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Zaragoza MV, Bui TA, Widyastuti HP, Mehrabi M, Cang Z, Sha Y, Grosberg A, Nie Q. LMNA -Related Dilated Cardiomyopathy: Single-Cell Transcriptomics during Patient-derived iPSC Differentiation Support Cell type and Lineage-specific Dysregulation of Gene Expression and Development for Cardiomyocytes and Epicardium-Derived Cells with Lamin A/C Haploinsufficiency. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598335. [PMID: 38915555 PMCID: PMC11195187 DOI: 10.1101/2024.06.12.598335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
LMNA -Related Dilated Cardiomyopathy (DCM) is an autosomal-dominant genetic condition with cardiomyocyte and conduction system dysfunction often resulting in heart failure or sudden death. The condition is caused by mutation in the Lamin A/C ( LMNA ) gene encoding Type-A nuclear lamin proteins involved in nuclear integrity, epigenetic regulation of gene expression, and differentiation. Molecular mechanisms of disease are not completely understood, and there are no definitive treatments to reverse progression or prevent mortality. We investigated possible mechanisms of LMNA -Related DCM using induced pluripotent stem cells derived from a family with a heterozygous LMNA c.357-2A>G splice-site mutation. We differentiated one LMNA mutant iPSC line derived from an affected female (Patient) and two non-mutant iPSC lines derived from her unaffected sister (Control) and conducted single-cell RNA sequencing for 12 samples (4 Patient and 8 Control) across seven time points: Day 0, 2, 4, 9, 16, 19, and 30. Our bioinformatics workflow identified 125,554 cells in raw data and 110,521 (88%) high-quality cells in sequentially processed data. Unsupervised clustering, cell annotation, and trajectory inference found complex heterogeneity: ten main cell types; many possible subtypes; and lineage bifurcation for Cardiac Progenitors to Cardiomyocytes (CM) and Epicardium-Derived Cells (EPDC). Data integration and comparative analyses of Patient and Control cells found cell type and lineage differentially expressed genes (DEG) with enrichment to support pathway dysregulation. Top DEG and enriched pathways included: 10 ZNF genes and RNA polymerase II transcription in Pluripotent cells (PP); BMP4 and TGF Beta/BMP signaling, sarcomere gene subsets and cardiogenesis, CDH2 and EMT in CM; LMNA and epigenetic regulation and DDIT4 and mTORC1 signaling in EPDC. Top DEG also included: XIST and other X-linked genes, six imprinted genes: SNRPN , PWAR6 , NDN , PEG10 , MEG3 , MEG8 , and enriched gene sets in metabolism, proliferation, and homeostasis. We confirmed Lamin A/C haploinsufficiency by allelic expression and Western blot. Our complex Patient-derived iPSC model for Lamin A/C haploinsufficiency in PP, CM, and EPDC provided support for dysregulation of genes and pathways, many previously associated with Lamin A/C defects, such as epigenetic gene expression, signaling, and differentiation. Our findings support disruption of epigenomic developmental programs as proposed in other LMNA disease models. We recognized other factors influencing epigenetics and differentiation; thus, our approach needs improvement to further investigate this mechanism in an iPSC-derived model.
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Deogharia M, Venegas-Zamora L, Agrawal A, Shi M, Jain AK, McHugh KJ, Altamirano F, Marian AJ, Gurha P. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization. Cardiovasc Res 2024; 120:630-643. [PMID: 38230606 PMCID: PMC11074792 DOI: 10.1093/cvr/cvae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/09/2023] [Accepted: 12/12/2023] [Indexed: 01/18/2024] Open
Abstract
AIMS Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation. METHODS AND RESULTS KDM5A, B, and C proteins were mainly expressed in the early post-natal stages, and their expressions were progressively downregulated in the post-natal CMs and were absent in adult hearts and CMs. In contrast, KDM5 proteins were persistently expressed in the iPSC-CMs up to 60 days after the induction of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor, induced differential expression of 2372 genes, including upregulation of genes involved in fatty acid oxidation (FAO), OXPHOS, and myogenesis in the iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the cleavage under targets and release using nuclease assay showed enriched of the H3K4me3 peaks at the promoter regions of genes encoding FAO, OXPHOS, and sarcomere proteins. Consistent with the chromatin and gene expression data, KDM5 inhibition increased the expression of multiple sarcomere proteins and enhanced myofibrillar organization. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene and increased its RNA and protein levels. Knockdown of ESRRA in KDM5-C70-treated iPSC-CM suppressed expression of a subset of the KDM5 targets. In conjunction with changes in gene expression, KDM5 inhibition increased oxygen consumption rate and contractility in iPSC-CMs. CONCLUSION KDM5 inhibition enhances maturation of iPSC-CMs by epigenetically upregulating the expressions of OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
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Affiliation(s)
- Manisha Deogharia
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
| | - Leslye Venegas-Zamora
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
| | - Akanksha Agrawal
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
| | - Miusi Shi
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Kevin J McHugh
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
- Department of Chemistry, Rice University, Houston, 6500 Main Street, Houston, TX 77030, USA
| | - Francisco Altamirano
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Avenue, Houston, Texas 77030, USA
- Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University, Ithaca, NY, USA
| | - Ali J Marian
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
| | - Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, 6770 Bertner Street, C950G, Houston, TX 77030, USA
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Husser MC, Pham NP, Law C, Araujo FRB, Martin VJJ, Piekny A. Endogenous tagging using split mNeonGreen in human iPSCs for live imaging studies. eLife 2024; 12:RP92819. [PMID: 38652106 PMCID: PMC11037917 DOI: 10.7554/elife.92819] [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] [Indexed: 04/25/2024] Open
Abstract
Endogenous tags have become invaluable tools to visualize and study native proteins in live cells. However, generating human cell lines carrying endogenous tags is difficult due to the low efficiency of homology-directed repair. Recently, an engineered split mNeonGreen protein was used to generate a large-scale endogenous tag library in HEK293 cells. Using split mNeonGreen for large-scale endogenous tagging in human iPSCs would open the door to studying protein function in healthy cells and across differentiated cell types. We engineered an iPS cell line to express the large fragment of the split mNeonGreen protein (mNG21-10) and showed that it enables fast and efficient endogenous tagging of proteins with the short fragment (mNG211). We also demonstrate that neural network-based image restoration enables live imaging studies of highly dynamic cellular processes such as cytokinesis in iPSCs. This work represents the first step towards a genome-wide endogenous tag library in human stem cells.
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Affiliation(s)
| | - Nhat P Pham
- Biology Department, Concordia University, Montreal, Canada
| | - Chris Law
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
| | - Flavia R B Araujo
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Biology Department, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
| | - Alisa Piekny
- Biology Department, Concordia University, Montreal, Canada
- Center for Microscopy and Cellular Imaging, Concordia University, Montreal, Canada
- Center for Applied Synthetic Biology, Concordia University, Montreal, Canada
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Kok CY, Ghossein G, Igoor S, Rao R, Titus T, Tsurusaki S, Chong JJ, Kizana E. Ghrelin mediated cardioprotection using in vitro models of oxidative stress. Gene Ther 2024; 31:165-174. [PMID: 38177343 PMCID: PMC10940144 DOI: 10.1038/s41434-023-00435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024]
Abstract
Ghrelin is commonly known as the 'hunger hormone' due to its role in stimulating food intake in humans. However, the roles of ghrelin extend beyond regulating hunger. Our aim was to investigate the ability of ghrelin to protect against hydrogen peroxide (H2O2), a reactive oxygen species commonly associated with cardiac injury. An in vitro model of oxidative stress was developed using H2O2 injured H9c2 cells. Despite lentiviral ghrelin overexpression, H9c2 cell viability and mitochondrial function were not protected following H2O2 injury. We found that H9c2 cells lack expression of the preproghrelin cleavage enzyme prohormone convertase 1 (encoded by PCSK1), required to convert ghrelin to its active form. In contrast, we found that primary rat cardiomyocytes do express PCSK1 and were protected from H2O2 injury by lentiviral ghrelin overexpression. In conclusion, we have shown that ghrelin expression can protect primary rat cardiomyocytes against H2O2, though this effect was not observed in other cell types tested.
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Affiliation(s)
- Cindy Y Kok
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Westmead Clinical School, the Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - George Ghossein
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Sindhu Igoor
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Renuka Rao
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Tracy Titus
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - Shinya Tsurusaki
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
| | - James Jh Chong
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Westmead Clinical School, the Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Cardiology, Westmead Hospital, Westmead, NSW, Australia
| | - Eddy Kizana
- Centre for Heart Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia.
- Westmead Clinical School, the Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- Department of Cardiology, Westmead Hospital, Westmead, NSW, Australia.
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Rapöhn M, Cyganek L, Voigt N, Hasenfuß G, Lehnart SE, Wegener JW. Noninvasive analysis of contractility during identical maturations revealed two phenotypes in ventricular but not in atrial iPSC-CM. Am J Physiol Heart Circ Physiol 2024; 326:H599-H611. [PMID: 38180453 PMCID: PMC11221812 DOI: 10.1152/ajpheart.00527.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
Patient-derived induced pluripotent stem cells (iPSCs) can be differentiated into atrial and ventricular cardiomyocytes to allow for personalized drug screening. A hallmark of differentiation is the manifestation of spontaneous beating in a two-dimensional (2-D) cell culture. However, an outstanding observation is the high variability in this maturation process. We valued that contractile parameters change during differentiation serving as an indicator of maturation. Consequently, we recorded noninvasively spontaneous motion activity during the differentiation of male iPSC toward iPSC cardiomyocytes (iPSC-CMs) to further analyze similar maturated iPSC-CMs. Surprisingly, our results show that identical differentiations into ventricular iPSC-CMs are variable with respect to contractile parameters resulting in two distinct subpopulations of ventricular-like cells. In contrast, differentiation into atrial iPSC-CMs resulted in only one phenotype. We propose that the noninvasive and cost-effective recording of contractile activity during maturation using a smartphone device may help to reduce the variability in results frequently reported in studies on ventricular iPSC-CMs.NEW & NOTEWORTHY Differentiation of induced pluripotent stem cells (iPSCs) into iPSC-derived cardiomyocytes (iPSC-CMs) exhibits a high variability in mature parameters. Here, we monitored noninvasively contractile parameters of iPSC-CM during full-time differentiation using a smartphone device. Our results show that parallel maturations of iPSCs into ventricular iPSC-CMs, but not into atrial iPSC-CMs, resulted in two distinct subpopulations of iPSC-CMs. These findings suggest that our cost-effective method may help to compare iPSC-CMs at the same maturation level.
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Affiliation(s)
- Marcel Rapöhn
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
| | - Lukas Cyganek
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Niels Voigt
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Department of Pharmacology and Toxicology, University Medical Center of Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Gerd Hasenfuß
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
| | - Stephan E Lehnart
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells," University of Göttingen, Göttingen, Germany
| | - Jörg W Wegener
- Department of Cardiology and Pulmonology, University Medical Center of Göttingen, Göttingen, Germany
- German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislaufforschung), Göttingen, Germany
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Yang J, Daily N, Pullinger TK, Wakatsuki T, Sobie EA. Creating cell-specific computational models of stem cell-derived cardiomyocytes using optical experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574577. [PMID: 38260376 PMCID: PMC10802448 DOI: 10.1101/2024.01.07.574577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) have gained traction as a powerful model in cardiac disease and therapeutics research, since iPSCs are self-renewing and can be derived from healthy and diseased patients without invasive surgery. However, current iPSC-CM differentiation methods produce cardiomyocytes with immature, fetal-like electrophysiological phenotypes, and the variety of maturation protocols in the literature results in phenotypic differences between labs. Heterogeneity of iPSC donor genetic backgrounds contributes to additional phenotypic variability. Several mathematical models of iPSC-CM electrophysiology have been developed to help understand the ionic underpinnings of, and to simulate, various cell responses, but these models individually do not capture the phenotypic variability observed in iPSC-CMs. Here, we tackle these limitations by developing a computational pipeline to calibrate cell preparation-specific iPSC-CM electrophysiological parameters. We used the genetic algorithm (GA), a heuristic parameter calibration method, to tune ion channel parameters in a mathematical model of iPSC-CM physiology. To systematically optimize an experimental protocol that generates sufficient data for parameter calibration, we created simulated datasets by applying various protocols to a population of in silico cells with known conductance variations, and we fitted to those datasets. We found that calibrating models to voltage and calcium transient data under 3 varied experimental conditions, including electrical pacing combined with ion channel blockade and changing buffer ion concentrations, improved model parameter estimates and model predictions of unseen channel block responses. This observation held regardless of whether the fitted data were normalized, suggesting that normalized fluorescence recordings, which are more accessible and higher throughput than patch clamp recordings, could sufficiently inform conductance parameters. Therefore, this computational pipeline can be applied to different iPSC-CM preparations to determine cell line-specific ion channel properties and understand the mechanisms behind variability in perturbation responses.
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Affiliation(s)
- Janice Yang
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neil Daily
- InvivoSciences Inc., Madison, WI 53719, USA
| | - Taylor K Pullinger
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric A Sobie
- Department of Pharmacological Sciences & Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Okuno S, Higo S, Kondo T, Shiba M, Kameda S, Inoue H, Tabata T, Ogawa S, Morishita Y, Sun C, Ishino S, Honda T, Miyagawa S, Sakata Y. SARS-CoV-2 spike receptor-binding domain is internalized and promotes protein ISGylation in human induced pluripotent stem cell-derived cardiomyocytes. Sci Rep 2023; 13:21397. [PMID: 38049441 PMCID: PMC10696029 DOI: 10.1038/s41598-023-48084-7] [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: 08/14/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023] Open
Abstract
Although an increased risk of myocarditis has been observed after vaccination with mRNA encoding severe acute respiratory syndrome coronavirus 2 spike protein, its underlying mechanism has not been elucidated. This study investigated the direct effects of spike receptor-binding domain (S-RBD) on human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs). Immunostaining experiments using ACE2 wild-type (WT) and knockout (KO) iPSC-CMs treated with purified S-RBD demonstrated that S-RBD was bound to ACE2 and internalized into the subcellular space in the iPSC-CMs, depending on ACE2. Immunostaining combined with live cell imaging using a recombinant S-RBD fused to the superfolder GFP (S-RBD-sfGFP) demonstrated that S-RBD was bound to the cell membrane, co-localized with RAB5A, and then delivered from the endosomes to the lysosomes in iPSC-CMs. Quantitative PCR array analysis followed by single cell RNA sequence analysis clarified that S-RBD-sfGFP treatment significantly upregulated the NF-kβ pathway-related gene (CXCL1) in the differentiated non-cardiomyocytes, while upregulated interferon (IFN)-responsive genes (IFI6, ISG15, and IFITM3) in the matured cardiomyocytes. S-RBD-sfGFP treatment promoted protein ISGylation, an ISG15-mediated post-translational modification in ACE2-WT-iPSC-CMs, which was suppressed in ACE2-KO-iPSC-CMs. Our experimental study demonstrates that S-RBD is internalized through the endolysosomal pathway, which upregulates IFN-responsive genes and promotes ISGylation in the iPSC-CMs.
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Affiliation(s)
- Shota Okuno
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shuichiro Higo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
- Department of Medical Therapeutics for Heart Failure, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - Takumi Kondo
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Mikio Shiba
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Satoshi Kameda
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hiroyuki Inoue
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Tomoka Tabata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shou Ogawa
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yu Morishita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Congcong Sun
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Saki Ishino
- CoMIT Omics Center, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Tomoyuki Honda
- Department of Virology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Kita-Ku, Okayama, 700-8558, Japan
- Department of Virology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Kita-Ku, Okayama, 700-8558, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
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Wang ZH, Zhao W, Combs CA, Zhang F, Knutson JR, Lilly MA, Xu H. Mechanical stimulation from the surrounding tissue activates mitochondrial energy metabolism in Drosophila differentiating germ cells. Dev Cell 2023; 58:2249-2260.e9. [PMID: 37647895 PMCID: PMC10843713 DOI: 10.1016/j.devcel.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/24/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
In multicellular lives, the differentiation of stem cells and progenitor cells is often accompanied by a transition from glycolysis to mitochondrial oxidative phosphorylation (OXPHOS). However, the underlying mechanism of this metabolic transition remains largely unknown. In this study, we investigate the role of mechanical stress in activating OXPHOS during differentiation of the female germline cyst in Drosophila. We demonstrate that the surrounding somatic cells flatten the 16-cell differentiating cyst, resulting in an increase of the membrane tension of germ cells inside the cyst. This mechanical stress is necessary to maintain cytosolic Ca2+ concentration in germ cells through a mechanically activated channel, transmembrane channel-like. The sustained cytosolic Ca2+ triggers a CaMKI-Fray-JNK signaling relay, leading to the transcriptional activation of OXPHOS in differentiating cysts. Our findings demonstrate a molecular link between cell mechanics and mitochondrial energy metabolism, with implications for other developmentally orchestrated metabolic transitions in mammals.
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Affiliation(s)
- Zong-Heng Wang
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenjing Zhao
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian A Combs
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fan Zhang
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jay R Knutson
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mary A Lilly
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hong Xu
- National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Deogharia M, Agrawal A, Shi M, Jain AK, McHugh KJ, Altamirano F, Marian AJ, Gurha P. Histone demethylase KDM5 regulates cardiomyocyte maturation by promoting fatty acid oxidation, oxidative phosphorylation, and myofibrillar organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.535169. [PMID: 37090524 PMCID: PMC10120725 DOI: 10.1101/2023.04.11.535169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Rationale Human pluripotent stem cell-derived CMs (iPSC-CMs) are a valuable tool for disease modeling, cell therapy and to reconstruct the CM maturation process and identify, characterize factors that regulate maturation. The transition from immature fetal to adult CM entails coordinated regulation of the mature gene programming, which is characterized by the induction of myofilament and OXPHOS gene expression among others. Recent studies in Drosophila , C. elegans, and C2C12 myoblast cell lines have implicated the histone H3K4me3 demethylase KDM5 and its homologs, as a potential regulator of developmental gene program and mitochondrial function. We speculated that KDM5 may potentiate the maturation of iPSC-CMs by targeting a conserved epigenetic program that encompass mitochondrial OXPHOS and other CM specific maturation genes. Objectives The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation. Methods and Results Immunoblot analysis revealed that KDM5A, B, and C expression was progressively downregulated in postnatal cardiomyocytes and absent in adult hearts and CMs. Additionally, KDM5 proteins were found to be persistently expressed in iPSC-CMs up to 60 days after the onset of myogenic differentiation, consistent with the immaturity of these cells. Inhibition of KDM5 by KDM5-C70 -a pan-KDM5 inhibitor-resulted in differential regulation of 2,372 genes including upregulation of Fatty acid oxidation (FAO), OXPHOS, and myogenic gene programs in iPSC-CMs. Likewise, genome-wide profiling of H3K4me3 binding sites by the CUT&RUN assay revealed enriched H3K4me3 peaks at the promoter regions of FAO, OXPHOS, and sarcomere genes. Consistent with the chromatin and gene expression data, KDM5 inhibition led to increased expression of multiple sarcomere proteins, enhanced myofibrillar organization and improved calcium handling. Furthermore, inhibition of KDM5 increased H3K4me3 deposits at the promoter region of the ESRRA gene, which is known to regulate OXPHOS and cardiomyocyte maturation, and resulted in its increased RNA and protein levels. Finally, KDM5 inhibition increased baseline, peak, and spare oxygen consumption rates in iPSC-CMs. Conclusions KDM5 regulates the maturation of iPSC-CMs by epigenetically regulating the expression of ESRRA, OXPHOS, FAO, and sarcomere genes and enhancing myofibril organization and mitochondrial function.
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Wang J, Morgan W, Saini A, Liu T, Lough J, Han L. Single-cell transcriptomic profiling reveals specific maturation signatures in human cardiomyocytes derived from LMNB2-inactivated induced pluripotent stem cells. Front Cell Dev Biol 2022; 10:895162. [PMID: 36518540 PMCID: PMC9742441 DOI: 10.3389/fcell.2022.895162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2023] Open
Abstract
Mammalian cardiomyocyte maturation entails phenotypic and functional optimization during the late fetal and postnatal phases of heart development, both processes driven and coordinated by complex gene regulatory networks. Cardiomyocytes derived from human induced pluripotent stem cells (iPSCs) are heterogenous and immature, barely resembling their adult in vivo counterparts. To characterize relevant developmental programs and maturation states during human iPSC-cardiomyocyte differentiation, we performed single-cell transcriptomic sequencing, which revealed six cardiomyocyte subpopulations, whose heterogeneity was defined by cell cycle and maturation states. Two of those subpopulations were characterized by a mature, non-proliferative transcriptional profile. To further investigate the proliferation-maturation transition in cardiomyocytes, we induced loss-of-function of LMNB2, which represses cell cycle progression in primary cardiomyocytes in vivo. This resulted in increased maturation in LMNB2-inactivated cardiomyocytes, characterized by transcriptional profiles related to myofibril structure and energy metabolism. Furthermore, we identified maturation signatures and maturational trajectories unique for control and LMNB2-inactivated cardiomyocytes. By comparing these datasets with single-cell transcriptomes of human fetal hearts, we were able to define spatiotemporal maturation states in human iPSC-cardiomyocytes. Our results provide an integrated approach for comparing in vitro-differentiated cardiomyocytes with their in vivo counterparts and suggest a strategy to promote cardiomyocyte maturation.
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Affiliation(s)
- Jie Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - William Morgan
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Ankur Saini
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - John Lough
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Lu Han
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
- Division of Pediatric Cardiology, Herma Heart Institute, Children’s Hospital of Wisconsin, Milwaukee, WI, United States
- Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
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11
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Ergir E, Oliver-De La Cruz J, Fernandes S, Cassani M, Niro F, Pereira-Sousa D, Vrbský J, Vinarský V, Perestrelo AR, Debellis D, Vadovičová N, Uldrijan S, Cavalieri F, Pagliari S, Redl H, Ertl P, Forte G. Generation and maturation of human iPSC-derived 3D organotypic cardiac microtissues in long-term culture. Sci Rep 2022; 12:17409. [PMID: 36257968 PMCID: PMC9579206 DOI: 10.1038/s41598-022-22225-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Cardiovascular diseases remain the leading cause of death worldwide; hence there is an increasing focus on developing physiologically relevant in vitro cardiovascular tissue models suitable for studying personalized medicine and pre-clinical tests. Despite recent advances, models that reproduce both tissue complexity and maturation are still limited. We have established a scaffold-free protocol to generate multicellular, beating human cardiac microtissues in vitro from hiPSCs-namely human organotypic cardiac microtissues (hOCMTs)-that show some degree of self-organization and can be cultured for long term. This is achieved by the differentiation of hiPSC in 2D monolayer culture towards cardiovascular lineage, followed by further aggregation on low-attachment culture dishes in 3D. The generated hOCMTs contain multiple cell types that physiologically compose the heart and beat without external stimuli for more than 100 days. We have shown that 3D hOCMTs display improved cardiac specification, survival and metabolic maturation as compared to standard monolayer cardiac differentiation. We also confirmed the functionality of hOCMTs by their response to cardioactive drugs in long-term culture. Furthermore, we demonstrated that they could be used to study chemotherapy-induced cardiotoxicity. Due to showing a tendency for self-organization, cellular heterogeneity, and functionality in our 3D microtissues over extended culture time, we could also confirm these constructs as human cardiac organoids (hCOs). This study could help to develop more physiologically-relevant cardiac tissue models, and represent a powerful platform for future translational research in cardiovascular biology.
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Affiliation(s)
- Ece Ergir
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic ,grid.5329.d0000 0001 2348 4034Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Vienna University of Technology, 1040 Vienna, Austria
| | - Jorge Oliver-De La Cruz
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Soraia Fernandes
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Marco Cassani
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Francesco Niro
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Faculty of Medicine, Department of Biomedical Sciences, Masaryk University, 62500 Brno, Czech Republic
| | - Daniel Pereira-Sousa
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic ,grid.10267.320000 0001 2194 0956Faculty of Medicine, Department of Biomedical Sciences, Masaryk University, 62500 Brno, Czech Republic
| | - Jan Vrbský
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Vladimír Vinarský
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Ana Rubina Perestrelo
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Doriana Debellis
- grid.25786.3e0000 0004 1764 2907Electron Microscopy Facility, Fondazione Istituto Italiano Di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Natália Vadovičová
- grid.10267.320000 0001 2194 0956Faculty of Medicine, Department of Biomedical Sciences, Masaryk University, 62500 Brno, Czech Republic
| | - Stjepan Uldrijan
- grid.10267.320000 0001 2194 0956Faculty of Medicine, Department of Biomedical Sciences, Masaryk University, 62500 Brno, Czech Republic
| | - Francesca Cavalieri
- grid.1008.90000 0001 2179 088XDepartment of Chemical Engineering, The University of Melbourne, Parkville, VIC 3010 Australia ,grid.6530.00000 0001 2300 0941Dipartimento di Scienze e Tecnologie Chimiche, Università degli Studi di Roma Tor Vergata, via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Stefania Pagliari
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic
| | - Heinz Redl
- grid.454388.6Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, 1200 Vienna, Austria ,grid.511951.8Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Peter Ertl
- grid.5329.d0000 0001 2348 4034Faculty of Technical Chemistry, Institute of Applied Synthetic Chemistry and Institute of Chemical Technologies and Analytics, Vienna University of Technology, 1040 Vienna, Austria ,grid.511951.8Austrian Cluster for Tissue Regeneration, 1200 Vienna, Austria
| | - Giancarlo Forte
- grid.412752.70000 0004 0608 7557Center for Translational Medicine (CTM), International Clinical Research Centre (FNUSA-ICRC), St. Anne’s University Hospital, Studentská 812/6, 62500 Brno, Czech Republic ,grid.1374.10000 0001 2097 1371Department of Biomaterials Science, Institute of Dentistry, University of Turku, 20014 Turku, Finland
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12
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Fluorescence Spectroscopy of Low-Level Endogenous β-adrenergic Receptor Expression at the Plasma Membrane of Differentiating Human iPSC-Derived Cardiomyocytes. Int J Mol Sci 2022; 23:ijms231810405. [PMID: 36142320 PMCID: PMC9499492 DOI: 10.3390/ijms231810405] [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: 07/24/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
The potential of human-induced pluripotent stem cells (hiPSCs) to be differentiated into cardiomyocytes (CMs) mimicking adult CMs functional morphology, marker genes and signaling characteristics has been investigated since over a decade. The evolution of the membrane localization of CM-specific G protein-coupled receptors throughout differentiation has received, however, only limited attention to date. We employ here advanced fluorescent spectroscopy, namely linescan Fluorescence Correlation Spectroscopy (FCS), to observe how the plasma membrane abundance of the β1- and β2-adrenergic receptors (β1/2-ARs), labelled using a bright and photostable fluorescent antagonist, evolves during the long-term monolayer culture of hiPSC-derived CMs. We compare it to the kinetics of observed mRNA levels in wildtype (WT) hiPSCs and in two CRISPR/Cas9 knock-in clones. We conduct these observations against the backdrop of our recent report of cell-to-cell expression variability, as well as of the subcellular localization heterogeneity of β-ARs in adult CMs.
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13
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Muñoz JJAM, Dariolli R, da Silva CM, Neri EA, Valadão IC, Turaça LT, Lima VM, de Carvalho MLP, Velho MR, Sobie EA, Krieger JE. Time-regulated transcripts with the potential to modulate human pluripotent stem cell-derived cardiomyocyte differentiation. Stem Cell Res Ther 2022; 13:437. [PMID: 36056380 PMCID: PMC9438174 DOI: 10.1186/s13287-022-03138-x] [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: 03/22/2022] [Accepted: 08/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are a promising disease model, even though hiPSC-CMs cultured for extended periods display an undifferentiated transcriptional landscape. MiRNA–target gene interactions contribute to fine-tuning the genetic program governing cardiac maturation and may uncover critical pathways to be targeted. Methods We analyzed a hiPSC-CM public dataset to identify time-regulated miRNA–target gene interactions based on three logical steps of filtering. We validated this process in silico using 14 human and mouse public datasets, and further confirmed the findings by sampling seven time points over a 30-day protocol with a hiPSC-CM clone developed in our laboratory. We then added miRNA mimics from the top eight miRNAs candidates in three cell clones in two different moments of cardiac specification and maturation to assess their impact on differentiation characteristics including proliferation, sarcomere structure, contractility, and calcium handling.
Results We uncovered 324 interactions among 29 differentially expressed genes and 51 miRNAs from 20,543 transcripts through 120 days of hiPSC-CM differentiation and selected 16 genes and 25 miRNAs based on the inverse pattern of expression (Pearson R-values < − 0.5) and consistency in different datasets. We validated 16 inverse interactions among eight genes and 12 miRNAs (Person R-values < − 0.5) during hiPSC-CMs differentiation and used miRNAs mimics to verify proliferation, structural and functional features related to maturation. We also demonstrated that miR-124 affects Ca2+ handling altering features associated with hiPSC-CMs maturation.
Conclusion We uncovered time-regulated transcripts influencing pathways affecting cardiac differentiation/maturation axis and showed that the top-scoring miRNAs indeed affect primarily structural features highlighting their role in the hiPSC-CM maturation. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03138-x.
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Affiliation(s)
- Juan J A M Muñoz
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil.,Universidad Señor de Sipán, Chiclayo, Perú
| | - Rafael Dariolli
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil.,Department of Pharmacological Sciences, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Caio Mateus da Silva
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Elida A Neri
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Iuri C Valadão
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Lauro Thiago Turaça
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Vanessa M Lima
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Mariana Lombardi Peres de Carvalho
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Mariliza R Velho
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Eric A Sobie
- Department of Pharmacological Sciences, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jose E Krieger
- Laboratory of Genetics and Molecular Cardiology/LIM 13, Heart Institute (InCor), University of São Paulo Medical School, Avenida Dr. Eneas C. Aguiar 44, São Paulo, SP, 05403-000, Brazil.
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14
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Hu Y, Zhang Y, Liu Y, Gao Y, San T, Li X, Song S, Yan B, Zhao Z. Advances in application of single-cell RNA sequencing in cardiovascular research. Front Cardiovasc Med 2022; 9:905151. [PMID: 35958408 PMCID: PMC9360414 DOI: 10.3389/fcvm.2022.905151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and identifying targets for disease treatment. In recent years, emerging single-cell RNA sequencing technologies have been used to make breakthroughs regarding decoding developmental trajectories, phenotypic transitions, and cellular interactions in the cardiovascular system, providing new insights into cardiovascular disease. This paper reviews the technical processes of single-cell RNA sequencing and the latest progress based on single-cell RNA sequencing in the field of cardiovascular system research, compares single-cell RNA sequencing with other single-cell technologies, and summarizes the extended applications and advantages and disadvantages of single-cell RNA sequencing. Finally, the prospects for applying single-cell RNA sequencing in the field of cardiovascular research are discussed.
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Affiliation(s)
- Yue Hu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Ying Zhang
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Yutong Liu
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Yan Gao
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Tiantian San
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
| | - Xiaoying Li
- Department of Research Center of Translational Medicine, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- Department of Emergency, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Sensen Song
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Binglong Yan
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
| | - Zhuo Zhao
- Department of Cardiology, Jinan Central Hospital, Shandong University, Jinan, China
- Department of Cardiology, Central Hospital Affiliated Shandong First Medical University, Jinan, China
- *Correspondence: Zhuo Zhao
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15
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Hsieh J, Becklin KL, Givens S, Komosa ER, Lloréns JEA, Kamdar F, Moriarity BS, Webber BR, Singh BN, Ogle BM. Myosin Heavy Chain Converter Domain Mutations Drive Early-Stage Changes in Extracellular Matrix Dynamics in Hypertrophic Cardiomyopathy. Front Cell Dev Biol 2022; 10:894635. [PMID: 35784482 PMCID: PMC9245526 DOI: 10.3389/fcell.2022.894635] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/24/2022] [Indexed: 11/24/2022] Open
Abstract
More than 60% of hypertrophic cardiomyopathy (HCM)-causing mutations are found in the gene loci encoding cardiac myosin-associated proteins including myosin heavy chain (MHC) and myosin binding protein C (MyBP-C). Moreover, patients with more than one independent HCM mutation may be at increased risk for more severe disease expression and adverse outcomes. However detailed mechanistic understanding, especially at early stages of disease progression, is limited. To identify early-stage HCM triggers, we generated single (MYH7 c.2167C > T [R723C] with a known pathogenic significance in the MHC converter domain) and double (MYH7 c.2167C > T [R723C]; MYH6 c.2173C > T [R725C] with unknown significance) myosin gene mutations in human induced pluripotent stem cells (hiPSCs) using a base-editing strategy. Cardiomyocytes (CMs) derived from hiPSCs with either single or double mutation exhibited phenotypic characteristics consistent with later-stage HCM including hypertrophy, multinucleation, altered calcium handling, metabolism, and arrhythmia. We then probed mutant CMs at time points prior to the detection of known HCM characteristics. We found MYH7/MYH6 dual mutation dysregulated extracellular matrix (ECM) remodeling, altered integrin expression, and interrupted cell-ECM adhesion by limiting the formation of focal adhesions. These results point to a new phenotypic feature of early-stage HCM and reveal novel therapeutic avenues aimed to delay or prohibit disease onset.
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Affiliation(s)
- Jeanne Hsieh
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Sophie Givens
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Elizabeth R. Komosa
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Juan E. Abrahante Lloréns
- University of Minnesota Informatics Institute (UMII), University of Minnesota, Minneapolis, MN, United States
| | - Forum Kamdar
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Bhairab N. Singh
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Bhairab N. Singh, ; Brenda M. Ogle,
| | - Brenda M. Ogle
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, United States
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Bhairab N. Singh, ; Brenda M. Ogle,
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16
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Jiang S, Feng W, Chang C, Li G. Modeling Human Heart Development and Congenital Defects Using Organoids: How Close Are We? J Cardiovasc Dev Dis 2022; 9:jcdd9050125. [PMID: 35621836 PMCID: PMC9145739 DOI: 10.3390/jcdd9050125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
The emergence of human-induced Pluripotent Stem Cells (hiPSCs) has dramatically improved our understanding of human developmental processes under normal and diseased conditions. The hiPSCs have been differentiated into various tissue-specific cells in vitro, and the advancement in three-dimensional (3D) culture has provided a possibility to generate those cells in an in vivo-like environment. Tissues with 3D structures can be generated using different approaches such as self-assembled organoids and tissue-engineering methods, such as bioprinting. We are interested in studying the self-assembled organoids differentiated from hiPSCs, as they have the potential to recapitulate the in vivo developmental process and be used to model human development and congenital defects. Organoids of tissues such as those of the intestine and brain were developed many years ago, but heart organoids were not reported until recently. In this review, we will compare the heart organoids with the in vivo hearts to understand the anatomical structures we still lack in the organoids. Specifically, we will compare the development of main heart structures, focusing on their marker genes and regulatory signaling pathways.
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17
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Floy ME, Shabnam F, Simmons AD, Bhute VJ, Jin G, Friedrich WA, Steinberg AB, Palecek SP. Advances in Manufacturing Cardiomyocytes from Human Pluripotent Stem Cells. Annu Rev Chem Biomol Eng 2022; 13:255-278. [PMID: 35320695 DOI: 10.1146/annurev-chembioeng-092120-033922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The emergence of human pluripotent stem cell (hPSC) technology over the past two decades has provided a source of normal and diseased human cells for a wide variety of in vitro and in vivo applications. Notably, hPSC-derived cardiomyocytes (hPSC-CMs) are widely used to model human heart development and disease and are in clinical trials for treating heart disease. The success of hPSC-CMs in these applications requires robust, scalable approaches to manufacture large numbers of safe and potent cells. Although significant advances have been made over the past decade in improving the purity and yield of hPSC-CMs and scaling the differentiation process from 2D to 3D, efforts to induce maturation phenotypes during manufacturing have been slow. Process monitoring and closed-loop manufacturing strategies are just being developed. We discuss recent advances in hPSC-CM manufacturing, including differentiation process development and scaling and downstream processes as well as separation and stabilization. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Martha E Floy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
| | - Fathima Shabnam
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
| | - Aaron D Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
| | - Vijesh J Bhute
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA; , .,Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Gyuhyung Jin
- Department of Chemical Engineering, Purdue University, West Lafayette, Indiana, USA;
| | - Will A Friedrich
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
| | - Alexandra B Steinberg
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA; , , , , ,
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18
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Fan Y, Zhou H, Liu X, Li J, Xu K, Fu X, Ye L, Li G. Applications of Single-Cell RNA Sequencing in Cardiovascular Research. Front Cell Dev Biol 2022; 9:810232. [PMID: 35174168 PMCID: PMC8841340 DOI: 10.3389/fcell.2021.810232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/14/2021] [Indexed: 11/28/2022] Open
Abstract
In recent years, cardiovascular disease (CVD) continues to be the leading cause of global disease burden. Extensive efforts have been made across basic, translational, and clinical research domains to curb the CVD epidemic and improve the health of the population. The successful completion of the Human Genome Project catapulted sequencing technology into the mainstream and aroused the interests of clinicians and scientific researchers alike. Advances in single-cell RNA sequencing (scRNA-seq), which is based on the transcriptional phenotypes of individual cells, have enabled the investigation of cellular fate, heterogeneity, and cell–cell interactions, as well as cell lineage determination, at a single-cell resolution. In this review, we summarize recent findings on the embryological development of the cardiovascular system and the pathogenesis and treatment of cardiovascular disease, as revealed by scRNA-seq technology. In particular, we discuss how scRNA-seq can help identify potential targets for the treatment of cardiovascular diseases and conclude with future perspectives for scRNA-seq.
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Affiliation(s)
- Yu Fan
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Obstetrics, Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Han Zhou
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Xuexue Liu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Jingyan Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Ke Xu
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Xiaodong Fu
- Department of Obstetrics, Sichuan Clinical Research Center for Birth Defects, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Lei Ye
- National Heart Research Institute of Singapore, Singapore, Singapore
- *Correspondence: Lei Ye, ; Guang Li,
| | - Guang Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education and Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention of Cardiovascular Diseases, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- *Correspondence: Lei Ye, ; Guang Li,
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Bremner SB, Mandrycky CJ, Leonard A, Padgett RM, Levinson AR, Rehn ES, Pioner JM, Sniadecki NJ, Mack DL. Full-length dystrophin deficiency leads to contractile and calcium transient defects in human engineered heart tissues. J Tissue Eng 2022; 13:20417314221119628. [PMID: 36003954 PMCID: PMC9393922 DOI: 10.1177/20417314221119628] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Cardiomyopathy is currently the leading cause of death for patients with Duchenne muscular dystrophy (DMD), a severe neuromuscular disorder affecting young boys. Animal models have provided insight into the mechanisms by which dystrophin protein deficiency causes cardiomyopathy, but there remains a need to develop human models of DMD to validate pathogenic mechanisms and identify therapeutic targets. Here, we have developed human engineered heart tissues (EHTs) from CRISPR-edited, human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) expressing a truncated dystrophin protein lacking part of the actin-binding domain. The 3D EHT platform enables direct measurement of contractile force, simultaneous monitoring of Ca2+ transients, and assessment of myofibril structure. Dystrophin-mutant EHTs produced less contractile force as well as delayed kinetics of force generation and relaxation, as compared to isogenic controls. Contractile dysfunction was accompanied by reduced sarcomere length, increased resting cytosolic Ca2+ levels, delayed Ca2+ release and reuptake, and increased beat rate irregularity. Transcriptomic analysis revealed clear differences between dystrophin-deficient and control EHTs, including downregulation of genes related to Ca2+ homeostasis and extracellular matrix organization, and upregulation of genes related to regulation of membrane potential, cardiac muscle development, and heart contraction. These findings indicate that the EHT platform provides the cues necessary to expose the clinically-relevant, functional phenotype of force production as well as mechanistic insights into the role of Ca2+ handling and transcriptomic dysregulation in dystrophic cardiac function, ultimately providing a powerful platform for further studies in disease modeling and drug discovery.
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Affiliation(s)
- Samantha B Bremner
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Christian J Mandrycky
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Andrea Leonard
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Ruby M Padgett
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
| | - Alan R Levinson
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Ethan S Rehn
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - J Manuel Pioner
- Department of Biology, University of Florence, Florence, Italy
| | - Nathan J Sniadecki
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David L Mack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, USA
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