Our study offers unique insights into a novel lncRNA-mediated regulatory mechanism promoting cardiomyocyte maturation and bears relevance to Charme locus for future theranostic applications.
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Affiliation(s)
- Valeria Taliani
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Giulia Buonaiuto
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Fabio Desideri
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Adriano Setti
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Tiziana Santini
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
| | - Silvia Galfrè
- Center for Life Nano- and Neuro-Science, Istituto Italiano di Tecnologia (IIT)RomeItaly
| | - Leonardo Schirone
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Davide Mariani
- Center for Human Technologies, Istituto Italiano di TecnologiaGenovaItaly
| | - Giacomo Frati
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Valentina Valenti
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Sebastiano Sciarretta
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of RomeLatinaItaly
| | - Emerald Perlas
- Epigenetics and Neurobiology Unit, EMBL-RomeMonterotondoItaly
| | - Carmine Nicoletti
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Antonio Musarò
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University of RomeRomeItaly
| | - Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of RomeRomeItaly
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23
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Bosada FM, van Duijvenboden K, Giovou AE, Rivaud MR, Uhm JS, Verkerk AO, Boukens BJ, Christoffels VM. An atrial fibrillation-associated regulatory region modulates cardiac Tbx5 levels and arrhythmia susceptibility. eLife 2023; 12:80317. [PMID: 36715501 PMCID: PMC9928424 DOI: 10.7554/elife.80317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/29/2023] [Indexed: 01/31/2023] Open
Abstract
Heart development and rhythm control are highly Tbx5 dosage-sensitive. TBX5 haploinsufficiency causes congenital conduction disorders, whereas increased expression levels of TBX5 in human heart samples has been associated with atrial fibrillation (AF). We deleted the conserved mouse orthologues of two independent AF-associated genomic regions in the Tbx5 locus, one intronic (RE(int)) and one downstream (RE(down)) of Tbx5. In both lines, we observed a modest (30%) increase of Tbx5 in the postnatal atria. To gain insight into the effects of slight dosage increase in vivo, we investigated the atrial transcriptional, epigenetic and electrophysiological properties of both lines. Increased atrial Tbx5 expression was associated with induction of genes involved in development, ion transport and conduction, with increased susceptibility to atrial arrhythmias, and increased action potential duration of atrial cardiomyocytes. We identified an AF-associated variant in the human RE(int) that increases its transcriptional activity. Expression of the AF-associated transcription factor Prrx1 was induced in Tbx5RE(int)KO cardiomyocytes. We found that some of the transcriptional and functional changes in the atria caused by increased Tbx5 expression were normalized when reducing cardiac Prrx1 expression in Tbx5RE(int)KO mice, indicating an interaction between these two AF genes. We conclude that modest increases in expression of dose-dependent transcription factors, caused by common regulatory variants, significantly impact on the cardiac gene regulatory network and disease susceptibility.
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Affiliation(s)
- Fernanda M Bosada
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Alexandra E Giovou
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Mathilde R Rivaud
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Jae-Sun Uhm
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Cardiology, Severance Hospital, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Arie O Verkerk
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
- Department of Physiology, University of Maastricht, Cardiovascular Research Institute Maastricht, Maastricht University Medical CenterMaastrichtNetherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of AmsterdamAmsterdamNetherlands
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24
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Deciphering Transcriptional Networks during Human Cardiac Development. Cells 2022; 11:cells11233915. [PMID: 36497174 PMCID: PMC9739390 DOI: 10.3390/cells11233915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Human heart development is governed by transcription factor (TF) networks controlling dynamic and temporal gene expression alterations. Therefore, to comprehensively characterize these transcriptional regulations, day-to-day transcriptomic profiles were generated throughout the directed cardiac differentiation, starting from three distinct human- induced pluripotent stem cell lines from healthy donors (32 days). We applied an expression-based correlation score to the chronological expression profiles of the TF genes, and clustered them into 12 sequential gene expression waves. We then identified a regulatory network of more than 23,000 activation and inhibition links between 216 TFs. Within this network, we observed previously unknown inferred transcriptional activations linking IRX3 and IRX5 TFs to three master cardiac TFs: GATA4, NKX2-5 and TBX5. Luciferase and co-immunoprecipitation assays demonstrated that these five TFs could (1) activate each other's expression; (2) interact physically as multiprotein complexes; and (3) together, finely regulate the expression of SCN5A, encoding the major cardiac sodium channel. Altogether, these results unveiled thousands of interactions between TFs, generating multiple robust hypotheses governing human cardiac development.
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25
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Scherba JC, Karra R, Turek JW, Bursac N. Toward improved understanding of cardiac development and congenital heart disease: The advent of cardiac organoids. J Thorac Cardiovasc Surg 2022; 164:2013-2018. [PMID: 35307217 PMCID: PMC9395547 DOI: 10.1016/j.jtcvs.2022.02.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
Human cardiac organoid systems hold significant promise for mechanistic studies of early heart morphogenesis and an improved understanding of congenital cardiac disease. During the past decade, we have witnessed remarkable progress in genome editing technology, stem cell research, and bioengineering. The fundamental basic research discoveries accelerate rapidly into clinical translation, paving the way for myocardial regeneration, better understanding of the structural heart disease, and bioengineering of heart structures and even entire hearts. The new horizon is vast and diverse, ranging from creating universal stem cell biobanking to genome edited heart xenotransplantation. Herein, a group of experts from Duke University discuss the state of the art and the possible influence of cardiac organoids on our understanding of structural heart disease. It may not be immediately clear now in what practical ways this technology will be translated into our daily work, yet the current progress in bioengineering will likely have a very significant influence on our surgical practice. Igor E. Konstantinov, MD, PhD, FRACS
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Affiliation(s)
- Jacob C Scherba
- Department of Biomedical Engineering, Duke University, Durham, NC; Duke University School of Medicine, Duke University, Durham, NC
| | - Ravi Karra
- Department of Medicine, Duke University Medical Center, Durham, NC; Department of Pathology, Duke University Medical Center, Durham, NC
| | - Joseph W Turek
- Duke University School of Medicine, Duke University, Durham, NC; Division of Cardiovascular and Thoracic Surgery, Duke University Medical Center, Durham, NC
| | - Nenad Bursac
- Department of Biomedical Engineering, Duke University, Durham, NC.
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Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nat Commun 2022; 13:4257. [PMID: 35871075 PMCID: PMC9308780 DOI: 10.1038/s41467-022-31938-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/11/2022] [Indexed: 11/26/2022] Open
Abstract
Fate-determining transcription factors (TFs) can promote lineage-restricted transcriptional programs from common progenitor states. The inner cell mass (ICM) of mouse blastocysts co-expresses the TFs NANOG and GATA6, which drive the bifurcation of the ICM into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, we induce GATA6 in embryonic stem cells–that also express NANOG–to characterize how a state of co-expression of opposing TFs resolves into divergent lineages. Surprisingly, we find that GATA6 and NANOG co-bind at the vast majority of Epi and PrE enhancers, a phenomenon we also observe in blastocysts. The co-bound state is followed by eviction and repression of Epi TFs, and quick remodeling of chromatin and enhancer-promoter contacts thus establishing the PrE lineage while repressing the Epi fate. We propose that co-binding of GATA6 and NANOG at shared enhancers maintains ICM plasticity and promotes the rapid establishment of Epi- and PrE-specific transcriptional programs. The authors show that the transcription factors NANOG and GATA6 co-bind the same enhancers in common progenitors before divergent epiblast and primitive endoderm lineages emerge. This may help maintain plasticity at early stages and facilitate bifurcation into distinct lineages
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Yin XY, Chen HX, Chen Z, Yang Q, Han J, He GW. Identification and functional analysis of genetic variants of ISL1 gene promoter in human atrial septal defects. J Gene Med 2022; 24:e3450. [PMID: 36170181 DOI: 10.1002/jgm.3450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 09/25/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Atrial septal defect (ASD) is a common type of congenital heart disease. A gene promoter plays pivotal role in the disease development. This study was designed to investigate the pathological role of variants of the ISL1 gene promoter region in ASD patients. METHODS Total DNA extracted from 625 subjects, including 332 ASD patients and 293 healthy controls, was sequenced to identify variants in the promoter region of ISL1 gene. Further functional analyses of the variants were performed with dual luciferase reporter assay and electrophoretic mobility shift assay (EMSA). All possible binding sites of transcription factor affected by the identified variants were predicted using the JASPAR database. RESULTS Four variants in the ISL1 gene promoter were found only in patients with ASD by sequencing. Three of the four variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] significantly decreased the transcriptional activities compared with the wild-type ISL1 gene promoter (p < 0.05). The EMSA revealed that these variants [g.4923 G > C (rs541081886), g.5079 A > G (rs1371835943) and g.5309 G > A (rs116222082)] in the ISL1 gene promoter affected the number and affinity of binding sites of transcription factors. Further analysis with the online JASPAR database demonstrated that a cluster of putative binding sites for transcription factors may be altered by these variants. CONCLUSIONS These sequence variants identified from the promoter region of ISL1 gene in ASD patients are probably involved in the development of ASD by affecting the transcriptional activity and altering ISL1 levels. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of ASD.
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Affiliation(s)
- Xiu-Yun Yin
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China & The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Zhuo Chen
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China & The Institute of Cardiovascular Diseases, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Jun Han
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu, Anhui, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
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Kim ED, Dorrity MW, Fitzgerald BA, Seo H, Sepuru KM, Queitsch C, Mitsuda N, Han SK, Torii KU. Dynamic chromatin accessibility deploys heterotypic cis/trans-acting factors driving stomatal cell-fate commitment. NATURE PLANTS 2022; 8:1453-1466. [PMID: 36522450 PMCID: PMC9788986 DOI: 10.1038/s41477-022-01304-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/28/2022] [Indexed: 05/12/2023]
Abstract
Chromatin architecture and transcription factor (TF) binding underpin cell-fate specification during development, but their mutual regulatory relationships remain unclear. Here we report an atlas of dynamic chromatin landscapes during stomatal cell-lineage progression, in which sequential cell-state transitions are governed by lineage-specific bHLH TFs. Major reprogramming of chromatin accessibility occurs at the proliferation-to-differentiation transition. We discover novel co-cis regulatory elements (CREs) signifying the early precursor stage, BBR/BPC (GAGA) and bHLH (E-box) motifs, where master-regulatory bHLH TFs, SPEECHLESS and MUTE, consecutively bind to initiate and terminate the proliferative state, respectively. BPC TFs complex with MUTE to repress SPEECHLESS expression through a local deposition of repressive histone marks. We elucidate the mechanism by which cell-state-specific heterotypic TF complexes facilitate cell-fate commitment by recruiting chromatin modifiers via key co-CREs.
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Affiliation(s)
- Eun-Deok Kim
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Bridget A Fitzgerald
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hyemin Seo
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Krishna Mohan Sepuru
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Soon-Ki Han
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Keiko U Torii
- Howard Hughes Medical Institute, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya, Aichi, Japan.
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Wu X, Chen Y, Luz A, Hu G, Tokar EJ. Cardiac Development in the Presence of Cadmium: An in Vitro Study Using Human Embryonic Stem Cells and Cardiac Organoids. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:117002. [PMID: 36321828 PMCID: PMC9628677 DOI: 10.1289/ehp11208] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND Exposure to cadmium (Cd) is associated with cardiovascular diseases. Maternal Cd exposure is a significant risk factor for congenital heart disease. However, mechanisms of Cd on developmental cardiotoxicity are not well defined. OBJECTIVES We evaluated the effects of Cd on the different stages (mesoderm, cardiac induction, cardiac function) of cardiac development using an early embryo development in vitro model and two- or three-dimensional (2- or 3D) cardiomyocyte and cardiac organoid formation models mimicking early cardiac development. METHODS Embryonic stem cells (ESCs) form 3D aggregates, called embryoid bodies, that recapitulate events involved with early embryogenesis (e.g., germ layer formation). This model was used for early germ layer formation and signaling pathway identification. The 2D cardiomyocyte differentiation from the NKX2-5eGFP/w human ESCs model was used to explore the effects of Cd exposure on cardiomyocyte formation and to model mesoderm differentiation and cardiac induction, allowing us to explore different developmental windows of Cd toxicity. The 3D cardiac organoid model was used in evaluating the effects of Cd exposure on contractility and cardiac development. RESULTS Cd (0.6μM; 110 ppb) lowered the differentiation of embryoid bodies to mesoderm via suppression of Wnt/β-catenin-signaling pathways. During early mesoderm induction, the mesoderm-associated transcription factors MESP1 and EOMES showed a transient up-regulation, which decreased later in the cardiac induction stage. Cd (0.15μM) lowered mesoderm formation and cardiac induction through suppression of the transcription factors and mesoderm marker genes HAND1, SNAI2, HOPX, and the cardiac-specific genes NKX2-5, GATA4, troponin T, and alpha-actinin. In addition, Cd-induced histone modifications for both gene activation (H3K4me3) and repression (H3K27me3), which play vital roles in regulating mesoderm commitment markers. The effects of Cd inhibition on cardiomyocyte differentiation were confirmed in 3D cardiac organoids. DISCUSSION In conclusion, using a human ESC-derived 2D/3D in vitro differentiation model system and cardiac organoids, we demonstrated that low-dose Cd suppressed mesoderm formation through mesoderm gene histone modification, thus inhibiting cardiomyocyte differentiation and cardiac induction. The studies provide valuable insights into cellular events and molecular mechanisms associated with Cd-induced congenital heart disease. https://doi.org/10.1289/EHP11208.
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Affiliation(s)
- Xian Wu
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute for Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Yichang Chen
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute for Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Anthony Luz
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute for Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, Division of Intramural Research, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Erik J. Tokar
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute for Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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30
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Crespo-García T, Cámara-Checa A, Dago M, Rubio-Alarcón M, Rapún J, Tamargo J, Delpón E, Caballero R. Regulation of cardiac ion channels by transcription factors: Looking for new opportunities of druggable targets for the treatment of arrhythmias. Biochem Pharmacol 2022; 204:115206. [PMID: 35963339 DOI: 10.1016/j.bcp.2022.115206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Cardiac electrical activity is governed by different ion channels that generate action potentials. Acquired or inherited abnormalities in the expression and/or function of ion channels usually result in electrophysiological changes that can cause cardiac arrhythmias. Transcription factors (TFs) control gene transcription by binding to specific DNA sequences adjacent to target genes. Linkage analysis, candidate-gene screening within families, and genome-wide association studies have linked rare and common genetic variants in the genes encoding TFs with genetically-determined cardiac arrhythmias. Besides its critical role in cardiac development, recent data demonstrated that they control cardiac electrical activity through the direct regulation of the expression and function of cardiac ion channels in adult hearts. This narrative review summarizes some studies showing functional data on regulation of the main human atrial and ventricular Na+, Ca2+, and K+ channels by cardiac TFs such as Pitx2c, Tbx20, Tbx5, Zfhx3, among others. The results have improved our understanding of the mechanisms regulating cardiac electrical activity and may open new avenues for therapeutic interventions in cardiac acquired or inherited arrhythmias through the identification of TFs as potential drug targets. Even though TFs have for a long time been considered as 'undruggable' targets, advances in structural biology have led to the identification of unique pockets in TFs amenable to be targeted with small-molecule drugs or peptides that are emerging as novel therapeutic drugs.
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Affiliation(s)
- T Crespo-García
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - A Cámara-Checa
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - M Dago
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - M Rubio-Alarcón
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - J Rapún
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - J Tamargo
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | - E Delpón
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain.
| | - R Caballero
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
| | -
- Department of Pharmacology and Toxicology. School of Medicine. Universidad Complutense de Madrid, Instituto de Investigación Sanitaria Gregorio Marañón. CIBERCV, 28040 Madrid, Spain
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31
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Hertweck A, Vila de Mucha M, Barber PR, Dagil R, Porter H, Ramos A, Lord GM, Jenner RG. The TH1 cell lineage-determining transcription factor T-bet suppresses TH2 gene expression by redistributing GATA3 away from TH2 genes. Nucleic Acids Res 2022; 50:4557-4573. [PMID: 35438764 PMCID: PMC9071441 DOI: 10.1093/nar/gkac258] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 03/28/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022] Open
Abstract
Lineage-determining transcription factors (LD-TFs) drive the differentiation of progenitor cells into a specific lineage. In CD4+ T cells, T-bet dictates differentiation of the TH1 lineage, whereas GATA3 drives differentiation of the alternative TH2 lineage. However, LD-TFs, including T-bet and GATA3, are frequently co-expressed but how this affects LD-TF function is not known. By expressing T-bet and GATA3 separately or together in mouse T cells, we show that T-bet sequesters GATA3 at its target sites, thereby removing GATA3 from TH2 genes. This redistribution of GATA3 is independent of GATA3 DNA binding activity and is instead mediated by the T-bet DNA binding domain, which interacts with the GATA3 DNA binding domain and changes GATA3's sequence binding preference. This mechanism allows T-bet to drive the TH1 gene expression program in the presence of GATA3. We propose that redistribution of one LD-TF by another may be a common mechanism that could explain how specific cell fate choices can be made even in the presence of other transcription factors driving alternative differentiation pathways.
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Affiliation(s)
- Arnulf Hertweck
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Maria Vila de Mucha
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Paul R Barber
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK.,Comprehensive Cancer Centre, School of Cancer & Pharmaceutical Sciences, King's College London, London, SE1 1UL, UK
| | - Robert Dagil
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Hayley Porter
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
| | - Andres Ramos
- Research Department of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London, WC1E 6XA, UK
| | - Graham M Lord
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9NT, UK
| | - Richard G Jenner
- UCL Cancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, WC1E 6BT, UK
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32
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Robbe ZL, Shi W, Wasson LK, Scialdone AP, Wilczewski CM, Sheng X, Hepperla AJ, Akerberg BN, Pu WT, Cristea IM, Davis IJ, Conlon FL. CHD4 is recruited by GATA4 and NKX2-5 to repress noncardiac gene programs in the developing heart. Genes Dev 2022; 36:468-482. [PMID: 35450884 PMCID: PMC9067406 DOI: 10.1101/gad.349154.121] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/31/2022] [Indexed: 12/23/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is one of the central chromatin remodeling complexes that mediates gene repression. NuRD is essential for numerous developmental events, including heart development. Clinical and genetic studies have provided direct evidence for the role of chromodomain helicase DNA-binding protein 4 (CHD4), the catalytic component of NuRD, in congenital heart disease (CHD), including atrial and ventricular septal defects. Furthermore, it has been demonstrated that CHD4 is essential for mammalian cardiomyocyte formation and function. A key unresolved question is how CHD4/NuRD is localized to specific cardiac target genes, as neither CHD4 nor NuRD can directly bind DNA. Here, we coupled a bioinformatics-based approach with mass spectrometry analyses to demonstrate that CHD4 interacts with the core cardiac transcription factors GATA4, NKX2-5, and TBX5 during embryonic heart development. Using transcriptomics and genome-wide occupancy data, we characterized the genomic landscape of GATA4, NKX2-5, and TBX5 repression and defined the direct cardiac gene targets of the GATA4-CHD4, NKX2-5-CHD4, and TBX5-CHD4 complexes. These data were used to identify putative cis-regulatory elements controlled by these complexes. We genetically interrogated two of these silencers in vivo: Acta1 and Myh11 We show that deletion of these silencers leads to inappropriate skeletal and smooth muscle gene misexpression, respectively, in the embryonic heart. These results delineate how CHD4/NuRD is localized to specific cardiac loci and explicates how mutations in the broadly expressed CHD4 protein lead to cardiac-specific disease states.
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Affiliation(s)
- Zachary L Robbe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Wei Shi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Lauren K Wasson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Angel P Scialdone
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Caralynn M Wilczewski
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Austin J Hepperla
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Frank L Conlon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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34
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Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell 2022; 185:794-814.e30. [PMID: 35182466 PMCID: PMC8923057 DOI: 10.1016/j.cell.2022.01.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/20/2021] [Accepted: 01/25/2022] [Indexed: 02/08/2023]
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.
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Affiliation(s)
- Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Maureen Pittman
- Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Franco Felix
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Desmond Richmond-Buccola
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Mauro W Costa
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michael Alexanian
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Clara Youngna Lee
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Bonnie E J Maven
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Kaitlen Samse-Knapp
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Sarah U Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Michael McGregor
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Casey A Gifford
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Brian L Black
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA
| | - Nevan J Krogan
- Gladstone Institutes, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Division of Cardiology, Department of Pediatrics, UCSF School of Medicine, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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Wu T, Liang Z, Zhang Z, Liu C, Zhang L, Gu Y, Peterson KL, Evans SM, Fu XD, Chen J. PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle. Circulation 2022; 145:586-602. [PMID: 34915728 PMCID: PMC8860879 DOI: 10.1161/circulationaha.121.056666] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/29/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Left ventricular noncompaction cardiomyopathy (LVNC) was discovered half a century ago as a cardiomyopathy with excessive trabeculation and a thin ventricular wall. In the decades since, numerous studies have demonstrated that LVNC primarily has an effect on left ventricles (LVs) and is often associated with LV dilation and dysfunction. However, in part because of the lack of suitable mouse models that faithfully mirror the selective LV vulnerability in patients, mechanisms underlying the susceptibility of LVs to dilation and dysfunction in LVNC remain unknown. Genetic studies have revealed that deletions and mutations in PRDM16 (PR domain-containing 16) cause LVNC, but previous conditional Prdm16 knockout mouse models do not mirror the LVNC phenotype in patients, and the underlying molecular mechanisms by which PRDM16 deficiency causes LVNC are still unclear. METHODS Prdm16 cardiomyocyte-specific knockout (Prdm16cKO) mice were generated and analyzed for cardiac phenotypes. RNA sequencing and chromatin immunoprecipitation deep sequencing were performed to identify direct transcriptional targets of PRDM16 in cardiomyocytes. Single-cell RNA sequencing in combination with spatial transcriptomics was used to determine cardiomyocyte identity at the single-cell level. RESULTS Cardiomyocyte-specific ablation of Prdm16 in mice caused LV-specific dilation and dysfunction, as well as biventricular noncompaction, which fully recapitulated LVNC in patients. PRDM16 functioned mechanistically as a compact myocardium-enriched transcription factor that activated compact myocardial genes while repressing trabecular myocardial genes in LV compact myocardium. Consequently, Prdm16cKO LV compact myocardial cardiomyocytes shifted from their normal transcriptomic identity to a transcriptional signature resembling trabecular myocardial cardiomyocytes or neurons. Chamber-specific transcriptional regulation by PRDM16 was attributable in part to its cooperation with LV-enriched transcription factors Tbx5 and Hand1. CONCLUSIONS These results demonstrate that disruption of proper specification of compact cardiomyocytes may play a key role in the pathogenesis of LVNC. They also shed light on underlying mechanisms of the LV-restricted transcriptional program governing LV chamber growth and maturation, providing a tangible explanation for the susceptibility of LV in a subset of LVNC cardiomyopathies.
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Affiliation(s)
- Tongbin Wu
- Department of Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zhengyu Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- These authors contributed equally
| | - Zengming Zhang
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Lunfeng Zhang
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Yusu Gu
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Kirk L. Peterson
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Sylvia M. Evans
- Department of Medicine, University of California San Diego, La Jolla, CA
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
- Institute of Genomic Medicine, University of California San Diego, La Jolla, CA
| | - Ju Chen
- Department of Medicine, University of California San Diego, La Jolla, CA
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Abstract
The Human Genome Project marked a major milestone in the scientific community as it unravelled the ~3 billion bases that are central to crucial aspects of human life. Despite this achievement, it only scratched the surface of understanding how each nucleotide matters, both individually and as part of a larger unit. Beyond the coding genome, which comprises only ~2% of the whole genome, scientists have realized that large portions of the genome, not known to code for any protein, were crucial for regulating the coding genes. These large portions of the genome comprise the 'non-coding genome'. The history of gene regulation mediated by proteins that bind to the regulatory non-coding genome dates back many decades to the 1960s. However, the original definition of 'enhancers' was first used in the early 1980s. In this Review, we summarize benchmark studies that have mapped the role of cardiac enhancers in disease and development. We highlight instances in which enhancer-localized genetic variants explain the missing link to cardiac pathogenesis. Finally, we inspire readers to consider the next phase of exploring enhancer-based gene therapy for cardiovascular disease.
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37
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Zheng H, Zhai W, Zhong C, Hong Q, Li H, Rui B, Zhu X, Que D, Feng L, Yu B, Huang G, Yin J, Li J, Yan J, Yang P. Nkx2-3 induces autophagy inhibiting proliferation and migration of vascular smooth muscle cells via AMPK/mTOR signaling pathway. J Cell Physiol 2021; 236:7342-7355. [PMID: 33928642 DOI: 10.1002/jcp.30400] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 12/25/2022]
Abstract
Vascular remodeling and restenosis are common complications after percutaneous coronary intervention. Excessive proliferation and migration of vascular smooth muscle cells (VSMCs) play important roles in intimal hyperplasia-induced vascular restenosis. NK2 Homeobox 3 (Nkx2-3), a critical member of Nkx family, is involved in tissue differentiation and organ development. However, the role of Nkx2-3 in VSMCs proliferation and migration remains unknown. In this study, we used carotid balloon injury model and platelet-derived growth factor-BB (PDGF)-treated VSMCs as in vivo and in vitro experimental models. EdU assay and CCK-8 assay were used to detect cell proliferation. Migration was measured by scratch test. Hematoxylin and eosin staining and immunohistochemistry staining were used to evaluate the intimal hyperplasia. The autophagy level was detected by fluorescent mRFP-GFP-LC3 in vitro and by transmission electron microscopy in vivo. It was shown that Nkx2-3 was upregulated both in balloon injured carotid arteries and PDGF-stimulated VSMCs. Adenovirus-mediated Nkx2-3 overexpression inhibited intimal hyperplasia after balloon injury, and suppressed VSMCs proliferation and migration induced by PDGF. Conversely, silencing of Nkx2-3 by small interfering RNA exaggerated proliferation and migration of VSMCs. Furthermore, we found that Nkx2-3 enhanced autophagy level, while the autophagy inhibitor 3-MA eliminated the inhibitory effect of Nkx2-3 on VSMCs proliferation and migration both in vivo and in vitro. Moreover, Nkx2-3 promoted autophagy in VSMCs by activating the AMP-activated protein kinase/mammalian target of rapamycin (AMPK/mTOR) signaling pathway. These results demonstrated for the first time that Nkx2-3 inhibited VSMCs proliferation and migration through AMPK/mTOR-mediated autophagy.
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MESH Headings
- AMP-Activated Protein Kinases/metabolism
- Animals
- Autophagy/drug effects
- Becaplermin/pharmacology
- Carotid Artery Injuries/enzymology
- Carotid Artery Injuries/genetics
- Carotid Artery Injuries/pathology
- Carotid Artery Injuries/prevention & control
- Cell Movement/drug effects
- Cell Proliferation/drug effects
- Cells, Cultured
- Disease Models, Animal
- Homeodomain Proteins/genetics
- Homeodomain Proteins/physiology
- Male
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/enzymology
- Muscle, Smooth, Vascular/ultrastructure
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/enzymology
- Myocytes, Smooth Muscle/ultrastructure
- Neointima
- Rats, Sprague-Dawley
- Signal Transduction
- TOR Serine-Threonine Kinases/metabolism
- Transcription Factors/genetics
- Transcription Factors/physiology
- Vascular Remodeling
- Rats
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Affiliation(s)
- Huajun Zheng
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Weicheng Zhai
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Chongbin Zhong
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Qingqing Hong
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Hekai Li
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Bowen Rui
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Xingxing Zhu
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Dongdong Que
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Liyun Feng
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Bin Yu
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Guanlin Huang
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Jianlong Yin
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Jiacheng Li
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Jing Yan
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
| | - Pingzhen Yang
- Department of Cardiology, Laboratory of Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Guangdong Provincial Biomedical Engineering Technology Research Center for Cardiovascular Disease, Guangzhou, Guangdong, China
- Heart Center of Zhujiang Hospital, Sino-Japanese Cooperation Platform for Translational Research in Heart Failure, Guangzhou, Guangdong, China
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Rowton M, Guzzetta A, Rydeen AB, Moskowitz IP. Control of cardiomyocyte differentiation timing by intercellular signaling pathways. Semin Cell Dev Biol 2021; 118:94-106. [PMID: 34144893 PMCID: PMC8968240 DOI: 10.1016/j.semcdb.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
Congenital Heart Disease (CHD), malformations of the heart present at birth, is the most common class of life-threatening birth defect (Hoffman (1995) [1], Gelb (2004) [2], Gelb (2014) [3]). A major research challenge is to elucidate the genetic determinants of CHD and mechanistically link CHD ontogeny to a molecular understanding of heart development. Although the embryonic origins of CHD are unclear in most cases, dysregulation of cardiovascular lineage specification, patterning, proliferation, migration or differentiation have been described (Olson (2004) [4], Olson (2006) [5], Srivastava (2006) [6], Dunwoodie (2007) [7], Bruneau (2008) [8]). Cardiac differentiation is the process whereby cells become progressively more dedicated in a trajectory through the cardiac lineage towards mature cardiomyocytes. Defects in cardiac differentiation have been linked to CHD, although how the complex control of cardiac differentiation prevents CHD is just beginning to be understood. The stages of cardiac differentiation are highly stereotyped and have been well-characterized (Kattman et al. (2011) [9], Wamstad et al. (2012) [10], Luna-Zurita et al. (2016) [11], Loh et al. (2016) [12], DeLaughter et al. (2016) [13]); however, the developmental and molecular mechanisms that promote or delay the transition of a cell through these stages have not been as deeply investigated. Tight temporal control of progenitor differentiation is critically important for normal organ size, spatial organization, and cellular physiology and homeostasis of all organ systems (Raff et al. (1985) [14], Amthor et al. (1998) [15], Kopan et al. (2014) [16]). This review will focus on the action of signaling pathways in the control of cardiomyocyte differentiation timing. Numerous signaling pathways, including the Wnt, Fibroblast Growth Factor, Hedgehog, Bone Morphogenetic Protein, Insulin-like Growth Factor, Thyroid Hormone and Hippo pathways, have all been implicated in promoting or inhibiting transitions along the cardiac differentiation trajectory. Gaining a deeper understanding of the mechanisms controlling cardiac differentiation timing promises to yield insights into the etiology of CHD and to inform approaches to restore function to damaged hearts.
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39
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Dixit R, Narasimhan C, Balekundri VI, Agrawal D, Kumar A, Mohapatra B. Functional analysis of novel genetic variants of NKX2-5 associated with nonsyndromic congenital heart disease. Am J Med Genet A 2021; 185:3644-3663. [PMID: 34214246 DOI: 10.1002/ajmg.a.62413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 01/26/2023]
Abstract
NKX2-5, a master cardiac regulatory transcription factor was the first known genetic cause of congenital heart diseases (CHDs). To further investigate its role in CHD pathogenesis, we performed mutational screening of 285 CHD probands and 200 healthy controls. Five coding sequence variants were identified in six CHD cases (2.1%), including three in the N-terminal region (p.A61G, p.R95L, and p.E131K) and one each in homeodomain (HD) (p.A148E) and tyrosine-rich domain (p.P247A). Variant-p.A148E showed tertiary structure changes and differential DNA binding affinity of mutant compared to wild type. Two N-terminal variants-p.A61G and p.E131K along with HD variant p.A148E demonstrated significantly reduced transcriptional activity of Nppa and Actc1 promoters in dual luciferase promoter assay supported by their reduced expression in qRT-PCR. Nonetheless, variant p.R95L affected the synergy of NKX2-5 with serum response factor and TBX5 leading to significantly decreased Actc1 promoter activity depicting a distinctive role of this region. The aberrant expression of other target genes-Irx4, Mef2c, Bmp10, Myh6, Myh7, and Myocd is also observed in response to NKX2-5 variants, possibly due to the defective gene regulatory network. Severely impaired downstream promoter activities and abnormal expression of target genes due to N-terminal variants supports the emerging role of this region during cardiac-developmental pathways.
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Affiliation(s)
- Ritu Dixit
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Chitra Narasimhan
- Department of Pediatric Cardiology, Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, Karnataka, India
| | - Vijayalakshmi I Balekundri
- Super Speciality Hospital, Pradhan Mantri Swasthya Suraksha Yojana (PMSSY), Medical College and Research Institute, Bengaluru, Karnataka, India
| | - Damyanti Agrawal
- Department of Cardiothoracic and Vascular Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ashok Kumar
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Bhagyalaxmi Mohapatra
- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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40
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Guo F, Hall AR, Tape CJ, Ling S, Pointon A. Intra- and intercellular signaling pathways associated with drug-induced cardiac pathophysiology. Trends Pharmacol Sci 2021; 42:675-687. [PMID: 34092416 DOI: 10.1016/j.tips.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022]
Abstract
Cardiac physiology and homeostasis are maintained by the interaction of multiple cell types, via both intra- and intercellular signaling pathways. Perturbations in these signaling pathways induced by oncology therapies can reduce cardiac function, ultimately leading to heart failure. As cancer survival increases, related cardiovascular complications are becoming increasingly prevalent, thus identifying the perturbations and cell signaling drivers of cardiotoxicity is increasingly important. Here, we discuss the homotypic and heterotypic cellular interactions that form the basis of intra- and intercellular cardiac signaling pathways, and how oncological agents disrupt these pathways, leading to heart failure. We also highlight the emerging systems biology techniques that can be applied, enabling a deeper understanding of the intra- and intercellular signaling pathways across multiple cell types associated with cardiovascular toxicity.
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Affiliation(s)
- Fei Guo
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, Research and Development, AstraZeneca, Cambridge, UK; Cell Communication Laboratory, Department of Oncology, University College London Cancer Institute, London, WC1E 6DD, UK
| | - Andrew R Hall
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, Research and Development, AstraZeneca, Cambridge, UK
| | - Christopher J Tape
- Cell Communication Laboratory, Department of Oncology, University College London Cancer Institute, London, WC1E 6DD, UK
| | - Stephanie Ling
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, Research and Development, AstraZeneca, Cambridge, UK
| | - Amy Pointon
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, Research and Development, AstraZeneca, Cambridge, UK.
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41
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Briganti F, Sun H, Wei W, Wu J, Zhu C, Liss M, Karakikes I, Rego S, Cipriano A, Snyder M, Meder B, Xu Z, Millat G, Gotthardt M, Mercola M, Steinmetz LM. iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy. Cell Rep 2021; 32:108117. [PMID: 32905764 PMCID: PMC8168789 DOI: 10.1016/j.celrep.2020.108117] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/11/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Recent advances in induced pluripotent stem cell (iPSC) technology and directed differentiation of iPSCs into cardiomyocytes (iPSC-CMs) make it possible to model genetic heart disease in vitro. We apply CRISPR/Cas9 genome editing technology to introduce three RBM20 mutations in iPSCs and differentiate them into iPSC-CMs to establish an in vitro model of RBM20 mutant dilated cardiomyopathy (DCM). In iPSC-CMs harboring a known causal RBM20 variant, the splicing of RBM20 target genes, calcium handling, and contractility are impaired consistent with the disease manifestation in patients. A variant (Pro633Leu) identified by exome sequencing of patient genomes displays the same disease phenotypes, thus establishing this variant as disease causing. We find that all-trans retinoic acid upregulates RBM20 expression and reverts the splicing, calcium handling, and contractility defects in iPSC-CMs with different causal RBM20 mutations. These results suggest that pharmacological upregulation of RBM20 expression is a promising therapeutic strategy for DCM patients with a heterozygous mutation in RBM20. Briganti et al. use iPSC and CRISPR/Cas9 to create a model of RBM20-deficient dilated cardiomyopathy (DCM) that recapitulates mRNA splicing and contractile defects of the disease. They evaluate pharmacological upregulation of RBM20 as a therapeutic strategy. All-trans retinoic acid upregulates RBM20 expression and ameliorates the in vitro hallmarks of disease.
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Affiliation(s)
- Francesca Briganti
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany; Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, USA
| | - Han Sun
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Wu Wei
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jingyan Wu
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Chenchen Zhu
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Martin Liss
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ioannis Karakikes
- Cardiovascular Institute and Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Shannon Rego
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Andrea Cipriano
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Benjamin Meder
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA; Institute for Cardiomyopathies Heidelberg and Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Zhenyu Xu
- SOPHiA Genetics, St. Sulpice, Switzerland
| | - Gilles Millat
- Laboratoire de Cardiogénétique Moléculaire, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Department of Cardiology, Charité-Universitätsmedizin Berlin, Berlin, Germany; DZHK: German Center for Cardiovascular Research, Partner Site Berlin, Berlin, Germany
| | - Mark Mercola
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany; Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, CA, USA; Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA; DZHK: German Center for Cardiovascular Research, Partner Site EMBL Heidelberg, Heidelberg, Germany.
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42
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Delgado I, Giovinazzo G, Temiño S, Gauthier Y, Balsalobre A, Drouin J, Torres M. Control of mouse limb initiation and antero-posterior patterning by Meis transcription factors. Nat Commun 2021; 12:3086. [PMID: 34035267 PMCID: PMC8149412 DOI: 10.1038/s41467-021-23373-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 04/21/2021] [Indexed: 12/31/2022] Open
Abstract
Meis1 and Meis2 are homeodomain transcription factors that regulate organogenesis through cooperation with Hox proteins. Elimination of Meis genes after limb induction has shown their role in limb proximo-distal patterning; however, limb development in the complete absence of Meis function has not been studied. Here, we report that Meis1/2 inactivation in the lateral plate mesoderm of mouse embryos leads to limb agenesis. Meis and Tbx factors converge in this function, extensively co-binding with Tbx to genomic sites and co-regulating enhancers of Fgf10, a critical factor in limb initiation. Limbs with three deleted Meis alleles show proximal-specific skeletal hypoplasia and agenesis of posterior skeletal elements. This failure in posterior specification results from an early role of Meis factors in establishing the limb antero-posterior prepattern required for Shh activation. Our results demonstrate roles for Meis transcription factors in early limb development and identify their involvement in previously undescribed interaction networks that regulate organogenesis.
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Affiliation(s)
- Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Giovanna Giovinazzo
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana Temiño
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Yves Gauthier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Aurelio Balsalobre
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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Man JCK, Bosada FM, Scholman KT, Offerhaus JA, Walsh R, van Duijvenboden K, van Eif VWW, Bezzina CR, Verkerk AO, Boukens BJ, Barnett P, Christoffels VM. Variant Intronic Enhancer Controls SCN10A-short Expression and Heart Conduction. Circulation 2021; 144:229-242. [PMID: 33910361 DOI: 10.1161/circulationaha.121.054083] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Genetic variants in SCN10A, encoding the neuronal voltage-gated sodium channel NaV1.8, are strongly associated with atrial fibrillation, Brugada syndrome, cardiac conduction velocities, and heart rate. The cardiac function of SCN10A has not been resolved, however, and diverging mechanisms have been proposed. Here, we investigated the cardiac expression of SCN10A and the function of a variant-sensitive intronic enhancer previously linked to the regulation of SCN5A, encoding the major essential cardiac sodium channel NaV1.5. METHODS The expression of SCN10A was investigated in mouse and human hearts. With the use of CRISPR/Cas9 genome editing, the mouse intronic enhancer was disrupted, and mutant mice were characterized by transcriptomic and electrophysiological analyses. The association of genetic variants at SCN5A-SCN10A enhancer regions and gene expression were evaluated by genome-wide association studies single-nucleotide polymorphism mapping and expression quantitative trait loci analysis. RESULTS We found that cardiomyocytes of the atria, sinoatrial node, and ventricular conduction system express a short transcript comprising the last 7 exons of the gene (Scn10a-short). Transcription occurs from an intronic enhancer-promoter complex, whereas full-length Scn10a transcript was undetectable in the human and mouse heart. Expression quantitative trait loci analysis revealed that the genetic variants in linkage disequilibrium with genetic variant rs6801957 in the intronic enhancer associate with SCN10A transcript levels in the heart. Genetic modification of the enhancer in the mouse genome led to reduced cardiac Scn10a-short expression in atria and ventricles, reduced cardiac sodium current in atrial cardiomyocytes, atrial conduction slowing and arrhythmia, whereas the expression of Scn5a, the presumed enhancer target gene, remained unaffected. In patch-clamp transfection experiments, expression of Scn10a-short-encoded NaV1.8-short increased NaV1.5-mediated sodium current. We propose that noncoding genetic variation modulates transcriptional regulation of Scn10a-short in cardiomyocytes that impacts NaV1.5-mediated sodium current and heart rhythm. CONCLUSIONS Genetic variants in and around SCN10A modulate enhancer function and expression of a cardiac-specific SCN10A-short transcript. We propose that noncoding genetic variation modulates transcriptional regulation of a functional C-terminal portion of NaV1.8 in cardiomyocytes that impacts on NaV1.5 function, cardiac conduction velocities, and arrhythmia susceptibility.
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Affiliation(s)
- Joyce C K Man
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Fernanda M Bosada
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Koen T Scholman
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Joost A Offerhaus
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Roddy Walsh
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Karel van Duijvenboden
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent W W van Eif
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Connie R Bezzina
- Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Arie O Verkerk
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Department of Experimental Cardiology (J.A.O., R.W., C.R.B., A.O.V., B.J.B.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Phil Barnett
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands.,Amsterdam Cardiovascular Sciences, Amsterdam Reproduction and Development (J.C.K.M., F.M.B., K.T.S., K.v.D., V.W.W.v.E., A.O.V., B.J.B., P.B., V.M.C.), Amsterdam UMC, University of Amsterdam, location AMC, The Netherlands
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44
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Rothenberg EV. Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment. Biophys J 2021; 120:4162-4181. [PMID: 33838137 PMCID: PMC8516641 DOI: 10.1016/j.bpj.2021.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/22/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Transcription factors are the major agents that read the regulatory sequence information in the genome to initiate changes in expression of specific genes, both in development and in physiological activation responses. Their actions depend on site-specific DNA binding and are largely guided by their individual DNA target sequence specificities. However, their action is far more conditional in a real developmental context than would be expected for simple reading of local genomic DNA sequence, which is common to all cells in the organism. They are constrained by slow-changing chromatin states and by interactions with other transcription factors, which affect their occupancy patterns of potential sites across the genome. These mechanisms lead to emergent discontinuities in function even for transcription factors with minimally changing expression. This is well revealed by diverse lineages of blood cells developing throughout life from hematopoietic stem cells, which use overlapping combinations of transcription factors to drive strongly divergent gene regulation programs. Here, using development of T lymphocytes from hematopoietic multipotent progenitor cells as a focus, recent evidence is reviewed on how binding specificity and dynamics, transcription factor cooperativity, and chromatin state changes impact the effective regulatory functions of key transcription factors including PU.1, Runx1, Notch-RBPJ, and Bcl11b.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.
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45
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Välimäki MJ, Leigh RS, Kinnunen SM, March AR, de Sande AH, Kinnunen M, Varjosalo M, Heinäniemi M, Kaynak BL, Ruskoaho H. GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line. Stem Cell Res Ther 2021; 12:190. [PMID: 33736688 PMCID: PMC7977156 DOI: 10.1186/s13287-021-02259-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Pharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. Compounds that target tissue-specific transcription factors could overcome non-specific effects of small molecules and lead to the regeneration of heart muscle following myocardial infarction. Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. Chemical compounds that modulate atrial and ventricular cell fate could be used to improve subtype-specific differentiation of endogenous or exogenously delivered progenitor cells in order to promote cardiac regeneration. Methods Transcription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression. Results GATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. More detailed structure-function analysis revealed a distinct subclass of GATA4/NKX2-5 inhibitory compounds with an acetyl lysine-like domain that contributed to ventricular cells (%Myl2-eGFP+). Additionally, BioID analysis indicated broad interaction between GATA4 and BET family of proteins, such as BRD4. This indicated the involvement of epigenetic modulators in the regulation of GATA-dependent transcription. In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression. Conclusions Collectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. The compound scaffolds described within this study could be used to develop regenerative strategies for myocardial regeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02259-z.
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Affiliation(s)
- Mika J Välimäki
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Robert S Leigh
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Sini M Kinnunen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Alexander R March
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Ana Hernández de Sande
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matias Kinnunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Bogac L Kaynak
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland.
| | - Heikki Ruskoaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland.
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46
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Yuan X, Scott IC, Wilson MD. Heart Enhancers: Development and Disease Control at a Distance. Front Genet 2021; 12:642975. [PMID: 33777110 PMCID: PMC7987942 DOI: 10.3389/fgene.2021.642975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
Bound by lineage-determining transcription factors and signaling effectors, enhancers play essential roles in controlling spatiotemporal gene expression profiles during development, homeostasis and disease. Recent synergistic advances in functional genomic technologies, combined with the developmental biology toolbox, have resulted in unprecedented genome-wide annotation of heart enhancers and their target genes. Starting with early studies of vertebrate heart enhancers and ending with state-of-the-art genome-wide enhancer discovery and testing, we will review how studying heart enhancers in metazoan species has helped inform our understanding of cardiac development and disease.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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47
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Jindal GA, Farley EK. Enhancer grammar in development, evolution, and disease: dependencies and interplay. Dev Cell 2021; 56:575-587. [PMID: 33689769 PMCID: PMC8462829 DOI: 10.1016/j.devcel.2021.02.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/19/2022]
Abstract
Each language has standard books describing that language's grammatical rules. Biologists have searched for similar, albeit more complex, principles relating enhancer sequence to gene expression. Here, we review the literature on enhancer grammar. We introduce dependency grammar, a model where enhancers encode information based on dependencies between enhancer features shaped by mechanistic, evolutionary, and biological constraints. Classifying enhancers based on the types of dependencies may identify unifying principles relating enhancer sequence to gene expression. Such rules would allow us to read the instructions for development within genomes and pinpoint causal enhancer variants underlying disease and evolutionary changes.
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Affiliation(s)
- Granton A Jindal
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Division of Cardiology, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA.
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48
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Hosokawa H, Rothenberg EV. How transcription factors drive choice of the T cell fate. Nat Rev Immunol 2021; 21:162-176. [PMID: 32918063 PMCID: PMC7933071 DOI: 10.1038/s41577-020-00426-6] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 12/21/2022]
Abstract
Recent evidence has elucidated how multipotent blood progenitors transform their identities in the thymus and undergo commitment to become T cells. Together with environmental signals, a core group of transcription factors have essential roles in this process by directly activating and repressing specific genes. Many of these transcription factors also function in later T cell development, but control different genes. Here, we review how these transcription factors work to change the activities of specific genomic loci during early intrathymic development to establish T cell lineage identity. We introduce the key regulators and highlight newly emergent insights into the rules that govern their actions. Whole-genome deep sequencing-based analysis has revealed unexpectedly rich relationships between inherited epigenetic states, transcription factor-DNA binding affinity thresholds and influences of given transcription factors on the activities of other factors in the same cells. Together, these mechanisms determine T cell identity and make the lineage choice irreversible.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ellen V Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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49
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Hosokawa H, Masuhara K, Koizumi M. Transcription factors regulate early T cell development via redeployment of other factors: Functional dynamics of constitutively required factors in cell fate decisions. Bioessays 2021; 43:e2000345. [PMID: 33624856 DOI: 10.1002/bies.202000345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/30/2021] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Establishment of cell lineage identity from multipotent progenitors is controlled by cooperative actions of lineage-specific and stably expressed transcription factors, combined with input from environmental signals. Lineage-specific master transcription factors activate and repress gene expression by recruiting consistently expressed transcription factors and chromatin modifiers to their target loci. Recent technical advances in genome-wide and multi-omics analysis have shed light on unexpected mechanisms that underlie more complicated actions of transcription factors in cell fate decisions. In this review, we discuss functional dynamics of stably expressed and continuously required factors, Notch and Runx family members, throughout developmental stages of early T cell development in the thymus. Pre- and post-commitment stage-specific transcription factors induce dynamic redeployment of Notch and Runx binding genomic regions. Thus, together with stage-specific transcription factors, shared transcription factors across distinct developmental stages regulate acquisition of T lineage identity.
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Affiliation(s)
- Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan.,Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, Japan
| | - Kaori Masuhara
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Maria Koizumi
- Department of Immunology, Tokai University School of Medicine, Isehara, Kanagawa, Japan
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50
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Kathiriya IS, Rao KS, Iacono G, Devine WP, Blair AP, Hota SK, Lai MH, Garay BI, Thomas R, Gong HZ, Wasson LK, Goyal P, Sukonnik T, Hu KM, Akgun GA, Bernard LD, Akerberg BN, Gu F, Li K, Speir ML, Haeussler M, Pu WT, Stuart JM, Seidman CE, Seidman JG, Heyn H, Bruneau BG. Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease. Dev Cell 2021; 56:292-309.e9. [PMID: 33321106 PMCID: PMC7878434 DOI: 10.1016/j.devcel.2020.11.020] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 01/10/2023]
Abstract
Haploinsufficiency of transcriptional regulators causes human congenital heart disease (CHD); however, the underlying CHD gene regulatory network (GRN) imbalances are unknown. Here, we define transcriptional consequences of reduced dosage of the CHD transcription factor, TBX5, in individual cells during cardiomyocyte differentiation from human induced pluripotent stem cells (iPSCs). We discovered highly sensitive dysregulation of TBX5-dependent pathways-including lineage decisions and genes associated with heart development, cardiomyocyte function, and CHD genetics-in discrete subpopulations of cardiomyocytes. Spatial transcriptomic mapping revealed chamber-restricted expression for many TBX5-sensitive transcripts. GRN analysis indicated that cardiac network stability, including vulnerable CHD-linked nodes, is sensitive to TBX5 dosage. A GRN-predicted genetic interaction between Tbx5 and Mef2c, manifesting as ventricular septation defects, was validated in mice. These results demonstrate exquisite and diverse sensitivity to TBX5 dosage in heterogeneous subsets of iPSC-derived cardiomyocytes and predicts candidate GRNs for human CHDs, with implications for quantitative transcriptional regulation in disease.
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Affiliation(s)
- Irfan S Kathiriya
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA.
| | - Kavitha S Rao
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Giovanni Iacono
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - W Patrick Devine
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, CA 94158, USA
| | - Andrew P Blair
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Swetansu K Hota
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Michael H Lai
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Bayardo I Garay
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA 94158, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | | | - Henry Z Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Piyush Goyal
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Tatyana Sukonnik
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Kevin M Hu
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Gunes A Akgun
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Laure D Bernard
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew L Speir
- Genomics Institute, University of California, Santa Cruz, CA 95064, USA
| | | | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02115, USA
| | - Joshua M Stuart
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - J G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, CA 94158, USA.
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