1
|
Laird J, Perera G, Batorsky R, Wang H, Arkun K, Chin MT. Spatial Transcriptomic Analysis of Focal and Normal Areas of Myocyte Disarray in Human Hypertrophic Cardiomyopathy. Int J Mol Sci 2023; 24:12625. [PMID: 37628806 PMCID: PMC10454036 DOI: 10.3390/ijms241612625] [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: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Hypertrophic Cardiomyopathy (HCM) is a common inherited disorder that can lead to heart failure and sudden cardiac death, characterized at the histological level by focal areas of myocyte disarray, hypertrophy and fibrosis, and only a few disease-targeted therapies exist. To identify the focal and spatially restricted alterations in the transcriptional pathways and reveal novel therapeutic targets, we performed a spatial transcriptomic analysis of the areas of focal myocyte disarray compared to areas of normal tissue using a commercially available platform (GeoMx, nanoString). We analyzed surgical myectomy tissue from four patients with HCM and the control interventricular septum tissue from two unused organ donor hearts that were free of cardiovascular disease. Histological sections were reviewed by an expert pathologist, and 72 focal areas with varying degrees of myocyte disarray (normal, mild, moderate, severe) were chosen for analysis. Areas of interest were interrogated with the Human Cancer Transcriptome Atlas designed to profile 1800 transcripts. Differential expression analysis revealed significant changes in gene expression between HCM and the control tissue, and functional enrichment analysis indicated that these genes were primarily involved in interferon production and mitochondrial energetics. Within the HCM tissue, differentially expressed genes between areas of normal and severe disarray were enriched for genes related to mitochondrial energetics and the extracellular matrix in severe disarray. An analysis of the gene expression of the ligand-receptor pair revealed that the HCM tissue exhibited downregulation of platelet-derived growth factor (PDGF), NOTCH, junctional adhesion molecule, and CD46 signaling while showing upregulation of fibronectin, CD99, cadherin, and amyloid precursor protein signaling. A deconvolution analysis utilizing the matched single nuclei RNA-sequencing (snRNA-seq) data to determine cell type composition in areas of interest revealed significant differences in fibroblast and vascular cell composition in areas of severe disarray when compared to normal areas in HCM samples. Cell composition in the normal areas of the control tissue was also divergent from the normal areas in HCM samples, which was consistent with the differential expression results. Overall, our data identify novel and potential disease-modifying targets for therapy in HCM.
Collapse
Affiliation(s)
- Jason Laird
- Research Technology, Tufts University, Medford, MA 02144, USA;
| | - Gayani Perera
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA;
| | - Rebecca Batorsky
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA; (R.B.); (H.W.)
| | - Hongjie Wang
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA; (R.B.); (H.W.)
| | - Knarik Arkun
- Department of Pathology, Tufts Medical Center, Boston, MA 02111, USA;
| | - Michael T. Chin
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA;
| |
Collapse
|
2
|
Perera G, Power L, Larson A, Codden CJ, Awata J, Batorsky R, Strathdee D, Chin MT. Single Cell Transcriptomic Analysis in a Mouse Model of Barth Syndrome Reveals Cell-Specific Alterations in Gene Expression and Intercellular Communication. Int J Mol Sci 2023; 24:11594. [PMID: 37511352 PMCID: PMC10380964 DOI: 10.3390/ijms241411594] [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: 06/21/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Barth Syndrome, a rare X-linked disorder affecting 1:300,000 live births, results from defects in Tafazzin, an acyltransferase that remodels cardiolipin and is essential for mitochondrial respiration. Barth Syndrome patients develop cardiomyopathy, muscular hypotonia and cyclic neutropenia during childhood, rarely surviving to middle age. At present, no effective therapy exists, and downstream transcriptional effects of Tafazzin dysfunction are incompletely understood. To identify novel, cell-specific, pathological pathways that mediate heart dysfunction, we performed single-nucleus RNA-sequencing (snRNA-seq) on wild-type (WT) and Tafazzin-knockout (Taz-KO) mouse hearts. We determined differentially expressed genes (DEGs) and inferred predicted cell-cell communication networks from these data. Surprisingly, DEGs were distributed heterogeneously across the cell types, with fibroblasts, cardiomyocytes, endothelial cells, macrophages, adipocytes and pericytes exhibiting the greatest number of DEGs between genotypes. One differentially expressed gene was detected for the lymphatic endothelial and mesothelial cell types, while no significant DEGs were found in the lymphocytes. A Gene Ontology (GO) analysis of these DEGs showed cell-specific effects on biological processes such as fatty acid metabolism in adipocytes and cardiomyocytes, increased translation in cardiomyocytes, endothelial cells and fibroblasts, in addition to other cell-specific processes. Analysis of ligand-receptor pair expression, to infer intercellular communication patterns, revealed the strongest dysregulated communication involved adipocytes and cardiomyocytes. For the knockout hearts, there was a strong loss of ligand-receptor pair expression involving adipocytes, and cardiomyocyte expression of ligand-receptor pairs underwent reorganization. These findings suggest that adipocyte and cardiomyocyte mitochondria may be most sensitive to mitochondrial Tafazzin deficiency and that rescuing adipocyte mitochondrial dysfunction, in addition to cardiomyocyte mitochondrial dysfunction, may provide therapeutic benefit in Barth Syndrome patients.
Collapse
Affiliation(s)
- Gayani Perera
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA; (G.P.); (A.L.); (C.J.C.); (J.A.)
| | - Liam Power
- Medical Scientist Training Program, Tufts University School of Medicine, Boston, MA 02111, USA;
| | - Amy Larson
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA; (G.P.); (A.L.); (C.J.C.); (J.A.)
| | - Christina J. Codden
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA; (G.P.); (A.L.); (C.J.C.); (J.A.)
| | - Junya Awata
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA; (G.P.); (A.L.); (C.J.C.); (J.A.)
| | - Rebecca Batorsky
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA;
| | | | - Michael T. Chin
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA; (G.P.); (A.L.); (C.J.C.); (J.A.)
| |
Collapse
|
3
|
Chou C, Martin GL, Perera G, Awata J, Larson A, Blanton R, Chin MT. A novel αB-crystallin R123W variant drives hypertrophic cardiomyopathy by promoting maladaptive calcium-dependent signal transduction. Front Cardiovasc Med 2023; 10:1223244. [PMID: 37435054 PMCID: PMC10331725 DOI: 10.3389/fcvm.2023.1223244] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 07/13/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disorder affecting 1 in 500 people in the general population. Characterized by asymmetric left ventricular hypertrophy, cardiomyocyte disarray and cardiac fibrosis, HCM is a highly complex disease with heterogenous clinical presentation, onset and complication. While mutations in sarcomere genes can account for a substantial proportion of familial cases of HCM, 40%-50% of HCM patients do not carry such sarcomere variants and the causal mutations for their diseases remain elusive. Recently, we identified a novel variant of the alpha-crystallin B chain (CRYABR123W) in a pair of monozygotic twins who developed concordant HCM phenotypes that manifested over a nearly identical time course. Yet, how CRYABR123W promotes the HCM phenotype remains unclear. Here, we generated mice carrying the CryabR123W knock-in allele and demonstrated that hearts from these animals exhibit increased maximal elastance at young age but reduced diastolic function with aging. Upon transverse aortic constriction, mice carrying the CryabR123W allele developed pathogenic left ventricular hypertrophy with substantial cardiac fibrosis and progressively decreased ejection fraction. Crossing of mice with a Mybpc3 frame-shift model of HCM did not potentiate pathological hypertrophy in compound heterozygotes, indicating that the pathological mechanisms in the CryabR123W model are independent of the sarcomere. In contrast to another well-characterized CRYAB variant (R120G) which induced Desmin aggregation, no evidence of protein aggregation was observed in hearts expressing CRYABR123W despite its potent effect on driving cellular hypertrophy. Mechanistically, we uncovered an unexpected protein-protein interaction between CRYAB and calcineurin. Whereas CRYAB suppresses maladaptive calcium signaling in response to pressure-overload, the R123W mutation abolished this effect and instead drove pathologic NFAT activation. Thus, our data establish the CryabR123W allele as a novel genetic model of HCM and unveiled additional sarcomere-independent mechanisms of cardiac pathological hypertrophy.
Collapse
Affiliation(s)
- Chun Chou
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
| | - Gregory L. Martin
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| | - Gayani Perera
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| | - Junya Awata
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| | - Amy Larson
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| | - Robert Blanton
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| | - Michael T. Chin
- Department of Medicine, Tufts University School of Medicine, Boston, MA, United States
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, United States
| |
Collapse
|
4
|
Moore J, Ewoldt J, Venturini G, Pereira AC, Padilha K, Lawton M, Lin W, Goel R, Luptak I, Perissi V, Seidman CE, Seidman J, Chin MT, Chen C, Emili A. Multi-Omics Profiling of Hypertrophic Cardiomyopathy Reveals Altered Mechanisms in Mitochondrial Dynamics and Excitation-Contraction Coupling. Int J Mol Sci 2023; 24. [PMID: 36902152 DOI: 10.3390/ijms24054724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Hypertrophic cardiomyopathy is one of the most common inherited cardiomyopathies and a leading cause of sudden cardiac death in young adults. Despite profound insights into the genetics, there is imperfect correlation between mutation and clinical prognosis, suggesting complex molecular cascades driving pathogenesis. To investigate this, we performed an integrated quantitative multi-omics (proteomic, phosphoproteomic, and metabolomic) analysis to illuminate the early and direct consequences of mutations in myosin heavy chain in engineered human induced pluripotent stem-cell-derived cardiomyocytes relative to late-stage disease using patient myectomies. We captured hundreds of differential features, which map to distinct molecular mechanisms modulating mitochondrial homeostasis at the earliest stages of pathobiology, as well as stage-specific metabolic and excitation-coupling maladaptation. Collectively, this study fills in gaps from previous studies by expanding knowledge of the initial responses to mutations that protect cells against the early stress prior to contractile dysfunction and overt disease.
Collapse
|
5
|
Chou C, Chin MT. Genetic and Molecular Mechanisms of Hypertrophic Cardiomyopathy. Int J Mol Sci 2023; 24:ijms24032522. [PMID: 36768840 PMCID: PMC9916656 DOI: 10.3390/ijms24032522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
The intention of this Special Issue is to highlight novel approaches and new paradigms for understanding the pathogenesis of hypertrophic cardiomyopathy (HCM) [...].
Collapse
Affiliation(s)
- Chun Chou
- Department of Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Michael Thomas Chin
- Department of Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
- Correspondence: ; Tel.: +1-617-636-8776
| |
Collapse
|
6
|
Long X, Yuan X, Du J. Single-cell and spatial transcriptomics: Advances in heart development and disease applications. Comput Struct Biotechnol J 2023; 21:2717-2731. [PMID: 37181659 PMCID: PMC10173363 DOI: 10.1016/j.csbj.2023.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Current transcriptomics technologies, including bulk RNA-seq, single-cell RNA sequencing (scRNA-seq), single-nucleus RNA-sequencing (snRNA-seq), and spatial transcriptomics (ST), provide novel insights into the spatial and temporal dynamics of gene expression during cardiac development and disease processes. Cardiac development is a highly sophisticated process involving the regulation of numerous key genes and signaling pathways at specific anatomical sites and developmental stages. Exploring the cell biological mechanisms involved in cardiogenesis also contributes to congenital heart disease research. Meanwhile, the severity of distinct heart diseases, such as coronary heart disease, valvular disease, cardiomyopathy, and heart failure, is associated with cellular transcriptional heterogeneity and phenotypic alteration. Integrating transcriptomic technologies in the clinical diagnosis and treatment of heart diseases will aid in advancing precision medicine. In this review, we summarize applications of scRNA-seq and ST in the cardiac field, including organogenesis and clinical diseases, and provide insights into the promise of single-cell and spatial transcriptomics in translational research and precision medicine.
Collapse
Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 4000l0, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
- Correspondence to: Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, 74 Lin Jiang Road Chongqing 400010, China.
| |
Collapse
|
7
|
Ke Y, Jian-yuan H, Ping Z, Yue W, Na X, Jian Y, Kai-xuan L, Yi-fan S, Han-bin L, Rong L. The progressive application of single-cell RNA sequencing technology in cardiovascular diseases. Biomed Pharmacother 2022; 154:113604. [DOI: 10.1016/j.biopha.2022.113604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/02/2022] Open
|
8
|
Pasqua T, Tropea T, Granieri MC, De Bartolo A, Spena A, Moccia F, Rocca C, Angelone T. Novel molecular insights and potential approaches for targeting hypertrophic cardiomyopathy: Focus on coronary modulators. Vascul Pharmacol 2022; 145:107003. [DOI: 10.1016/j.vph.2022.107003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 11/26/2022]
|
9
|
Safabakhsh S, Sar F, Martelotto L, Haegert A, Singhera G, Hanson P, Parker J, Collins C, Rohani L, Laksman Z. Isolating Nuclei From Frozen Human Heart Tissue for Single-Nucleus RNA Sequencing. Curr Protoc 2022; 2:e480. [PMID: 35816165 DOI: 10.1002/cpz1.480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Heart disease is the leading cause of global morbidity and mortality. This is in part because, despite an abundance of animal and in vitro models, it has been a challenge to date to study human heart tissue with sufficient depth and resolution to develop disease-modifying therapies for common cardiac conditions. Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful tool capable of analyzing cellular function and signaling in health and disease, and has already contributed to significant advances in areas such as oncology and hematology. Employing snRNA-seq technology on flash-frozen human tissue has the potential to unlock novel disease mechanisms and pathways in any organ. Studying the human heart using snRNA-seq is a key priority for the field of cardiovascular sciences; however, progress to date has been slowed by numerous barriers. One key challenge is the fact that the human heart is very resistant to shearing and stress, making tissue dissociation and nuclear isolation difficult. Here, we describe a tissue dissociation method allowing the efficient and cost-effective isolation of high-quality nuclei from flash-frozen human heart tissue collected in surgical operating rooms. Our protocol addresses the challenge of nuclear isolation from human hearts, enables snRNA-seq of the human heart, and paves the way for an improved understanding of the human heart in health and disease. Ultimately, this will be key to uncovering signaling pathways and networks amenable to therapeutic intervention and the development of novel biomarkers and disease-modifying therapies. © 2022 Wiley Periodicals LLC. Basic Protocol: Human heart tissue dissociation and nuclear isolation for snRNA-seq.
Collapse
Affiliation(s)
- Sina Safabakhsh
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Funda Sar
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | | | - Anne Haegert
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | | | | | - Jeremy Parker
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Colin Collins
- Vancouver Prostate Centre, UBC, Vancouver, British Columbia, Canada
| | - Leili Rohani
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary Laksman
- University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|