1
|
Manda V, Pavelka J, Lau E. Proteomics applications in next generation induced pluripotent stem cell models. Expert Rev Proteomics 2024; 21:217-228. [PMID: 38511670 PMCID: PMC11065590 DOI: 10.1080/14789450.2024.2334033] [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: 06/14/2023] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
INTRODUCTION Induced pluripotent stem (iPS) cell technology has transformed biomedical research. New opportunities now exist to create new organoids, microtissues, and body-on-a-chip systems for basic biology investigations and clinical translations. AREAS COVERED We discuss the utility of proteomics for attaining an unbiased view into protein expression changes during iPS cell differentiation, cell maturation, and tissue generation. The ability to discover cell-type specific protein markers during the differentiation and maturation of iPS-derived cells has led to new strategies to improve cell production yield and fidelity. In parallel, proteomic characterization of iPS-derived organoids is helping to realize the goal of bridging in vitro and in vivo systems. EXPERT OPINIONS We discuss some current challenges of proteomics in iPS cell research and future directions, including the integration of proteomic and transcriptomic data for systems-level analysis.
Collapse
Affiliation(s)
- Vyshnavi Manda
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jay Pavelka
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Edward Lau
- Department of Medicine, Division of Cardiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, Colorado, USA
| |
Collapse
|
2
|
Nakanishi-Koakutsu M, Miki K, Naka Y, Sasaki M, Wakimizu T, Napier SC, Okubo C, Narita M, Nishikawa M, Hata R, Chonabayashi K, Hotta A, Imahashi K, Nishimoto T, Yoshida Y. CD151 expression marks atrial- and ventricular- differentiation from human induced pluripotent stem cells. Commun Biol 2024; 7:231. [PMID: 38418926 PMCID: PMC10901864 DOI: 10.1038/s42003-024-05809-2] [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: 09/03/2022] [Accepted: 01/11/2024] [Indexed: 03/02/2024] Open
Abstract
Current differentiation protocols for human induced pluripotent stem cells (hiPSCs) produce heterogeneous cardiomyocytes (CMs). Although chamber-specific CM selection using cell surface antigens enhances biomedical applications, a cell surface marker that accurately distinguishes between hiPSC-derived atrial CMs (ACMs) and ventricular CMs (VCMs) has not yet been identified. We have developed an approach for obtaining functional hiPSC-ACMs and -VCMs based on CD151 expression. For ACM differentiation, we found that ACMs are enriched in the CD151low population and that CD151 expression is correlated with the expression of Notch4 and its ligands. Furthermore, Notch signaling inhibition followed by selecting the CD151low population during atrial differentiation leads to the highly efficient generation of ACMs as evidenced by gene expression and electrophysiology. In contrast, for VCM differentiation, VCMs exhibiting a ventricular-related gene signature and uniform action potentials are enriched in the CD151high population. Our findings enable the production of high-quality ACMs and VCMs appropriate for hiPSC-derived chamber-specific disease models and other applications.
Collapse
Affiliation(s)
- Misato Nakanishi-Koakutsu
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Kenji Miki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
- Center for Organ Engineering, Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, 02114, USA.
- Premium Research Institute for Human Metaverse Medicine, Osaka University, Suita, 565-0871, Japan.
| | - Yuki Naka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Masako Sasaki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Takayuki Wakimizu
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Stephanie C Napier
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Global Advanced Platform, Takeda Pharmaceutical Company Limited, Fujisawa, 251-8555, Japan
| | - Chikako Okubo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Megumi Narita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Reo Hata
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
| | - Kazuhisa Chonabayashi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Akitsu Hotta
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
| | - Kenichi Imahashi
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Global Advanced Platform, Takeda Pharmaceutical Company Limited, Fujisawa, 251-8555, Japan
| | - Tomoyuki Nishimoto
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan
- Orizuru Therapeutics Incorporated, Fujisawa, 251-8555, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan.
- Takeda-CiRA Joint program (T-CiRA), Fujisawa, 251-8555, Japan.
| |
Collapse
|
3
|
Liew LC, Poh BM, An O, Ho BX, Lim CYY, Pang JKS, Beh LY, Yang HH, Soh BS. JAK2 as a surface marker for enrichment of human pluripotent stem cells-derived ventricular cardiomyocytes. Stem Cell Res Ther 2023; 14:367. [PMID: 38093391 PMCID: PMC10720068 DOI: 10.1186/s13287-023-03610-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) hold great promise for cardiac disease modelling, drug discovery and regenerative medicine. Despite the advancement in various differentiation protocols, the heterogeneity of the generated population composed of diverse cardiac subtypes poses a significant challenge to their practical applications. Mixed populations of cardiac subtypes can compromise disease modelling and drug discovery, while transplanting them may lead to undesired arrhythmias as they may not integrate and synchronize with the host tissue's contractility. It is therefore crucial to identify cell surface markers that could enable high purity of ventricular CMs for subsequent applications. METHODS By exploiting the fact that immature CMs expressing myosin light chain 2A (MLC2A) will gradually express myosin light chain 2 V (MLC2V) protein as they mature towards ventricular fate, we isolated signal regulatory protein alpha (SIRPA)-positive CMs expressing intracellular MLC2A or MLC2V using MARIS (method for analysing RNA following intracellular sorting). Subsequently, RNA sequencing analysis was performed to examine the gene expression profile of MLC2A + and MLC2V + sorted CMs. We identified genes that were significantly up-regulated in MLC2V + samples to be potential surface marker candidates for ventricular specification. To validate these surface markers, we performed immunostaining and western blot analysis to measure MLC2A and MLC2V protein expressions in SIRPA + CMs that were either positive or negative for the putative surface markers, JAK2 (Janus kinase 2) or CD200. We then characterized the electrophysiological properties of surface marker-sorted CMs, using fluo-4 AM, a green-fluorescent calcium indicator, to measure the cellular calcium transient at the single cell level. For functional validation, we investigated the response of the surface marker-sorted CMs to vernakalant, an atrial-selective anti-arrhythmic agent. RESULTS In this study, while JAK2 and CD200 were identified as potential surface markers for the purification of ventricular-like CMs, the SIRPA+/JAK2+ population showed a higher percentage of MLC2V-expressing cells (~ 90%) compared to SIRPA+/CD200+ population (~ 75%). SIRPA+/JAK2+ sorted CMs exhibited ventricular-like electrophysiological properties, including slower beating rate, slower calcium depolarization and longer calcium repolarization duration. Importantly, vernakalant had limited to no significant effect on the calcium repolarization duration of SIRPA+/JAK2+ population, indicating their enrichment for ventricular-like CMs. CONCLUSION Our study lays the groundwork for the identification of cardiac subtype surface markers that allow purification of cardiomyocyte sub-populations. Our findings suggest that JAK2 can be employed as a cell surface marker for enrichment of hPSC-derived ventricular-like CMs.
Collapse
Affiliation(s)
- Lee Chuen Liew
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Boon Min Poh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Beatrice Xuan Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Christina Ying Yan Lim
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jeremy Kah Sheng Pang
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Leslie Y Beh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Henry He Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Republic of Singapore
| | - Boon-Seng Soh
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore.
| |
Collapse
|
4
|
Pan Z, Liang P. Human-Induced Pluripotent Stem Cell-Based Differentiation of Cardiomyocyte Subtypes for Drug Discovery and Cell Therapy. Handb Exp Pharmacol 2023; 281:209-233. [PMID: 37421443 DOI: 10.1007/164_2023_663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Drug attrition rates have increased over the past few years, accompanied with growing costs for the pharmaceutical industry and consumers. Lack of in vitro models connecting the results of toxicity screening assays with clinical outcomes accounts for this high attrition rate. The emergence of cardiomyocytes derived from human pluripotent stem cells provides an amenable source of cells for disease modeling, drug discovery, and cardiotoxicity screening. Functionally similar to to embryonic stem cells, but with fewer ethical concerns, induced pluripotent stem cells (iPSCs) can recapitulate patient-specific genetic backgrounds, which would be a huge revolution for personalized medicine. The generated iPSC-derived cardiomyocytes (iPSC-CMs) represent different subtypes including ventricular-, atrial-, and nodal-like cardiomyocytes. Purifying these subtypes for chamber-specific drug screening presents opportunities and challenges. In this chapter, we discuss the strategies for the purification of iPSC-CMs, the use of iPSC-CMs for drug discovery and cardiotoxicity test, and the current limitations of iPSC-CMs that should be overcome for wider and more precise cardiovascular applications.
Collapse
Affiliation(s)
- Ziwei Pan
- Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China
| | - Ping Liang
- Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Institute of Translational Medicine, Zhejiang University, Hangzhou, China.
| |
Collapse
|
5
|
Destici E, Zhu F, Tran S, Preissl S, Farah EN, Zhang Y, Hou X, Poirion OB, Lee AY, Grinstein JD, Bloomekatz J, Kim HS, Hu R, Evans SM, Ren B, Benner C, Chi NC. Human-gained heart enhancers are associated with species-specific cardiac attributes. NATURE CARDIOVASCULAR RESEARCH 2022; 1:830-843. [PMID: 36817700 PMCID: PMC9937543 DOI: 10.1038/s44161-022-00124-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
The heart, a vital organ which is first to develop, has adapted its size, structure and function in order to accommodate the circulatory demands for a broad range of animals. Although heart development is controlled by a relatively conserved network of transcriptional/chromatin regulators, how the human heart has evolved species-specific features to maintain adequate cardiac output and function remains to be defined. Here, we show through comparative epigenomic analysis the identification of enhancers and promoters that have gained activity in humans during cardiogenesis. These cis-regulatory elements (CREs) are associated with genes involved in heart development and function, and may account for species-specific differences between human and mouse hearts. Supporting these findings, genetic variants that are associated with human cardiac phenotypic/disease traits, particularly those differing between human and mouse, are enriched in human-gained CREs. During early stages of human cardiogenesis, these CREs are also gained within genomic loci of transcriptional regulators, potentially expanding their role in human heart development. In particular, we discovered that gained enhancers in the locus of the early human developmental regulator ZIC3 are selectively accessible within a subpopulation of mesoderm cells which exhibits cardiogenic potential, thus possibly extending the function of ZIC3 beyond its conserved left-right asymmetry role. Genetic deletion of these enhancers identified a human gained enhancer that was required for not only ZIC3 and early cardiac gene expression at the mesoderm stage but also cardiomyocyte differentiation. Overall, our results illuminate how human gained CREs may contribute to human-specific cardiac attributes, and provide insight into how transcriptional regulators may gain cardiac developmental roles through the evolutionary acquisition of enhancers.
Collapse
Affiliation(s)
- Eugin Destici
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Fugui Zhu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shaina Tran
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elie N. Farah
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Xiameng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Olivier B. Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Jonathan D. Grinstein
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Hong Sook Kim
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert Hu
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Chris Benner
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Neil C. Chi
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Institute of Genomic Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| |
Collapse
|
6
|
Cardiac Cell Therapy with Pluripotent Stem Cell-Derived Cardiomyocytes: What Has Been Done and What Remains to Do? Curr Cardiol Rep 2022; 24:445-461. [PMID: 35275365 PMCID: PMC9068652 DOI: 10.1007/s11886-022-01666-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 01/14/2023]
Abstract
PURPOSE OF REVIEW Exciting pre-clinical data presents pluripotent stem cell-derived cardiomyocytes (PSC-CM) as a novel therapeutic prospect following myocardial infarction, and worldwide clinical trials are imminent. However, despite notable advances, several challenges remain. Here, we review PSC-CM pre-clinical studies, identifying key translational hurdles. We further discuss cell production and characterization strategies, identifying markers that may help generate cells which overcome these barriers. RECENT FINDINGS PSC-CMs can robustly repopulate infarcted myocardium with functional, force generating cardiomyocytes. However, current differentiation protocols produce immature and heterogenous cardiomyocytes, creating related issues such as arrhythmogenicity, immunogenicity and poor engraftment. Recent efforts have enhanced our understanding of cardiovascular developmental biology. This knowledge may help implement novel differentiation or gene editing strategies that could overcome these limitations. PSC-CMs are an exciting therapeutic prospect. Despite substantial recent advances, limitations of the technology remain. However, with our continued and increasing biological understanding, these issues are addressable, with several worldwide clinical trials anticipated in the coming years.
Collapse
|
7
|
Floy ME, Dunn KK, Mateyka TD, Reichardt IM, Steinberg AB, Palecek SP. Direct coculture of human pluripotent stem cell-derived cardiac progenitor cells with epicardial cells induces cardiomyocyte proliferation and reduces sarcomere organization. J Mol Cell Cardiol 2022; 162:144-157. [PMID: 34560089 PMCID: PMC8766908 DOI: 10.1016/j.yjmcc.2021.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 01/03/2023]
Abstract
Epicardial cells (EpiCs) are necessary for myocardium formation, yet little is known about crosstalk between EpiCs and cardiomyocytes (CMs) during development and the potential impact of EpiCs on CM maturation. To investigate the effects of EpiCs on CM commitment and maturation, we differentiated human pluripotent stem cells (hPSCs) to cardiac progenitor cells (CPCs) and EpiCs, and cocultured EpiCs and CPCs for two weeks. When EpiCs were allowed to form epicardial-derived cells, we observed increased expression of cTnI in developing CMs. In the presence of the TGFβ inhibitor A83-01, EpiCs remained in the epicardial state and induced CM proliferation, increased MLC2v expression, and led to less organized sarcomeres. These effects were not observed if CPCs were treated with EpiC-conditioned medium or if CPCs were indirectly cocultured with EpiCs. Finally, single cell RNA sequencing identified that EpiC-CPC coculture had bi-directional effects on transcriptional programs in EpiCs and CMs, and biased EpiC lineages from a SFRP2-enriched population to a DLK1- or C3-enriched population. This work suggests important crosstalk between EpiCs and CMs during differentiation which can be used to influence cell fate and improve the ability to generate cardiac cells and tissues for in vitro models and development of cardiac cellular therapies.
Collapse
Affiliation(s)
- Martha E. Floy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America
| | - Kaitlin K. Dunn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America
| | - Taylor D. Mateyka
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America
| | - Isabella M. Reichardt
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America
| | - Alexandra B. Steinberg
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States of America,Correspondence:
| |
Collapse
|
8
|
Zhang XD, Thai PN, Lieu DK, Chiamvimonvat N. Model Systems for Addressing Mechanism of Arrhythmogenesis in Cardiac Repair. Curr Cardiol Rep 2021; 23:72. [PMID: 34050853 PMCID: PMC8164614 DOI: 10.1007/s11886-021-01498-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 11/09/2022]
Abstract
PURPOSE OF REVIEW Cardiac cell-based therapy represents a promising approach for cardiac repair. However, one of the main challenges is cardiac arrhythmias associated with stem cell transplantation. The current review summarizes the recent progress in model systems for addressing mechanisms of arrhythmogenesis in cardiac repair. RECENT FINDINGS Animal models have been extensively developed for mechanistic studies of cardiac arrhythmogenesis. Advances in human induced pluripotent stem cells (hiPSCs), patient-specific disease models, tissue engineering, and gene editing have greatly enhanced our ability to probe the mechanistic bases of cardiac arrhythmias. Additionally, recent development in multiscale computational studies and machine learning provides yet another powerful tool to quantitatively decipher the mechanisms of cardiac arrhythmias. Advancing efforts towards the integrations of experimental and computational studies are critical to gain insights into novel mitigation strategies for cardiac arrhythmias in cell-based therapy.
Collapse
Affiliation(s)
- Xiao-Dong Zhang
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA 95616 USA
- Department of Veterans Affairs, Veterans Affairs Northern California Health Care System, Mather, CA 95655 USA
| | - Phung N. Thai
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA 95616 USA
- Department of Veterans Affairs, Veterans Affairs Northern California Health Care System, Mather, CA 95655 USA
| | - Deborah K. Lieu
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA 95616 USA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular Medicine, Department of Internal Medicine, School of Medicine, University of California, Davis, Davis, CA 95616 USA
- Department of Veterans Affairs, Veterans Affairs Northern California Health Care System, Mather, CA 95655 USA
- Department of Pharmacology, School of Medicine, University of California, Davis, Davis, CA 95616 USA
| |
Collapse
|
9
|
Myosin light chain 2 marks differentiating ventricular cardiomyocytes derived from human embryonic stem cells. Pflugers Arch 2021; 473:991-1007. [PMID: 34031754 DOI: 10.1007/s00424-021-02578-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/01/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have great value for studies of human cardiac development, drug discovery, disease modeling, and cell therapy. However, the mixed cardiomyocyte subtypes (ventricular-, atrial-, and nodal-like myocytes) and the maturation heterogeneity of hPSC-CMs restrain their application in vitro and in vivo. Myosin light chain 2 (MYL2, encoding the ventricular/cardiac muscle isoform MLC2v protein) is regarded as a ventricular-specific marker of cardiac myocardium; however, its restricted localization to ventricles during human heart development has been questioned. Consequently, it is currently unclear whether MYL2 definitively marks ventricular hESC-CMs. Here, by using a MYL2-Venus hESC reporter line, we characterized a time-dependent increase of the MYL2-Venus positive (MLC2v-Venus+) hESC-CMs during differentiation. We also compared the molecular, cellular, and functional properties between the MLC2v-Venus+ and MYL2-Venus negative (MLC2v-Venus-) hESC-CMs. At early differentiation stages of hESC-CMs, we reported that both MLC2v-Venus- and MLC2v-Venus+ CMs displayed ventricular-like traits but the ventricular-like cells from MLC2v-Venus+ hESC-CMs displayed more developed action potential (AP) properties than that from MLC2v-Venus- hESC-CMs. Meanwhile, about a half MLC2v-Venus- hESC-CM population displayed atrial-like AP properties, and a half showed ventricular-like AP properties, whereas only ~ 20% of the MLC2v-Venus- hESC-CMs expressed the atrial marker nuclear receptor subfamily 2 group F member 2 (NR2F2, also named as COUPTFII). At late time points, almost all MLC2v-Venus+ hESC-CMs exhibited ventricular-like AP properties. Further analysis demonstrates that the MLC2v-Venus+ hESC-CMs had enhanced Ca2+ transients upon increase of the MLC2v level during cultivation. Concomitantly, the MLC2v-Venus+ hESC-CMs showed more defined sarcomeric structures and better mitochondrial function than those in the MLC2v-Venus- hESC-CMs. Moreover, the MLC2v-Venus+ hESC-CMs were more sensitive to hypoxic stimulus than the MLC2v-Venus- hESC-CMs. These results provide new insights into the development of human ventricular myocytes and reveal a direct correlation between the expression profile of MLC2v and ventricular hESC-CM development. Our findings that MLC2v is predominantly a ventricular marker in developmentally immature hESC-CMs have implications for human development, drug screening, and disease modeling, and this marker should prove useful in overcoming issues associated with hESC-CM heterogeneity.
Collapse
|
10
|
Hocker JD, Poirion OB, Zhu F, Buchanan J, Zhang K, Chiou J, Wang TM, Zhang Q, Hou X, Li YE, Zhang Y, Farah EN, Wang A, McCulloch AD, Gaulton KJ, Ren B, Chi NC, Preissl S. Cardiac cell type-specific gene regulatory programs and disease risk association. SCIENCE ADVANCES 2021; 7:eabf1444. [PMID: 33990324 PMCID: PMC8121433 DOI: 10.1126/sciadv.abf1444] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/25/2021] [Indexed: 05/07/2023]
Abstract
Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease-associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type-specific gene regulation in human hearts during health and disease.
Collapse
Affiliation(s)
- James D Hocker
- Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Fugui Zhu
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin Buchanan
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
| | - Tsui-Min Wang
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qingquan Zhang
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Elie N Farah
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
| | - Andrew D McCulloch
- Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, CA, USA
- Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
11
|
Cell surface markers for immunophenotyping human pluripotent stem cell-derived cardiomyocytes. Pflugers Arch 2021; 473:1023-1039. [PMID: 33928456 DOI: 10.1007/s00424-021-02549-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/09/2021] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Human pluripotent stem cells (hPSC) self-renew and represent a potentially unlimited source for the production of cardiomyocytes (CMs) suitable for studies of human cardiac development, drug discovery, cardiotoxicity testing, and disease modelling and for cell-based therapies. However, most cardiac differentiation protocols yield mixed cultures of atrial-, ventricular-, and pacemaker-like cells at various stages of development, as well as non-CMs. The proportions and maturation states of these cell types result from disparities among differentiation protocols and time of cultivation, as well as hPSC reprogramming inconsistencies and genetic background variations. The reproducible use of hPSC-CMs for research and therapy is therefore limited by issues of cell population heterogeneity and functional states of maturation. A validated method that overcomes issues of cell heterogeneity is immunophenotyping coupled with live cell sorting, an approach that relies on accessible surface markers restricted to the desired cell type(s). Here we review current progress in unravelling heterogeneity in hPSC-cardiac cultures and in the identification of surface markers suitable for defining cardiac identity, subtype specificity, and maturation states.
Collapse
|
12
|
Regulatory Light Chains in Cardiac Development and Disease. Int J Mol Sci 2021; 22:ijms22094351. [PMID: 33919432 PMCID: PMC8122660 DOI: 10.3390/ijms22094351] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/18/2022] Open
Abstract
The role of regulatory light chains (RLCs) in cardiac muscle function has been elucidated progressively over the past decade. The RLCs are among the earliest expressed markers during cardiogenesis and persist through adulthood. Failing hearts have shown reduced RLC phosphorylation levels and that restoring baseline levels of RLC phosphorylation is necessary for generating optimal force of muscle contraction. The signalling mechanisms triggering changes in RLC phosphorylation levels during disease progression remain elusive. Uncovering this information may provide insights for better management of heart failure patients. Given the cardiac chamber-specific expression of RLC isoforms, ventricular RLCs have facilitated the identification of mature ventricular cardiomyocytes, opening up possibilities of regenerative medicine. This review consolidates the standing of RLCs in cardiac development and disease and highlights knowledge gaps and potential therapeutic advancements in targeting RLCs.
Collapse
|
13
|
Kit-Anan W, Mazo MM, Wang BX, Leonardo V, Pence IJ, Gopal S, Gelmi A, Nagelkerke A, Becce M, Chiappini C, Harding SE, Terracciano CM, Stevens MM. Multiplexing physical stimulation on single human induced pluripotent stem cell-derived cardiomyocytes for phenotype modulation. Biofabrication 2021; 13:025004. [PMID: 33710972 PMCID: PMC7610872 DOI: 10.1088/1758-5090/abce0a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/11/2020] [Accepted: 11/25/2020] [Indexed: 12/02/2022]
Abstract
Traditional in vitro bioengineering approaches whereby only individual biophysical cues are manipulated at any one time are highly inefficient, falling short when recapitulating the complexity of the cardiac environment. Multiple biophysical cues are present in the native myocardial niche and are essential during development, as well as in maintenance of adult cardiomyocyte (CM) phenotype in both health and disease. This study establishes a novel biofabrication workflow to study and manipulate hiPSC-CMs and to understand how these cells respond to a multiplexed biophysical environment, namely 3D shape and substrate stiffness, at a single cell level. Silicon masters were fabricated and developed to generate inverse patterns of the desired 3D shapes in bas relief, which then were used to mold the designed microwell arrays into a hydrogel. Polyacrylamide (PAAm) was modified with the incorporation of acrylic acid to provide a carboxylic group conjugation site for adhesion motifs, without compromising capacity to modulate stiffness. In this manner, two individual parameters can be finely tuned independently within the hydrogel: the shape of the 3D microwell and its stiffness. The design allows the platform to isolate single hiPSC-CMs to study solely biophysical cues in the absence of cell-cell physical interaction. Under physiologic-like physical conditions (3D shape resembling that of adult CM and 9.83 kPa substrate stiffness that mimics muscle stiffness), isolated single hiPSC-CMs exhibit increased Cx-43 density, cell membrane stiffness and calcium transient amplitude; co-expression of the subpopulation-related MYL2-MYL7 proteins; and higher anisotropism than cells in pathologic-like conditions (flat surface and 112 kPa substrate stiffness). This demonstrates that supplying a physiologic or pathologic microenvironment to an isolated single hiPSC-CM in the absence of any physical cell-to-cell communication in this biofabricated platform leads to a significantly different set of cellular features, thus presenting a differential phenotype. Importantly, this demonstrates the high plasticity of hiPSC-CMs even in isolation. The ability of multiple biophysical cues to significantly influence isolated single hiPSC-CM phenotype and functionality highlights the importance of fine-tuning such cues for specific applications. This has the potential to produce more fit-for-purpose hiPSC-CMs. Further understanding of human cardiac development is enabled by the robust, versatile and reproducible biofabrication techniques applied here. We envision that this system could be easily applied to other tissues and cell types where the influence of cellular shape and stiffness of the surrounding environment is hypothesized to play an important role in physiology.
Collapse
Affiliation(s)
- Worrapong Kit-Anan
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Manuel M Mazo
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Brian X Wang
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Vincent Leonardo
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Isaac J Pence
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Sahana Gopal
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Amy Gelmi
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
- Current Address: Applied Chemistry and Environmental Science, School of Science, RMIT University, Melbourne, VIC 3001, Australia
| | - Anika Nagelkerke
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Michele Becce
- Department of Materials, Imperial College London, London, United Kingdom
| | - Ciro Chiappini
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Sian E Harding
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Cesare M Terracciano
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| |
Collapse
|
14
|
Jæger KH, Charwat V, Wall S, Healy KE, Tveito A. Identifying Drug Response by Combining Measurements of the Membrane Potential, the Cytosolic Calcium Concentration, and the Extracellular Potential in Microphysiological Systems. Front Pharmacol 2021; 11:569489. [PMID: 33628168 PMCID: PMC7898238 DOI: 10.3389/fphar.2020.569489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/16/2020] [Indexed: 01/01/2023] Open
Abstract
Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) offer a new means to study and understand the human cardiac action potential, and can give key insight into how compounds may interact with important molecular pathways to destabilize the electrical function of the heart. Important features of the action potential can be readily measured using standard experimental techniques, such as the use of voltage sensitive dyes and fluorescent genetic reporters to estimate transmembrane potentials and cytosolic calcium concentrations. Using previously introduced computational procedures, such measurements can be used to estimate the current density of major ion channels present in hiPSC-CMs, and how compounds may alter their behavior. However, due to the limitations of optical recordings, resolving the sodium current remains difficult from these data. Here we show that if these optical measurements are complemented with observations of the extracellular potential using multi electrode arrays (MEAs), we can accurately estimate the current density of the sodium channels. This inversion of the sodium current relies on observation of the conduction velocity which turns out to be straightforwardly computed using measurements of extracellular waves across the electrodes. The combined data including the membrane potential, the cytosolic calcium concentration and the extracellular potential further opens up for the possibility of accurately estimating the effect of novel drugs applied to hiPSC-CMs.
Collapse
Affiliation(s)
| | - Verena Charwat
- Department of Bioengineering, University of California, Berkeley, CA, United States
| | | | - Kevin E. Healy
- Department of Bioengineering, University of California, Berkeley, CA, United States
- Department of Material Science and Engineering, University of California, Berkeley, CA, United States
| | - Aslak Tveito
- Simula Research Laboratory, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| |
Collapse
|
15
|
Galdos FX, Darsha AK, Paige SL, Wu SM. Purification of Pluripotent Stem Cell-Derived Cardiomyocytes Using CRISPR/Cas9-Mediated Integration of Fluorescent Reporters. Methods Mol Biol 2021; 2158:223-240. [PMID: 32857377 DOI: 10.1007/978-1-0716-0668-1_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes have become critically important for the detailed study of cardiac development, disease modeling, and drug screening. However, directed differentiation of hiPSCs into cardiomyocytes often results in mixed populations of cardiomyocytes and other cell types, which may confound experiments that require pure populations of cardiomyocytes. Here, we detail the use of a CRISPR/Cas9 genome editing strategy to develop cardiomyocyte-specific reporters that allow for the isolation of hiPSC-derived cardiomyocytes and chamber-specific myocytes. Moreover, we describe a cardiac differentiation protocol to derive cardiomyocytes from hiPSCs, as well as a strategy to use fluorescence-activated cell sorting to isolate pure populations of fluorescently labeled cardiomyocytes for downstream applications.
Collapse
Affiliation(s)
- Francisco X Galdos
- Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA.
- Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Adrija K Darsha
- Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
- Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sharon L Paige
- Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
- Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Cardiovascular Medicine, Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean M Wu
- Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
- Institute of Stem Cell and Regenerative Biology, School of Medicine, Stanford University, Stanford, CA, USA
- Departments of Pediatrics and Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
16
|
Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
Collapse
Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
| |
Collapse
|
17
|
Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T. Cell type-specific genetic regulation of gene expression across human tissues. Science 2020; 369:eaaz8528. [PMID: 32913075 PMCID: PMC8051643 DOI: 10.1126/science.aaz8528] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 07/31/2020] [Indexed: 12/15/2022]
Abstract
The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci in cis (QTLs) for the majority of genes across a wide range of human tissues. However, the functional characterization of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. We mapped interactions between computational estimates of cell type abundance and genotype to identify cell type-interaction QTLs for seven cell types and show that cell type-interaction expression QTLs (eQTLs) provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations with 87 complex traits show a contribution from cell type-interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.
Collapse
Affiliation(s)
- Sarah Kim-Hellmuth
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany.
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - François Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meritxell Oliva
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Manuel Muñoz-Aguirre
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Department of Statistics and Operations Research, Universitat Politècnica de Catalunya (UPC), Barcelona, Catalonia, Spain
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Stephane E Castel
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Andrew R Hamel
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Ana Viñuela
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Amy L Roberts
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Gao Wang
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Diego Garrido-Martín
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Brian B Nadel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuxin Zou
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Rodrigo Bonazzola
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jie Quan
- Inflammation & Immunology, Pfizer, Cambridge, MA, USA
| | - Andrew Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Population Health and Genomics, University of Dundee, Dundee, Scotland, UK
| | - Angel Martinez-Perez
- Unit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - José Manuel Soria
- Unit of Genomic of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Hualin S Xi
- Foundational Neuroscience Center, AbbVie, Cambridge, MA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Ayellet V Segrè
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, USA
| |
Collapse
|
18
|
Optimizing the Use of iPSC-CMs for Cardiac Regeneration in Animal Models. Animals (Basel) 2020; 10:ani10091561. [PMID: 32887495 PMCID: PMC7552322 DOI: 10.3390/ani10091561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/29/2020] [Accepted: 08/31/2020] [Indexed: 12/29/2022] Open
Abstract
Simple Summary In 2006, the first induced pluripotent stem cells were generated by reprogramming skin cells. Induced pluripotent stem cells undergo fast cell division, can differentiate into many different cell types, can be patient-specific, and do not raise ethical issues. Thus, they offer great promise as in vitro disease models, drug toxicity testing platforms, and for autologous tissue regeneration. Heart failure is one of the major causes of death worldwide. It occurs when the heart cannot meet the body’s metabolic demands. Induced pluripotent stem cells can be differentiated into cardiac myocytes, can form patches resembling native cardiac tissue, and can engraft to the damaged heart. However, despite correct host/graft coupling, most animal studies demonstrate an arrhythmogenicity of the engrafted tissue and variable survival. This is partially because of the heterogeneity and immaturity of the cells. New evidence suggests that by modulating induced pluripotent stem cells-cardiac myocytes (iPSC-CM) metabolism by switching substrates and changing metabolic pathways, you can decrease iPSC-CM heterogeneity and arrhythmogenicity. Novel culture methods and tissue engineering along with animal models of heart failure are needed to fully unlock the potential of cardiac myocytes derived from induced pluripotent stem cells for cardiac regeneration. Abstract Heart failure (HF) is a common disease in which the heart cannot meet the metabolic demands of the body. It mostly occurs in individuals 65 years or older. Cardiac transplantation is the best option for patients with advanced HF. High numbers of patient-specific cardiac myocytes (CMs) can be generated from induced pluripotent stem cells (iPSCs) and can possibly be used to treat HF. While some studies found iPSC-CMS can couple efficiently to the damaged heart and restore cardiac contractility, almost all found iPSC-CM transplantation is arrhythmogenic, thus hampering the use of iPSC-CMs for cardiac regeneration. Studies show that iPSC-CM cultures are highly heterogeneous containing atrial-, ventricular- and nodal-like CMs. Furthermore, they have an immature phenotype, resembling more fetal than adult CMs. There is an urgent need to overcome these issues. To this end, a novel and interesting avenue to increase CM maturation consists of modulating their metabolism. Combined with careful engineering and animal models of HF, iPSC-CMs can be assessed for their potential for cardiac regeneration and a cure for HF.
Collapse
|
19
|
Branco MA, Cabral JM, Diogo MM. From Human Pluripotent Stem Cells to 3D Cardiac Microtissues: Progress, Applications and Challenges. Bioengineering (Basel) 2020; 7:E92. [PMID: 32785039 PMCID: PMC7552661 DOI: 10.3390/bioengineering7030092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022] Open
Abstract
The knowledge acquired throughout the years concerning the in vivo regulation of cardiac development has promoted the establishment of directed differentiation protocols to obtain cardiomyocytes (CMs) and other cardiac cells from human pluripotent stem cells (hPSCs), which play a crucial role in the function and homeostasis of the heart. Among other developments in the field, the transition from homogeneous cultures of CMs to more complex multicellular cardiac microtissues (MTs) has increased the potential of these models for studying cardiac disorders in vitro and for clinically relevant applications such as drug screening and cardiotoxicity tests. This review addresses the state of the art of the generation of different cardiac cells from hPSCs and the impact of transitioning CM differentiation from 2D culture to a 3D environment. Additionally, current methods that may be employed to generate 3D cardiac MTs are reviewed and, finally, the adoption of these models for in vitro applications and their adaptation to medium- to high-throughput screening settings are also highlighted.
Collapse
Affiliation(s)
| | | | - Maria Margarida Diogo
- iBB-Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (M.A.B.); (J.M.S.C.)
| |
Collapse
|
20
|
Sung TC, Su HC, Ling QD, Kumar SS, Chang Y, Hsu ST, Higuchi A. Efficient differentiation of human pluripotent stem cells into cardiomyocytes on cell sorting thermoresponsive surface. Biomaterials 2020; 253:120060. [PMID: 32450407 DOI: 10.1016/j.biomaterials.2020.120060] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 03/18/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022]
Abstract
The current differentiation process of human pluripotent stem cells (hPSCs) into cardiomyocytes to enhance the purity of hPSC-derived cardiomyocytes requires some purification processes, which are laborious processes. We developed cell sorting plates, which are prepared from coating thermoresponsive poly(N-isopropylacrylamide) and extracellular matrix proteins. After hPSCs were induced into cardiomyocytes on the thermoresponsive surface coated with laminin-521 for 15 days, the temperature of the cell culture plates was decreased to 8-9 °C to detach the cells partially from the thermoresponsive surface. The detached cells exhibited a higher cardiomyocyte marker of cTnT than the remaining cells on the thermoresponsive surface as well as the cardiomyocytes after purification using conventional cell selection. The detached cells expressed several cardiomyocyte markers, such as α-actinin, MLC2a and NKX2.5. This study suggested that the purification of hPSC-derived cardiomyocytes using cell sorting plates with the thermoresponsive surface is a promising method for the purification of hPSC-derived cardiomyocytes without conventional laborious processes.
Collapse
Affiliation(s)
- Tzu-Cheng Sung
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China; Department of Chemical and Materials Engineering, National Central University, No. 300, Jhongda RD., Jhongli, Taoyuan, 32001, Taiwan
| | - Huan Chiao Su
- Department of Chemical and Materials Engineering, National Central University, No. 300, Jhongda RD., Jhongli, Taoyuan, 32001, Taiwan
| | - Qing-Dong Ling
- Cathay Medical Research Institute, Cathay General Hospital, No. 32, Ln 160, Jian-Cheng Road, Hsi-Chi City, Taipei 221, Taiwan
| | - S Suresh Kumar
- Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, Serdang, 43400, Selangor, Malaysia
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, 200, Chung-Bei Rd., Chungli, Taoyuan, 320, Taiwan
| | - Shih-Tien Hsu
- Department of Internal Medicine, Taiwan Landseed Hospital, 77, Kuangtai Road, Pingjen City, Taoyuan, 32405, Taiwan
| | - Akon Higuchi
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China; Department of Chemical and Materials Engineering, National Central University, No. 300, Jhongda RD., Jhongli, Taoyuan, 32001, Taiwan; Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, 200, Chung-Bei Rd., Chungli, Taoyuan, 320, Taiwan; Wenzhou Institute, University of Chinese Academy of Science, No. 16, Xinsan Road, Hi-tech Industry Park, Wenzhou, Zhejiang, China; Center for Emergent Matter Science, Riken, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| |
Collapse
|
21
|
Zhao MT, Shao NY, Garg V. Subtype-specific cardiomyocytes for precision medicine: Where are we now? Stem Cells 2020; 38:822-833. [PMID: 32232889 DOI: 10.1002/stem.3178] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 11/12/2022]
Abstract
Patient-derived pluripotent stem cells (PSCs) have greatly transformed the current understanding of human heart development and cardiovascular disease. Cardiomyocytes derived from personalized PSCs are powerful tools for modeling heart disease and performing patient-based cardiac toxicity testing. However, these PSC-derived cardiomyocytes (PSC-CMs) are a mixed population of atrial-, ventricular-, and pacemaker-like cells in the dish, hindering the future of precision cardiovascular medicine. Recent insights gleaned from the developing heart have paved new avenues to refine subtype-specific cardiomyocytes from patients with known pathogenic genetic variants and clinical phenotypes. Here, we discuss the recent progress on generating subtype-specific (atrial, ventricular, and nodal) cardiomyocytes from the perspective of embryonic heart development and how human pluripotent stem cells will expand our current knowledge on molecular mechanisms of cardiovascular disease and the future of precision medicine.
Collapse
Affiliation(s)
- Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute and The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Ning-Yi Shao
- Faculty of Health Sciences, University of Macau, Macau, People's Republic of China
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute and The Heart Center, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Department of Molecular Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| |
Collapse
|
22
|
Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure. Nat Commun 2020; 11:1122. [PMID: 32111823 PMCID: PMC7048760 DOI: 10.1038/s41467-020-14843-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/27/2020] [Indexed: 12/02/2022] Open
Abstract
Heart failure is a major public health problem affecting over 23 million people worldwide. In this study, we present the results of a large scale meta-analysis of heart failure GWAS and replication in a comparable sized cohort to identify one known and two novel loci associated with heart failure. Heart failure sub-phenotyping shows that a new locus in chromosome 1 is associated with left ventricular adverse remodeling and clinical heart failure, in response to different initial cardiac muscle insults. Functional characterization and fine-mapping of that locus reveal a putative causal variant in a cardiac muscle specific regulatory region activated during cardiomyocyte differentiation that binds to the ACTN2 gene, a crucial structural protein inside the cardiac sarcolemma (Hi-C interaction p-value = 0.00002). Genome-editing in human embryonic stem cell-derived cardiomyocytes confirms the influence of the identified regulatory region in the expression of ACTN2. Our findings extend our understanding of biological mechanisms underlying heart failure. Heart failure has a heterogeneous etiology and the genetic underpinnings are not well understood. Here, Arvanitis et al. perform GWAS meta-analysis including 10,976 heart failure cases and 437,573 controls, identify new loci near ABO and ACTN2 and show that deletion of a ACTN2 enhancer leads to reduced ACTN2 expression in differentiating cardiomyocytes.
Collapse
|
23
|
Wang J, Jiang X, Zhao L, Zuo S, Chen X, Zhang L, Lin Z, Zhao X, Qin Y, Zhou X, Yu XY. Lineage reprogramming of fibroblasts into induced cardiac progenitor cells by CRISPR/Cas9-based transcriptional activators. Acta Pharm Sin B 2020; 10:313-326. [PMID: 32082976 PMCID: PMC7016296 DOI: 10.1016/j.apsb.2019.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/26/2019] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Overexpression of exogenous lineage-determining factors succeeds in directly reprogramming fibroblasts to various cell types. Several studies have reported reprogramming of fibroblasts into induced cardiac progenitor cells (iCPCs). CRISPR/Cas9-mediated gene activation is a potential approach for cellular reprogramming due to its high precision and multiplexing capacity. Here we show lineage reprogramming to iCPCs through a dead Cas9 (dCas9)-based transcription activation system. Targeted and robust activation of endogenous cardiac factors, including GATA4, HAND2, MEF2C and TBX5 (G, H, M and T; GHMT), can reprogram human fibroblasts toward iCPCs. The iCPCs show potentials to differentiate into cardiomyocytes, smooth muscle cells and endothelial cells in vitro. Addition of MEIS1 to GHMT induces cell cycle arrest in G2/M and facilitates cardiac reprogramming. Lineage reprogramming of human fibroblasts into iCPCs provides a promising cellular resource for disease modeling, drug discovery and individualized cardiac cell therapy.
Collapse
|
24
|
Pan J, Lee YC, Lee HHC, Sung TC, Jen SH, Ban LK, Su HY, Chen DC, Hsu ST, Higuchi A, Chen H. Culture and differentiation of purified human adipose-derived stem cells by membrane filtration via nylon mesh filters. J Mater Chem B 2020; 8:5204-5214. [PMID: 32490480 DOI: 10.1039/d0tb00947d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Human adipose derived stem cells purified by the membrane migration method through filter membranes coated with vitronectin showed high osteogenic differentiation.
Collapse
|
25
|
Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. Nat Genet 2019; 51:1380-1388. [PMID: 31427791 PMCID: PMC6722002 DOI: 10.1038/s41588-019-0479-7] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022]
Abstract
Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated. Here, by interrogating chromatin reorganization during human pluripotent stem cell (hPSC) differentiation, we discover a role for the primate-specific endogenous retrotransposon human endogenous retrovirus subfamily H (HERV-H) in creating topologically associating domains (TADs) in hPSCs. Deleting these HERV-H elements eliminates their corresponding TAD boundaries and reduces the transcription of upstream genes, while de novo insertion of HERV-H elements can introduce new TAD boundaries. The ability of HERV-H to create TAD boundaries depends on high transcription, as transcriptional repression of HERV-H elements prevents the formation of boundaries. This ability is not limited to hPSCs, as these actively transcribed HERV-H elements and their corresponding TAD boundaries also appear in pluripotent stem cells from other hominids but not in more distantly related species lacking HERV-H elements. Overall, our results provide direct evidence for retrotransposons in actively shaping cell type- and species-specific chromatin architecture.
Collapse
Affiliation(s)
- Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ting Li
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maria Luisa Amaral
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Jonathan D Grinstein
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Elie N Farah
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Eugin Destici
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sora Chee
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Kaiyue Ma
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Quan Zhu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Hui Huang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sylvia M Evans
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
26
|
Ren J, Han P, Ma X, Farah EN, Bloomekatz J, Zeng XXI, Zhang R, Swim MM, Witty AD, Knight HG, Deshpande R, Xu W, Yelon D, Chen S, Chi NC. Canonical Wnt5b Signaling Directs Outlying Nkx2.5+ Mesoderm into Pacemaker Cardiomyocytes. Dev Cell 2019; 50:729-743.e5. [PMID: 31402282 DOI: 10.1016/j.devcel.2019.07.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/01/2019] [Accepted: 07/11/2019] [Indexed: 12/21/2022]
Abstract
Pacemaker cardiomyocytes that create the sinoatrial node are essential for the initiation and maintenance of proper heart rhythm. However, illuminating developmental cues that direct their differentiation has remained particularly challenging due to the unclear cellular origins of these specialized cardiomyocytes. By discovering the origins of pacemaker cardiomyocytes, we reveal an evolutionarily conserved Wnt signaling mechanism that coordinates gene regulatory changes directing mesoderm cell fate decisions, which lead to the differentiation of pacemaker cardiomyocytes. We show that in zebrafish, pacemaker cardiomyocytes derive from a subset of Nkx2.5+ mesoderm that responds to canonical Wnt5b signaling to initiate the cardiac pacemaker program, including activation of pacemaker cell differentiation transcription factors Isl1 and Tbx18 and silencing of Nkx2.5. Moreover, applying these developmental findings to human pluripotent stem cells (hPSCs) notably results in the creation of hPSC-pacemaker cardiomyocytes, which successfully pace three-dimensional bioprinted hPSC-cardiomyocytes, thus providing potential strategies for biological cardiac pacemaker therapy.
Collapse
Affiliation(s)
- Jie Ren
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peidong Han
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuanyi Ma
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elie N Farah
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joshua Bloomekatz
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Xin-Xin I Zeng
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ruilin Zhang
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Megan M Swim
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alec D Witty
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hannah G Knight
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rima Deshpande
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Weizhe Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Deborah Yelon
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shaochen Chen
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of NanoEngineering, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neil C Chi
- Department of Medicine, Division of Cardiology, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
27
|
Wang Z, Huang J. Apela Promotes Cardiomyocyte Differentiation from Transgenic Human Embryonic Stem Cell Lines. Appl Biochem Biotechnol 2019; 189:396-410. [PMID: 31025171 DOI: 10.1007/s12010-019-03012-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/27/2019] [Indexed: 12/22/2022]
Abstract
Although embryonic stem (ES) cells (ESCs) may be a promising donor source for the repair of infarcted or ischemic heart tissues, their successful application in regenerative medicine has been hampered by difficulties in enriching, identifying, and selecting cardiomyocytes from the differentiating cells. We established transgenic human ES cell lines by transcriptional control of the α-cardiac myosin heavy chain (α-MHC) promoter driving green fluorescent protein (GFP) expression. Differentiated GFP-expressing cells display the characteristics of cardiomyocytes (CMs). Apela, a recently identified short peptide, up-regulated the expression of the cardiac-restricted transcription factors Tbx5 and GATA4 as well as differentiated the cardiomyocyte markers α-MHC and β-MHC. Flow cytometric analysis showed that apela increased the percentage of GFP-expressing cells in the beating foci of the embryoid bodies. The percentage of cardiac troponin T (TNT)-positive cells and the protein expression of TNT were increased in the ES cell-derived CMs with apela treatment. Functionally, the contractile frequency of the ES-derived CMs responded appropriately to the vasoactive drugs isoprenaline and carbachol. Our work presented a protocol for specially labelling and enriching CMs by combining transgenic human ES cell lines and exogenous growth factor treatment.
Collapse
Affiliation(s)
- Zhi Wang
- Department of Cardiovascular Medicine, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, People's Republic of China. .,Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, People's Republic of China. .,Department of Cardiology, Nanjing Brain Hospital, Nanjing Medical University, No. 264 Guangzhou Road, Nanjing, 210029, People's Republic of China.
| | - Jin Huang
- Department of Cardiovascular Medicine, Nanjing Brain Hospital, Nanjing Medical University, Nanjing, People's Republic of China. .,Department of Cardiovascular Medicine, Nanjing Chest Hospital, Nanjing, People's Republic of China.
| |
Collapse
|
28
|
Biendarra-Tiegs SM, Li X, Ye D, Brandt EB, Ackerman MJ, Nelson TJ. Single-Cell RNA-Sequencing and Optical Electrophysiology of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Discordance Between Cardiac Subtype-Associated Gene Expression Patterns and Electrophysiological Phenotypes. Stem Cells Dev 2019; 28:659-673. [PMID: 30892143 PMCID: PMC6534093 DOI: 10.1089/scd.2019.0030] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The ability to accurately phenotype cells differentiated from human induced pluripotent stem cells (hiPSCs) is essential for their application in modeling developmental and disease processes, yet also poses a particular challenge without the context of anatomical location. Our specific objective was to determine if single-cell gene expression was sufficient to predict the electrophysiology of iPSC-derived cardiac lineages, to evaluate the concordance between molecular and functional surrogate markers. To this end, we used the genetically encoded voltage indicator ArcLight to profile hundreds of hiPSC-derived cardiomyocytes (hiPSC-CMs), thus identifying patterns of electrophysiological maturation and increased prevalence of cells with atrial-like action potentials (APs) between days 11 and 42 of differentiation. To profile expression patterns of cardiomyocyte subtype-associated genes, single-cell RNA-seq was performed at days 12 and 40 after the populations were fully characterized with the high-throughput ArcLight platform. Although we could detect global gene expression changes supporting progressive differentiation, individual cellular expression patterns alone were not able to delineate the individual cardiomyocytes into atrial, ventricular, or nodal subtypes as functionally documented by electrophysiology measurements. Furthermore, our efforts to understand the distinct electrophysiological properties associated with day 12 versus day 40 hiPSC-CMs revealed that ion channel regulators SLMAP, FGF12, and FHL1 were the most significantly increased genes at day 40, categorized by electrophysiology-related gene functions. Notably, FHL1 knockdown during differentiation was sufficient to significantly modulate APs toward ventricular-like electrophysiology. Thus, our results establish the inability of subtype-associated gene expression patterns to specifically categorize hiPSC-derived cells according to their functional electrophysiology, and yet, altered FHL1 expression is able to redirect electrophysiological maturation of these developing cells. Therefore, noncanonical gene expression patterns of cardiac maturation may be sufficient to direct functional maturation of cardiomyocytes, with canonical gene expression patterns being insufficient to temporally define cardiac subtypes of in vitro differentiation.
Collapse
Affiliation(s)
- Sherri M Biendarra-Tiegs
- 1 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,2 Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Xing Li
- 2 Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota.,3 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Dan Ye
- 4 Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Emma B Brandt
- 1 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,2 Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Michael J Ackerman
- 4 Windland Smith Rice Sudden Death Genomics Laboratory, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,5 Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,6 Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota
| | - Timothy J Nelson
- 1 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota.,2 Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota.,5 Division of Heart Rhythm Services, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota.,6 Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota.,7 Division of General Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
29
|
Addressing Variability and Heterogeneity of Induced Pluripotent Stem Cell-Derived Cardiomyocytes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1212:1-29. [DOI: 10.1007/5584_2019_350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
30
|
Are These Cardiomyocytes? Protocol Development Reveals Impact of Sample Preparation on the Accuracy of Identifying Cardiomyocytes by Flow Cytometry. Stem Cell Reports 2019; 12:395-410. [PMID: 30686762 PMCID: PMC6373208 DOI: 10.1016/j.stemcr.2018.12.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 11/20/2022] Open
Abstract
Several protocols now support efficient differentiation of human pluripotent stem cells to cardiomyocytes (hPSC-CMs) but these still indicate line-to-line variability. As the number of studies implementing this technology expands, accurate assessment of cell identity is paramount to well-defined studies that can be replicated among laboratories. While flow cytometry is apt for routine assessment, a standardized protocol for assessing cardiomyocyte identity has not yet been established. Therefore, the current study leveraged targeted mass spectrometry to confirm the presence of troponin proteins in day 25 hPSC-CMs and systematically evaluated multiple anti-troponin antibodies and sample preparation protocols for their suitability in assessing cardiomyocyte identity. Results demonstrate challenges to interpreting data generated by published methods and inform the development of a robust protocol for routine assessment of hPSC-CMs. The data, workflow for antibody evaluation, and standardized protocol described here should benefit investigators new to this field and those with expertise in hPSC-CM differentiation. TNNI3 and TNNT2 proteins are present in day 25 hPSC-CMs Commonly used reagents can lead to non-specific binding of anti-troponin antibodies A fit-for-purpose workflow describes how to develop a flow cytometry protocol A robust protocol for routine quality control testing was validated for hPSC-CMs
Collapse
|