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Pereira IT, Gomes-Júnior R, Hansel-Frose A, França RSV, Liu M, Soliman HAN, Chan SSK, Dudley SC, Kyba M, Dallagiovanna B. Cardiac Development Long Non-Coding RNA ( CARDEL) Is Activated during Human Heart Development and Contributes to Cardiac Specification and Homeostasis. Cells 2024; 13:1050. [PMID: 38920678 PMCID: PMC11201801 DOI: 10.3390/cells13121050] [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: 03/15/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Successful heart development depends on the careful orchestration of a network of transcription factors and signaling pathways. In recent years, in vitro cardiac differentiation using human pluripotent stem cells (hPSCs) has been used to uncover the intricate gene-network regulation involved in the proper formation and function of the human heart. Here, we searched for uncharacterized cardiac-development genes by combining a temporal evaluation of human cardiac specification in vitro with an analysis of gene expression in fetal and adult heart tissue. We discovered that CARDEL (CARdiac DEvelopment Long non-coding RNA; LINC00890; SERTM2) expression coincides with the commitment to the cardiac lineage. CARDEL knockout hPSCs differentiated poorly into cardiac cells, and hPSC-derived cardiomyocytes showed faster beating rates after controlled overexpression of CARDEL during differentiation. Altogether, we provide physiological and molecular evidence that CARDEL expression contributes to sculpting the cardiac program during cell-fate commitment.
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Affiliation(s)
- Isabela T. Pereira
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Rubens Gomes-Júnior
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Aruana Hansel-Frose
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Rhaíza S. V. França
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Man Liu
- Department of Medicine, Division of Cardiology, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (S.C.D.J.)
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
| | - Hossam A. N. Soliman
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sunny S. K. Chan
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C. Dudley
- Department of Medicine, Division of Cardiology, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (S.C.D.J.)
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruno Dallagiovanna
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
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2
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Mabry SA, Pavon N. Exploring the prospects, advancements, and challenges of in vitro modeling of the heart-brain axis. Front Cell Neurosci 2024; 18:1386355. [PMID: 38766369 PMCID: PMC11099243 DOI: 10.3389/fncel.2024.1386355] [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: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Research on bidirectional communication between the heart and brain has often relied on studies involving nonhuman animals. Dependance on animal models offer limited applicability to humans and a lack of high-throughput screening. Recently, the field of 3D cell biology, specifically organoid technology, has rapidly emerged as a valuable tool for studying interactions across organ systems, i.e., gut-brain axis. The initial success of organoid models indicates the usefulness of 3D cultures for elucidating the intricate interactivity of the autonomic nervous system and overall health. This perspective aims to explore the potential of advancing in vitro modeling of the heart-brain axis by discussing the benefits, applications, and adaptability of organoid technologies. We closely examine the current state of brain organoids in conjunction with the advancements of cardiac organoids. Moreover, we explore the use of combined organoid systems to investigate pathophysiology and provide a platform for treatment discovery. Finally, we address the challenges that accompany the use of 3D models for studying the heart-brain axis with an emphasis on generating tailored engineering strategies for further refinement of dynamic organ system modeling in vitro.
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Affiliation(s)
- Senegal Alfred Mabry
- Affect and Cognition Laboratory, Department of Psychology and Human Development, College of Human Ecology, Cornell University, Ithaca, NY, United States
| | - Narciso Pavon
- ChangHui Pak Laboratory, Department of Biochemistry and Molecular Biology, College of Natural Sciences, University of Massachusetts-Amherst, Amherst, MA, United States
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3
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Kumar A, He S, Mali P. Systematic discovery of transcription factors that improve hPSC-derived cardiomyocyte maturation via temporal analysis of bioengineered cardiac tissues. APL Bioeng 2023; 7:026109. [PMID: 37252678 PMCID: PMC10219684 DOI: 10.1063/5.0137458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have the potential to become powerful tools for disease modeling, drug testing, and transplantation; however, their immaturity limits their applications. Transcription factor (TF) overexpression can improve hPSC-CM maturity, but identifying these TFs has been elusive. Toward this, we establish here an experimental framework for systematic identification of maturation enhancing factors. Specifically, we performed temporal transcriptome RNAseq analyses of progressively matured hPSC-derived cardiomyocytes across 2D and 3D differentiation systems and further compared these bioengineered tissues to native fetal and adult-derived tissues. These analyses revealed 22 TFs whose expression did not increase in 2D differentiation systems but progressively increased in 3D culture systems and adult mature cell types. Individually overexpressing each of these TFs in immature hPSC-CMs identified five TFs (KLF15, ZBTB20, ESRRA, HOPX, and CAMTA2) as regulators of calcium handling, metabolic function, and hypertrophy. Notably, the combinatorial overexpression of KLF15, ESRRA, and HOPX improved all three maturation parameters simultaneously. Taken together, we introduce a new TF cocktail that can be used in solo or in conjunction with other strategies to improve hPSC-CM maturation and anticipate that our generalizable methodology can also be implemented to identify maturation-associated TFs for other stem cell progenies.
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Affiliation(s)
- Aditya Kumar
- Department of Bioengineering, University of California, San Diego, California 92093, USA
| | - Starry He
- Department of Bioengineering, University of California, San Diego, California 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, California 92093, USA
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4
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Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res 2023; 119:64-78. [PMID: 35325060 DOI: 10.1093/cvr/cvac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
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Affiliation(s)
- Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalie D Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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5
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Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F. A transcription factor atlas of directed differentiation. Cell 2023; 186:209-229.e26. [PMID: 36608654 PMCID: PMC10344468 DOI: 10.1016/j.cell.2022.11.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 01/07/2023]
Abstract
Transcription factors (TFs) regulate gene programs, thereby controlling diverse cellular processes and cell states. To comprehensively understand TFs and the programs they control, we created a barcoded library of all annotated human TF splice isoforms (>3,500) and applied it to build a TF Atlas charting expression profiles of human embryonic stem cells (hESCs) overexpressing each TF at single-cell resolution. We mapped TF-induced expression profiles to reference cell types and validated candidate TFs for generation of diverse cell types, spanning all three germ layers and trophoblasts. Targeted screens with subsets of the library allowed us to create a tailored cellular disease model and integrate mRNA expression and chromatin accessibility data to identify downstream regulators. Finally, we characterized the effects of combinatorial TF overexpression by developing and validating a strategy for predicting combinations of TFs that produce target expression profiles matching reference cell types to accelerate cellular engineering efforts.
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Affiliation(s)
- Julia Joung
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Sai Ma
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tristan Tay
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kathryn R Geiger-Schuller
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paul C Kirchgatterer
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Vanessa K Verdine
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Baolin Guo
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mario A Arias-Garcia
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E Allen
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA; Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Ankita Singh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Olena Kuksenko
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Omar O Abudayyeh
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Zhanyan Fu
- McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rhiannon K Macrae
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aviv Regev
- Department of Biology, MIT, Cambridge, MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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6
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Kambis TN, Mishra PK. Genome Editing and Diabetic Cardiomyopathy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:103-114. [PMID: 36454462 PMCID: PMC10155862 DOI: 10.1007/978-981-19-5642-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Differential gene expression is associated with diabetic cardiomyopathy (DMCM) and culminates in adverse remodeling in the diabetic heart. Genome editing is a technology utilized to alter endogenous genes. Genome editing also provides an option to induce cardioprotective genes or inhibit genes linked to adverse cardiac remodeling and thus has promise in ameliorating DMCM. Non-coding genes have emerged as novel regulators of cellular signaling and may serve as potential therapeutic targets for DMCM. Specifically, there is a widespread change in the gene expression of fetal cardiac genes and microRNAs, termed genetic reprogramming, that promotes pathological remodeling and contributes to heart failure in diabetes. This genetic reprogramming of both coding and non-coding genes varies with the progression and severity of DMCM. Thus, genetic editing provides a promising option to investigate the role of specific genes/non-coding RNAs in DMCM initiation and progression as well as developing therapeutics to mitigate cardiac remodeling and ameliorate DMCM. This chapter will summarize the research progress in genome editing and DMCM and provide future directions for utilizing genome editing as an approach to prevent and/or treat DMCM.
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Affiliation(s)
- Tyler N Kambis
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paras K Mishra
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA.
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7
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Berg Luecke L, Waas M, Littrell J, Wojtkiewicz M, Castro C, Burkovetskaya M, Schuette EN, Buchberger AR, Churko JM, Chalise U, Waknitz M, Konfrst S, Teuben R, Morrissette-McAlmon J, Mahr C, Anderson DR, Boheler KR, Gundry RL. Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts. NATURE CARDIOVASCULAR RESEARCH 2023; 2:76-95. [PMID: 36950336 PMCID: PMC10030153 DOI: 10.1038/s44161-022-00200-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 11/29/2022] [Indexed: 01/19/2023]
Abstract
Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) profiling of cells present in limited quantities, and we apply it to isolated primary human heart cells. We report experimental evidence of surface localization and extracellular domains for 1,144 N-glycoproteins, including cell-type-restricted and region-restricted glycoproteins. We identified a surface protein specific for healthy cardiomyocytes, LSMEM2, and validated an anti-LSMEM2 monoclonal antibody for flow cytometry and imaging. Surfaceome comparisons among pluripotent stem cell derivatives and their primary counterparts highlighted important differences with direct implications for drug screening and disease modeling. Finally, 20% of cell surface proteins, including LSMEM2, were differentially abundant between failing and non-failing cardiomyocytes. These results represent a rich resource to advance development of cell type and organ-specific targets for drug delivery, disease modeling, immunophenotyping and in vivo imaging.
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Affiliation(s)
- Linda Berg Luecke
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI USA
| | - Matthew Waas
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Present Address: Princess Margaret Cancer Centre, University Health Network, Toronto, ON Canada
| | - Jack Littrell
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Melinda Wojtkiewicz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Chase Castro
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Maria Burkovetskaya
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Erin N. Schuette
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Amanda Rae Buchberger
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI USA
- Present Address: Department of Chemistry, University of Wisconsin-Madison, Madison, WI USA
| | - Jared M. Churko
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program, University of Arizona, Tucson, AZ USA
| | - Upendra Chalise
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Michelle Waknitz
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Shelby Konfrst
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
| | - Roald Teuben
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
| | - Justin Morrissette-McAlmon
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
| | - Claudius Mahr
- Department of Mechanical Engineering, Division of Cardiology, University of Washington, Seattle, WA USA
| | - Daniel R. Anderson
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE USA
| | - Kenneth R. Boheler
- Department of Biomedical Engineering, Whiting School of Engineering, The Johns Hopkins University, Baltimore, MD USA
- Department of Medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, MD USA
| | - Rebekah L. Gundry
- CardiOmics Program, Center for Heart and Vascular Research and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE USA
- Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE USA
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8
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Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept. NPJ Genom Med 2022; 7:74. [PMID: 36577754 PMCID: PMC9797484 DOI: 10.1038/s41525-022-00347-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts. The number of well-expressed genes in AF cells was comparable to that in fibroblasts and much higher than that in blood across different disease categories. We found AF cells RNA-seq feasible and beneficial in prenatal diagnosis (n = 4) as transcriptomic data elucidated the molecular consequence leading to the pathogenicity upgrade of variants in CHD7 and COL1A2 and revising the in silico prediction of a variant in MYRF. AF cells RNA-seq could become a reasonable choice for postnatal patients with advantages over fibroblasts and blood as it prevents invasive procedures.
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9
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Spendlove SJ, Bondhus L, Lluri G, Sul JH, Arboleda VA. Polygenic risk scores of endo-phenotypes identify the effect of genetic background in congenital heart disease. HGG ADVANCES 2022; 3:100112. [PMID: 35599848 PMCID: PMC9118152 DOI: 10.1016/j.xhgg.2022.100112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/19/2022] [Indexed: 01/28/2023] Open
Abstract
Congenital heart disease (CHD) is a rare structural defect that occurs in ∼1% of live births. Studies on CHD genetic architecture have identified pathogenic single-gene mutations in less than 30% of cases. Single-gene mutations often show incomplete penetrance and variable expressivity. Therefore, we hypothesize that genetic background may play a role in modulating disease expression. Polygenic risk scores (PRSs) aggregate effects of common genetic variants to investigate whether, cumulatively, these variants are associated with disease penetrance or severity. However, the major limitations in this field have been in generating sufficient sample sizes for these studies. Here we used CHD-phenotype matched genome-wide association study (GWAS) summary statistics from the UK Biobank (UKBB) as our base study and whole-genome sequencing data from the CHD cohort (n1 = 711 trios, n2 = 362 European trios) of the Gabriella Miller Kids First dataset as our target study to develop PRSs for CHD. PRSs estimated using a GWAS for heart valve problems and heart murmur explain 2.5% of the variance in case-control status of CHD (all SNVs, p = 7.90 × 10-3; fetal cardiac SNVs, p = 8.00 × 10-3) and 1.8% of the variance in severity of CHD (fetal cardiac SNVs, p = 6.20 × 10-3; all SNVs, p = 0.015). These results show that common variants captured in CHD phenotype-matched GWASs have a modest but significant contribution to phenotypic expression of CHD. Further exploration of the cumulative effect of common variants is necessary for understanding the complex genetic etiology of CHD and other rare diseases.
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Affiliation(s)
- Sarah J Spendlove
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leroy Bondhus
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gentian Lluri
- Ahmanson/UCLA Adult Congenital Heart Disease Center, Division of Cardiology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jae Hoon Sul
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Valerie A Arboleda
- Interdepartmental Bioinformatics Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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10
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Astro V, Ramirez-Calderon G, Pennucci R, Caroli J, Saera-Vila A, Cardona-Londoño K, Forastieri C, Fiacco E, Maksoud F, Alowaysi M, Sogne E, Andrea Falqui, Gonzàlez F, Montserrat N, Battaglioli E, Andrea Mattevi, Adamo A. Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism. iScience 2022; 25:104665. [PMID: 35856020 PMCID: PMC9287196 DOI: 10.1016/j.isci.2022.104665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/31/2022] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
The histone demethylase KDM1A is a multi-faceted regulator of vital developmental processes, including mesodermal and cardiac tube formation during gastrulation. However, it is unknown whether the fine-tuning of KDM1A splicing isoforms, already shown to regulate neuronal maturation, is crucial for the specification and maintenance of cell identity during cardiogenesis. Here, we discovered a temporal modulation of ubKDM1A and KDM1A+2a during human and mice fetal cardiac development and evaluated their impact on the regulation of cardiac differentiation. We revealed a severely impaired cardiac differentiation in KDM1A−/− hESCs that can be rescued by re-expressing ubKDM1A or catalytically impaired ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. Conversely, KDM1A+2a−/− hESCs give rise to functional cardiac cells, displaying increased beating amplitude and frequency and enhanced expression of critical cardiogenic markers. Our findings prove the existence of a divergent scaffolding role of KDM1A splice variants, independent of their enzymatic activity, during hESC differentiation into cardiac cells. ubKDM1A and KDM1A+2a isoforms are fine-tuned during fetal cardiac development Depletion of KDM1A isoforms impairs hESC differentiation into cardiac cells KDM1A+2a ablation enhances the expression of key cardiac markers KDM1A isoforms exhibit enzymatic-independent divergent roles during cardiogenesis
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11
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The phylogenetic position of zebrafish (Danio rerio) from south african pet shops. Mol Biol Rep 2022; 49:7327-7336. [PMID: 35596052 DOI: 10.1007/s11033-022-07522-x] [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: 01/04/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Zebrafish (Danio rerio), a small freshwater fish that originates from India, Bangladesh, Nepal, Bhutan and northern Myanmar, have been widely used as a model organism for studies of developmental biology and genetics. The current study aimed to determine the origin of South African pet shop stock that are currently being used to establish a laboratory population founded from diverse sources available locally. METHODS AND RESULTS Zebrafish DNA was extracted from 65 specimens housed at the University of the Free State (UFS) Department of Genetics. For phylogenetic analysis, cytb sequences were generated from all samples. A further 178 sequences were downloaded from the GenBank database, including sequences of an outgroup species (Danio kyathit). Five microsatellite markers were used to further assess the genetic diversity of the UFS zebrafish specimens. A maximum likelihood analysis was performed for the cytb data. Results of the phylogenetic analyses divided the sequences into three major genetic groups, which was congruent with a previous study on laboratory zebrafish provenance. The SA pet shop fish grouped with the lines from the northern and north-eastern regions of India. High levels of microsatellite genetic diversity were observed for the pet shop sourced population, correlating to what has previously been observed in zebrafish. CONCLUSION These results can be used to guide the future development of laboratory lines suited to the needs at the UFS.
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12
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Yang H, Liu W, Song S, Bai L, Nie Y, Bai Y, Zhang G. Proteogenomics Integrating Reveal a Complex Network, Alternative Splicing, Hub Genes Regulating Heart Maturation. Genes (Basel) 2022; 13:genes13020250. [PMID: 35205300 PMCID: PMC8872128 DOI: 10.3390/genes13020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/01/2022] [Accepted: 01/21/2022] [Indexed: 11/23/2022] Open
Abstract
Heart maturation is an essentially biological process for neonatal heart transition to adult heart, thus illustrating the mechanism of heart maturation may be helpful to explore postnatal heart development and cardiac cardiomyopathy. This study combined proteomic analysis based on isobaric tags for relative and absolute quantitation (iTRAQ) and transcriptome analysis based on RNA sequencing to detect the proteins and genes associated with heart maturation in mice. The proteogenomics integrating analysis identified 254 genes/proteins as commonly differentially expressed between neonatal and adult hearts. Functional and pathway analysis demonstrated that these identified genes/proteins contribute to heart maturation mainly by regulating mRNA processing and energy metabolism. Genome-wide alternative splicing (AS) analysis showed that some important sarcomere and energy-associated genes undergo different AS events. Through the Cytoscape plug-in CytoHubba, a total of 23 hub genes were found and further confirmed by RT-qPCR. Next, we verified that the most up-regulated hub gene, Ogdhl, plays an essential role in heart maturation by detecting energy metabolism phenotype changes in the Ogdhl-interfering cardiomyocytes. Together, we revealed a complex gene network, AS genes and patterns, and candidate hub genes controlling heart maturation by proteome and transcriptome combination analysis.
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Affiliation(s)
- Huijun Yang
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha 410008, China;
| | - Weijing Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; (W.L.); (S.S.); (L.B.); (Y.N.)
| | - Shen Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; (W.L.); (S.S.); (L.B.); (Y.N.)
| | - Lina Bai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; (W.L.); (S.S.); (L.B.); (Y.N.)
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China; (W.L.); (S.S.); (L.B.); (Y.N.)
| | - Yongping Bai
- Department of Geriatric Medicine, Xiangya Hospital, National Clinical Research Center for Geriatric Disorders, Central South University, Changsha 410008, China;
| | - Guogang Zhang
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha 410008, China;
- Correspondence:
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13
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Sunny S, Challa AK, Qiao A, Jyothidasan A, Krishnamurthy P, Ramamurthy MT, Crossman DK, Pogwizd S, Cinghu S, Rajasekaran NS. Transcriptional Regulation of Structural and Functional Adaptations in a Developing Adulthood Myocardium. ACTA ACUST UNITED AC 2021; 5:454-470. [PMID: 34497977 PMCID: PMC8423094 DOI: 10.26502/fccm.92920215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The development of the heart follows a synergic action of several signaling pathways during gestational, pre- & postnatal stages. The current study aimed to investigate whether the myocardium experiences transcriptional changes during the transition from post-natal to adult hood stages. Herein, we used C57/B16/J mice at 4 (28- days; post-natal/PN) and 20 weeks (adulthood/AH) of ages and employed the next generation RNAseq (NGS) to profile the transcriptome and echocardiography analysis to monitor the structural/functional changes in the heart. NGS-based RNA-seq revealed that 1215 genes were significantly upregulated and 2549 were down regulated in the AH versus PN hearts, indicating a significant transcriptional change during this transition. A synchronized cardiac transcriptional regulation through cell cycle, growth hormones, redox homeostasis and metabolic pathways was noticed in both PN and AH hearts. Echocardiography reveals significant structural and functional (i.e. systolic/diastolic) changes during the transition of PN to adult stage. Particularly, a progressive decline in ejection fraction and cardiac output was observed in AH hearts. These structural adaptations are in line with critical signaling pathways that drive the maturation of heart during AH. Overall, we have presented a comprehensive transcriptomic analysis along with structural-functional relationship during the myocardial development in adult mice.
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Affiliation(s)
- Sini Sunny
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Anil Kumar Challa
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | - Aijun Qiao
- Department of Biomedical Engineering, University of Alabama at Birmingham, AL, USA
| | - Arun Jyothidasan
- Department of Pathology, University of Alabama at Birmingham, AL, USA
| | | | | | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, AL, USA
| | - Steven Pogwizd
- Department of Medicine, University of Alabama at Birmingham, AL, USA
| | - Senthilkumar Cinghu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, USA
| | - Namakkal S Rajasekaran
- Department of Pathology, University of Alabama at Birmingham, AL, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Utah, UT, USA
- Center for Free Radical Biology, University of Alabama at Birmingham, AL, USA
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14
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Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes. Sci Rep 2021; 11:15845. [PMID: 34349150 PMCID: PMC8338992 DOI: 10.1038/s41598-021-94732-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
We performed a comprehensive analysis of the transcriptional changes occurring during human induced pluripotent stem cell (hiPSC) differentiation to cardiomyocytes. Using single cell RNA-seq, we sequenced > 20,000 single cells from 55 independent samples representing two differentiation protocols and multiple hiPSC lines. Samples included experimental replicates ranging from undifferentiated hiPSCs to mixed populations of cells at D90 post-differentiation. Differentiated cell populations clustered by time point, with differential expression analysis revealing markers of cardiomyocyte differentiation and maturation changing from D12 to D90. We next performed a complementary cluster-independent sparse regression analysis to identify and rank genes that best assigned cells to differentiation time points. The two highest ranked genes between D12 and D24 (MYH7 and MYH6) resulted in an accuracy of 0.84, and the three highest ranked genes between D24 and D90 (A2M, H19, IGF2) resulted in an accuracy of 0.94, revealing that low dimensional gene features can identify differentiation or maturation stages in differentiating cardiomyocytes. Expression levels of select genes were validated using RNA FISH. Finally, we interrogated differences in cardiac gene expression resulting from two differentiation protocols, experimental replicates, and three hiPSC lines in the WTC-11 background to identify sources of variation across these experimental variables.
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Affiliation(s)
| | | | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,, Parse Biosciences, Seattle, WA, USA
| | - Charles M Roco
- , Parse Biosciences, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Matthew Hirano
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA
| | | | - Joyce Tang
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Julie A Theriot
- Allen Institute for Cell Science, Seattle, WA, USA.,Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, Seattle, WA, USA
| | - Vilas Menon
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin - Madison, Madison, WI, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA.,Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
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15
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Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg TA, Rafelski SM, Theriot JA, Gunawardane RN. Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes. Cell Syst 2021; 12:670-687.e10. [PMID: 34043964 DOI: 10.1016/j.cels.2021.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/11/2022]
Abstract
Although some cell types may be defined anatomically or by physiological function, a rigorous definition of cell state remains elusive. Here, we develop a quantitative, imaging-based platform for the systematic and automated classification of subcellular organization in single cells. We use this platform to quantify subcellular organization and gene expression in >30,000 individual human induced pluripotent stem cell-derived cardiomyocytes, producing a publicly available dataset that describes the population distributions of local and global sarcomere organization, mRNA abundance, and correlations between these traits. While the mRNA abundance of some phenotypically important genes correlates with subcellular organization (e.g., the beta-myosin heavy chain, MYH7), these two cellular metrics are heterogeneous and often uncorrelated, which suggests that gene expression alone is not sufficient to classify cell states. Instead, we posit that cell state should be defined by observing full distributions of quantitative, multidimensional traits in single cells that also account for space, time, and function.
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Affiliation(s)
- Kaytlyn A Gerbin
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Tanya Grancharova
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | - Helen G Anderson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jackson M Brown
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jianxu Chen
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Stephanie Q Dinh
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Jamie L Gehring
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Gregory R Johnson
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - HyeonWoo Lee
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Aditya Nath
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | - M Filip Sluzewski
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Matheus P Viana
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | - Calysta Yan
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA
| | | | | | | | | | | | - Julie A Theriot
- Allen Institute for Cell Science, 615 Westlake Ave N, Seattle, WA, USA; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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16
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Schuman ML, Peres Diaz LS, Aisicovich M, Ingallina F, Toblli JE, Landa MS, García SI. Cardiac Thyrotropin-releasing Hormone Inhibition Improves Ventricular Function and Reduces Hypertrophy and Fibrosis After Myocardial Infarction in Rats. J Card Fail 2021; 27:796-807. [PMID: 33865967 DOI: 10.1016/j.cardfail.2021.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/11/2021] [Accepted: 04/06/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cardiac thyrotropin-releasing hormone (TRH) is a tripeptide with still unknown functions. We demonstrated that the left ventricle (LV) TRH system is hyperactivated in spontaneously hypertensive rats and its inhibition prevented cardiac hypertrophy and fibrosis. Therefore, we evaluated whether in vivo cardiac TRH inhibition could improve myocardial function and attenuate ventricular remodeling in a rat model of myocardial infarction (MI). METHODS AND RESULTS In Wistar rats, MI was induced by a permanent left anterior descending coronary artery ligation. A coronary injection of a specific small interfering RNA against TRH was applied simultaneously. The control group received a scrambled small interfering RNA. Cardiac remodeling variables were evaluated one week later. In MI rats, TRH inhibition decreased LV end-diastolic (1.049 ± 0.102 mL vs 1.339 ± 0.102 mL, P < .05), and end-systolic volumes (0.282 ± 0.043 mL vs 0.515 ± 0.037 mL, P < .001), and increased LV ejection fraction (71.89 ± 2.80% vs 65.69 ± 2.85%, P < .05). Although both MI groups presented similar infarct size, small interfering RNA against TRH treatment attenuated the cardiac hypertrophy index and myocardial interstitial collagen deposition in the peri-infarct myocardium. These effects were accompanied by attenuation in the rise of transforming growth factor-β, collagen I, and collagen III, as well as the fetal genes (atrial natriuretic peptide, B-type natriuretic peptide, and beta myosin heavy chain) expression in the peri-infarct region. In addition, the expression of Hif1α and vascular endothelial growth factor significantly increased compared with all groups. CONCLUSIONS Cardiac TRH inhibition improves LV systolic function and attenuates ventricular remodeling after MI. These novel findings support the idea that TRH inhibition may serve as a new therapeutic strategy against the progression of heart failure.
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Affiliation(s)
- Mariano L Schuman
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Cardiology, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ludmila S Peres Diaz
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Cardiology, Ciudad Autónoma de Buenos Aires, Argentina
| | - Maia Aisicovich
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Cardiology, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Ingallina
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; University of Buenos Aires (UBA), School of Medicine, Institute of Medical Research "Alfredo Lanari," Department of Cardiology, Ciudad Autonoma de Buenos Aires, Argentina
| | - Jorge E Toblli
- Laboratory of Experimental Medicine, Hospital Alemán, Ciudad Autonoma de Buenos Aires, Argentina
| | - Maria S Landa
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Cardiology, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Genetics and Biology of Complex Diseases, Ciudad Autonoma de Buenos Aires, Argentina
| | - Silvia I García
- University of Buenos Aires, School of Medicine, Institute of Medical Research A. Lanari, Ciudad Autónoma de Buenos Aires, Argentina; National Scientific and Technical Research Council (CONICET), University of Buenos Aires (UBA), Institute of Medical Research (IDIM), Department of Molecular Cardiology, Ciudad Autónoma de Buenos Aires, Argentina; Laboratory of Experimental Medicine, Hospital Alemán, Ciudad Autonoma de Buenos Aires, Argentina.
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17
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Yang Y, Kurian J, Schena G, Johnson J, Kubo H, Travers JG, Kang C, Lucchese AM, Eaton DM, Lv M, Li N, Leynes LG, Yu D, Yang F, McKinsey TA, Kishore R, Khan M, Mohsin S, Houser SR. Cardiac Remodeling During Pregnancy With Metabolic Syndrome: Prologue of Pathological Remodeling. Circulation 2021; 143:699-712. [PMID: 33587660 PMCID: PMC7888689 DOI: 10.1161/circulationaha.120.051264] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/30/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND The heart undergoes physiological hypertrophy during pregnancy in healthy individuals. Metabolic syndrome (MetS) is now prevalent in women of child-bearing age and might add risks of adverse cardiovascular events during pregnancy. The present study asks if cardiac remodeling during pregnancy in obese individuals with MetS is abnormal and whether this predisposes them to a higher risk for cardiovascular disorders. METHODS The idea that MetS induces pathological cardiac remodeling during pregnancy was studied in a long-term (15 weeks) Western diet-feeding animal model that recapitulated features of human MetS. Pregnant female mice with Western diet (45% kcal fat)-induced MetS were compared with pregnant and nonpregnant females fed a control diet (10% kcal fat). RESULTS Pregnant mice fed a Western diet had increased heart mass and exhibited key features of pathological hypertrophy, including fibrosis and upregulation of fetal genes associated with pathological hypertrophy. Hearts from pregnant animals with WD-induced MetS had a distinct gene expression profile that could underlie their pathological remodeling. Concurrently, pregnant female mice with MetS showed more severe cardiac hypertrophy and exacerbated cardiac dysfunction when challenged with angiotensin II/phenylephrine infusion after delivery. CONCLUSIONS These results suggest that preexisting MetS could disrupt physiological hypertrophy during pregnancy to produce pathological cardiac remodeling that could predispose the heart to chronic disorders.
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Affiliation(s)
- Yijun Yang
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Justin Kurian
- Center for Metabolic Disease and Department of Physiology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Giana Schena
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Jaslyn Johnson
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Hajime Kubo
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Joshua G. Travers
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Chunya Kang
- Medical University of Lublin, Lublin, Poland
| | - Anna Maria Lucchese
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Deborah M. Eaton
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Maoting Lv
- Second Ultrasound Department, Cangzhou Central Hospital, Hebei, China
| | - Na Li
- Second Department of Obstetrics, Cangzhou Central Hospital, Hebei, China
| | - Lorianna G. Leynes
- Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Daohai Yu
- Department of Clinical Sciences, Lewis Katz School of Medicine at Temple University, PA, United States
| | - Fengzhen Yang
- Second Department of Obstetrics, Cangzhou Central Hospital, Hebei, China
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology, and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Mohsin Khan
- Center for Metabolic Disease and Department of Physiology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Sadia Mohsin
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
| | - Steven R. Houser
- Independence Blue Cross Cardiovascular Research Center and Department of Pharmacology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, United States
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18
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Chen Z, Wei L, Duru F, Chen L. Single-cell RNA Sequencing: In-depth Decoding of Heart Biology and Cardiovascular Diseases. Curr Genomics 2020; 21:585-601. [PMID: 33414680 PMCID: PMC7770632 DOI: 10.2174/1389202921999200604123914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background The cardiac system is a combination of a complex structure, various cells, and versatile specified functions and sophisticated regulatory mechanisms. Moreover, cardiac diseases that encompass a wide range of endogenous conditions, remain a serious health burden worldwide. Recent genome-wide profiling techniques have taken the lead in uncovering a new realm of cell types and molecular programs driving physiological and pathological processes in various organs and diseases. In particular, the emerging technique single-cell RNA sequencing dominates a breakthrough in decoding the cell heterogeneity, phenotype transition, and developmental dynamics in cardiovascular science. Conclusion Herein, we review recent advances in single cellular studies of cardiovascular system and summarize new insights provided by single-cell RNA sequencing in heart developmental sciences, stem-cell researches as well as normal or disease-related working mechanisms.
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Affiliation(s)
- Zhongli Chen
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Liang Wei
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Firat Duru
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Liang Chen
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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19
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Weitzner EL, Fanter CE, Hindle AG. Pinniped Ontogeny as a Window into the Comparative Physiology and Genomics of Hypoxia Tolerance. Integr Comp Biol 2020; 60:1414-1424. [PMID: 32559283 DOI: 10.1093/icb/icaa083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Diving physiology has received considerable scientific attention as it is a central element of the extreme phenotype of marine mammals. Many scientific discoveries have illuminated physiological mechanisms supporting diving, such as massive, internally bound oxygen stores and dramatic cardiovascular regulation. However, the cellular and molecular mechanisms that support the diving phenotype remain mostly unexplored as logistic and legal restrictions limit the extent of scientific manipulation possible. With next-generation sequencing (NGS) tools becoming more widespread and cost-effective, there are new opportunities to explore the diving phenotype. Genomic investigations come with their own challenges, particularly those including cross-species comparisons. Studying the regulatory pathways that underlie diving mammal ontogeny could provide a window into the comparative physiology of hypoxia tolerance. Specifically, in pinnipeds, which shift from terrestrial pups to elite diving adults, there is potential to characterize the transcriptional, epigenetic, and posttranslational differences between contrasting phenotypes while leveraging a common genome. Here we review the current literature detailing the maturation of the diving phenotype in pinnipeds, which has primarily been explored via biomarkers of metabolic capability including antioxidants, muscle fiber typing, and key aerobic and anaerobic metabolic enzymes. We also discuss how NGS tools have been leveraged to study phenotypic shifts within species through ontogeny, and how this approach may be applied to investigate the biochemical and physiological mechanisms that develop as pups become elite diving adults. We conclude with a specific example of the Antarctic Weddell seal by overlapping protein biomarkers with gene regulatory microRNA datasets.
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Affiliation(s)
- Emma L Weitzner
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Cornelia E Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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20
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Greenig M, Melville A, Huntley D, Isalan M, Mielcarek M. Cross-Sectional Transcriptional Analysis of the Aging Murine Heart. Front Mol Biosci 2020; 7:565530. [PMID: 33102519 PMCID: PMC7545256 DOI: 10.3389/fmolb.2020.565530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Cardiovascular disease accounts for millions of deaths each year and is currently the leading cause of mortality worldwide. The aging process is clearly linked to cardiovascular disease, however, the exact relationship between aging and heart function is not fully understood. Furthermore, a holistic view of cardiac aging, linking features of early life development to changes observed in old age, has not been synthesized. Here, we re-purpose RNA-sequencing data previously-collected by our group, investigating gene expression differences between wild-type mice of different age groups that represent key developmental milestones in the murine lifespan. DESeq2's generalized linear model was applied with two hypothesis testing approaches to identify differentially-expressed (DE) genes, both between pairs of age groups and across mice of all ages. Pairwise comparisons identified genes associated with specific age transitions, while comparisons across all age groups identified a large set of genes associated with the aging process more broadly. An unsupervised machine learning approach was then applied to extract common expression patterns from this set of age-associated genes. Sets of genes with both linear and non-linear expression trajectories were identified, suggesting that aging not only involves the activation of gene expression programs unique to different age groups, but also the re-activation of gene expression programs from earlier ages. Overall, we present a comprehensive transcriptomic analysis of cardiac gene expression patterns across the entirety of the murine lifespan.
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Affiliation(s)
- Matthew Greenig
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Andrew Melville
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Derek Huntley
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Center for Synthetic Biology, Imperial College London, London, United Kingdom
| | - Michal Mielcarek
- Department of Life Sciences, Imperial College London, London, United Kingdom
- Imperial College Center for Synthetic Biology, Imperial College London, London, United Kingdom
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21
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Tsang HG, Clark EL, Markby GR, Bush SJ, Hume DA, Corcoran BM, MacRae VE, Summers KM. Expression of Calcification and Extracellular Matrix Genes in the Cardiovascular System of the Healthy Domestic Sheep ( Ovis aries). Front Genet 2020; 11:919. [PMID: 33101359 PMCID: PMC7506100 DOI: 10.3389/fgene.2020.00919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
The maintenance of a healthy cardiovascular system requires expression of genes that contribute to essential biological activities and repression of those that are associated with functions likely to be detrimental to cardiovascular homeostasis. Vascular calcification is a major disruption to cardiovascular homeostasis, where tissues of the cardiovascular system undergo ectopic calcification and consequent dysfunction, but little is known about the expression of calcification genes in the healthy cardiovascular system. Large animal models are of increasing importance in cardiovascular disease research as they demonstrate more similar cardiovascular features (in terms of anatomy, physiology and size) to humans than do rodent species. We used RNA sequencing results from the sheep, which has been utilized extensively to examine calcification of prosthetic cardiac valves, to explore the transcriptome of the heart and cardiac valves in this large animal, in particular looking at expression of calcification and extracellular matrix genes. We then examined genes implicated in the process of vascular calcification in a wide array of cardiovascular tissues and across multiple developmental stages, using RT-qPCR. Our results demonstrate that there is a balance between genes that promote and those that suppress mineralization during development and across cardiovascular tissues. We show extensive expression of genes encoding proteins involved in formation and maintenance of the extracellular matrix in cardiovascular tissues, and high expression of hematopoietic genes in the cardiac valves. Our analysis will support future research into the functions of implicated genes in the development of valve calcification, and increase the utility of the sheep as a large animal model for understanding ectopic calcification in cardiovascular disease. This study provides a foundation to explore the transcriptome of the developing cardiovascular system and is a valuable resource for the fields of mammalian genomics and cardiovascular research.
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Affiliation(s)
- Hiu-Gwen Tsang
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Emily L. Clark
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Greg R. Markby
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Brendan M. Corcoran
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Vicky E. MacRae
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- The Roslin Institute and R(D)SVS, The University of Edinburgh, Edinburgh, United Kingdom
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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22
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Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med 2020; 22:1181-1190. [PMID: 32225167 DOI: 10.1038/s41436-020-0780-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/14/2023] Open
Abstract
PURPOSE RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing. RNA-seq is typically performed on clinically accessible tissues (CATs) from blood and skin. RNA tissue specificity makes it difficult to identify aberrations in relevant but nonaccessible tissues (non-CATs). We determined how RNA-seq from CATs represent splicing in and across genes and non-CATs. METHODS We quantified RNA splicing in 801 RNA-seq samples from 56 different adult and fetal tissues from Genotype-Tissue Expression Project (GTEx) and ArrayExpress. We identified genes and splicing events in each non-CAT and determined when RNA-seq in each CAT would inadequately represent them. We developed an online resource, MAJIQ-CAT, for exploring our analysis for specific genes and tissues. RESULTS In non-CATs, 40.2% of genes have splicing that is inadequately represented by at least one CAT; 6.3% of genes have splicing inadequately represented by all CATs. A majority (52.1%) of inadequately represented genes are lowly expressed in CATs (transcripts per million (TPM) < 1), but 5.8% are inadequately represented despite being well expressed (TPM > 10). CONCLUSION Many splicing events in non-CATs are inadequately evaluated using RNA-seq from CATs. MAJIQ-CAT allows users to explore which accessible tissues, if any, best represent splicing in genes and tissues of interest.
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Ronaldson-Bouchard K, Yeager K, Teles D, Chen T, Ma S, Song L, Morikawa K, Wobma HM, Vasciaveo A, Ruiz EC, Yazawa M, Vunjak-Novakovic G. Engineering of human cardiac muscle electromechanically matured to an adult-like phenotype. Nat Protoc 2019; 14:2781-2817. [PMID: 31492957 PMCID: PMC7195192 DOI: 10.1038/s41596-019-0189-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
The application of tissue-engineering approaches to human induced pluripotent stem (hiPS) cells enables the development of physiologically relevant human tissue models for in vitro studies of development, regeneration, and disease. However, the immature phenotype of hiPS-derived cardiomyocytes (hiPS-CMs) limits their utility. We have developed a protocol to generate engineered cardiac tissues from hiPS cells and electromechanically mature them toward an adult-like phenotype. This protocol also provides optimized methods for analyzing these tissues' functionality, ultrastructure, and cellular properties. The approach relies on biological adaptation of cultured tissues subjected to biomimetic cues, applied at an increasing intensity, to drive accelerated maturation. hiPS cells are differentiated into cardiomyocytes and used immediately after the first contractions are observed, when they still have developmental plasticity. This starting cell population is combined with human dermal fibroblasts, encapsulated in a fibrin hydrogel and allowed to compact under passive tension in a custom-designed bioreactor. After 7 d of tissue formation, the engineered tissues are matured for an additional 21 d by increasingly intense electromechanical stimulation. Tissue properties can be evaluated by measuring contractile function, responsiveness to electrical stimuli, ultrastructure properties (sarcomere length, mitochondrial density, networks of transverse tubules), force-frequency and force-length relationships, calcium handling, and responses to β-adrenergic agonists. Cell properties can be evaluated by monitoring gene/protein expression, oxidative metabolism, and electrophysiology. The protocol takes 4 weeks and requires experience in advanced cell culture and machining methods for bioreactor fabrication. We anticipate that this protocol will improve modeling of cardiac diseases and testing of drugs.
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Affiliation(s)
| | - Keith Yeager
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Diogo Teles
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Timothy Chen
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Stephen Ma
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - LouJin Song
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kumi Morikawa
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Holly M Wobma
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Edward C Ruiz
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Masayuki Yazawa
- Departments of Rehabilitation and Regenerative Medicine, and of Pharmacology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
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24
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Pervolaraki E, Hall SP, Foresteire D, Saito T, Saido TC, Whittington MA, Lever C, Dachtler J. Insoluble Aβ overexpression in an App knock-in mouse model alters microstructure and gamma oscillations in the prefrontal cortex, affecting anxiety-related behaviours. Dis Model Mech 2019; 12:dmm040550. [PMID: 31439589 PMCID: PMC6765200 DOI: 10.1242/dmm.040550] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
We studied a new amyloid-beta precursor protein (App) knock-in mouse model of Alzheimer's disease (AppNL-G-F ), containing the Swedish KM670/671NL mutation, the Iberian I716F mutation and the Artic E693G mutation, which generates elevated levels of amyloid beta (Aβ)40 and Aβ42 without the confounds associated with APP overexpression. This enabled us to assess changes in anxiety-related and social behaviours, and neural alterations potentially underlying such changes, driven specifically by Aβ accumulation. AppNL-G-F knock-in mice exhibited subtle deficits in tasks assessing social olfaction, but not in social motivation tasks. In anxiety-assessing tasks, AppNL-G-F knock-in mice exhibited: (1) increased thigmotaxis in the open field (OF), yet; (2) reduced closed-arm, and increased open-arm, time in the elevated plus maze (EPM). Their ostensibly anxiogenic OF profile, yet ostensibly anxiolytic EPM profile, could hint at altered cortical mechanisms affecting decision-making (e.g. 'disinhibition'), rather than simple core deficits in emotional motivation. Consistent with this possibility, alterations in microstructure, glutamatergic-dependent gamma oscillations and glutamatergic gene expression were all observed in the prefrontal cortex, but not the amygdala, of AppNL-G-F knock-in mice. Thus, insoluble Aβ overexpression drives prefrontal cortical alterations, potentially underlying changes in social and anxiety-related behavioural tasks.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Stephen P Hall
- Hull York Medical School, University of York, Heslington, YO10 5DD, UK
| | - Denise Foresteire
- Department of Psychology, Durham University, South Road, Durham, DH1 3LE, UK
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
| | | | - Colin Lever
- Department of Psychology, Durham University, South Road, Durham, DH1 3LE, UK
| | - James Dachtler
- Department of Psychology, Durham University, South Road, Durham, DH1 3LE, UK
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