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Harris S, Anwar I, Baksh SS, Pratt RE, Dzau VJ, Hodgkinson CP. Skeletal muscle differentiation induces wide-ranging nucleosome repositioning in muscle gene promoters. Sci Rep 2024; 14:9396. [PMID: 38658615 PMCID: PMC11043329 DOI: 10.1038/s41598-024-60236-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
In a previous report, we demonstrated that Cbx1, PurB and Sp3 inhibited cardiac muscle differentiation by increasing nucleosome density around cardiac muscle gene promoters. Since cardiac and skeletal muscle express many of the same proteins, we asked if Cbx1, PurB and Sp3 similarly regulated skeletal muscle differentiation. In a C2C12 model of skeletal muscle differentiation, Cbx1 and PurB knockdown increased myotube formation. In contrast, Sp3 knockdown inhibited myotube formation, suggesting that Sp3 played opposing roles in cardiac muscle and skeletal muscle differentiation. Consistent with this finding, Sp3 knockdown also inhibited various muscle-specific genes. The Cbx1, PurB and Sp3 proteins are believed to influence gene-expression in part by altering nucleosome position. Importantly, we developed a statistical approach to determine if changes in nucleosome positioning were significant and applied it to understanding the architecture of muscle-specific genes. Through this novel statistical approach, we found that during myogenic differentiation, skeletal muscle-specific genes undergo a set of unique nucleosome changes which differ significantly from those shown in commonly expressed muscle genes. While Sp3 binding was associated with nucleosome loss, there appeared no correlation with the aforementioned nucleosome changes. In summary, we have identified a novel role for Sp3 in skeletal muscle differentiation and through the application of quantifiable MNase-seq have discovered unique fingerprints of nucleosome changes for various classes of muscle genes during myogenic differentiation.
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Affiliation(s)
- Sonalí Harris
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Iqra Anwar
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Syeda S Baksh
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Richard E Pratt
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Victor J Dzau
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA
| | - Conrad P Hodgkinson
- Mandel Center for Heart and Vascular Research, The Duke Cardiovascular Research Center, Duke University Medical Center, Duke University, CaRL Building, 213 Research Drive, Durham, NC, 27710, USA.
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Viswanathan G, Kirshner HF, Nazo N, Ali S, Ganapathi A, Cumming I, Zhuang Y, Choi I, Warman A, Jassal C, Almeida-Peters S, Haney J, Corcoran D, Yu YR, Rajagopal S. Single-Cell Analysis Reveals Distinct Immune and Smooth Muscle Cell Populations that Contribute to Chronic Thromboembolic Pulmonary Hypertension. Am J Respir Crit Care Med 2023; 207:1358-1375. [PMID: 36803741 PMCID: PMC10595445 DOI: 10.1164/rccm.202203-0441oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/21/2023] [Indexed: 02/23/2023] Open
Abstract
Rationale: Chronic thromboembolic pulmonary hypertension (CTEPH) is a sequela of acute pulmonary embolism (PE) in which the PE remodels into a chronic scar in the pulmonary arteries. This results in vascular obstruction, pulmonary microvasculopathy, and pulmonary hypertension. Objectives: Our current understanding of CTEPH pathobiology is primarily derived from cell-based studies limited by the use of specific cell markers or phenotypic modulation in cell culture. Therefore, our main objective was to identify the multiple cell types that constitute CTEPH thrombusy and to study their dysfunction. Methods: Here we used single-cell RNA sequencing of tissue removed at the time of pulmonary endarterectomy surgery from five patients to identify the multiple cell types. Using in vitro assays, we analyzed differences in phenotype between CTEPH thrombus and healthy pulmonary vascular cells. We studied potential therapeutic targets in cells isolated from CTEPH thrombus. Measurements and Main Results: Single-cell RNA sequencing identified multiple cell types, including macrophages, T cells, and smooth muscle cells (SMCs), that constitute CTEPH thrombus. Notably, multiple macrophage subclusters were identified but broadly split into two categories, with the larger group characterized by an upregulation of inflammatory signaling predicted to promote pulmonary vascular remodeling. CD4+ and CD8+ T cells were identified and likely contribute to chronic inflammation in CTEPH. SMCs were a heterogeneous population, with a cluster of myofibroblasts that express markers of fibrosis and are predicted to arise from other SMC clusters based on pseudotime analysis. Additionally, cultured endothelial, smooth muscle, and myofibroblast cells isolated from CTEPH fibrothrombotic material have distinct phenotypes from control cells with regard to angiogenic potential and rates of proliferation and apoptosis. Last, our analysis identified PAR1 (protease-activated receptor 1) as a potential therapeutic target that links thrombosis to chronic PE in CTEPH, with PAR1 inhibition decreasing SMC and myofibroblast proliferation and migration. Conclusions: These findings suggest a model for CTEPH similar to atherosclerosis, with chronic inflammation promoted by macrophages and T cells driving vascular remodeling through SMC modulation, and suggest new approaches for pharmacologically targeting this disease.
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Affiliation(s)
| | | | - Nour Nazo
- Division of Cardiology, Department of Medicine
| | - Saba Ali
- Division of Cardiology, Department of Medicine
| | | | - Ian Cumming
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Yonghua Zhuang
- Biostatistics Shared Resource, University of Colorado Cancer Center
- Department of Pediatrics, and
| | - Issac Choi
- Division of Cardiology, Department of Medicine
| | | | | | - Susana Almeida-Peters
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - John Haney
- Division of Cardiothoracic Surgery, Department of Surgery
| | | | - Yen-Rei Yu
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Sudarshan Rajagopal
- Division of Cardiology, Department of Medicine
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina; and
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DeBenedittis P, Karpurapu A, Henry A, Thomas MC, McCord TJ, Brezitski K, Prasad A, Baker CE, Kobayashi Y, Shah SH, Kontos CD, Tata PR, Lumbers RT, Karra R. Coupled myovascular expansion directs cardiac growth and regeneration. Development 2022; 149:dev200654. [PMID: 36134690 PMCID: PMC10692274 DOI: 10.1242/dev.200654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/15/2022] [Indexed: 12/04/2023]
Abstract
Heart regeneration requires multiple cell types to enable cardiomyocyte (CM) proliferation. How these cells interact to create growth niches is unclear. Here, we profile proliferation kinetics of cardiac endothelial cells (CECs) and CMs in the neonatal mouse heart and find that they are spatiotemporally coupled. We show that coupled myovascular expansion during cardiac growth or regeneration is dependent upon VEGF-VEGFR2 signaling, as genetic deletion of Vegfr2 from CECs or inhibition of VEGFA abrogates both CEC and CM proliferation. Repair of cryoinjury displays poor spatial coupling of CEC and CM proliferation. Boosting CEC density after cryoinjury with virus encoding Vegfa enhances regeneration. Using Mendelian randomization, we demonstrate that circulating VEGFA levels are positively linked with human myocardial mass, suggesting that Vegfa can stimulate human cardiac growth. Our work demonstrates the importance of coupled CEC and CM expansion and reveals a myovascular niche that may be therapeutically targeted for heart regeneration.
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Affiliation(s)
- Paige DeBenedittis
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Anish Karpurapu
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert Henry
- Institute of Cardiovascular Science, University College London, London WC1E 6BT, UK
- Institute of Health Informatics, University College London, London WC1E 6BT, UK
| | - Michael C. Thomas
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy J. McCord
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kyla Brezitski
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Anil Prasad
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Caroline E. Baker
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Svati H. Shah
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Christopher D. Kontos
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
- Regeneration Next, Duke University, Durham, NC 27710, USA
- Center for Aging, Duke University Medical Center, Durham, NC 27710, USA
| | - R. Thomas Lumbers
- Institute of Health Informatics, University College London, London WC1E 6BT, UK
- Health Data Research UK London, University College London, London, WC1E 6BT, UK
- British Heart Foundation Research Accelerator, University College London, London WC1E 6BT, UK
| | - Ravi Karra
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Regeneration Next, Duke University, Durham, NC 27710, USA
- Center for Aging, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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