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Kiskin FN, Yang Y, Yang H, Zhang JZ. Cracking the code of the cardiovascular enigma: hPSC-derived endothelial cells unveil the secrets of endothelial dysfunction. J Mol Cell Cardiol 2024; 192:65-78. [PMID: 38761989 DOI: 10.1016/j.yjmcc.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Endothelial dysfunction is a central contributor to the development of most cardiovascular diseases and is characterised by the reduced synthesis or bioavailability of the vasodilator nitric oxide together with other abnormalities such as inflammation, senescence, and oxidative stress. The use of patient-specific and genome-edited human pluripotent stem cell-derived endothelial cells (hPSC-ECs) has shed novel insights into the role of endothelial dysfunction in cardiovascular diseases with strong genetic components such as genetic cardiomyopathies and pulmonary arterial hypertension. However, their utility in studying complex multifactorial diseases such as atherosclerosis, metabolic syndrome and heart failure poses notable challenges. In this review, we provide an overview of the different methods used to generate and characterise hPSC-ECs before comprehensively assessing their effectiveness in cardiovascular disease modelling and high-throughput drug screening. Furthermore, we explore current obstacles that will need to be overcome to unleash the full potential of hPSC-ECs in facilitating patient-specific precision medicine. Addressing these challenges holds great promise in advancing our understanding of intricate cardiovascular diseases and in tailoring personalised therapeutic strategies.
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Affiliation(s)
- Fedir N Kiskin
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Yuan Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Hao Yang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Joe Z Zhang
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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2
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Cai Z, Zhu M, Xu L, Wang Y, Xu Y, Yim WY, Cao H, Guo R, Qiu X, He X, Shi J, Qiao W, Dong N. Directed Differentiation of Human Induced Pluripotent Stem Cells to Heart Valve Cells. Circulation 2024; 149:1435-1456. [PMID: 38357822 PMCID: PMC11062615 DOI: 10.1161/circulationaha.123.065143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND A main obstacle in current valvular heart disease research is the lack of high-quality homogeneous functional heart valve cells. Human induced pluripotent stem cells (hiPSCs)-derived heart valve cells may help with this dilemma. However, there are no well-established protocols to induce hiPSCs to differentiate into functional heart valve cells, and the networks that mediate the differentiation have not been fully elucidated. METHODS To generate heart valve cells from hiPSCs, we sequentially activated the Wnt, BMP4, VEGF (vascular endothelial growth factor), and NFATc1 signaling pathways using CHIR-99021, BMP4, VEGF-165, and forskolin, respectively. The transcriptional and functional similarity of hiPSC-derived heart valve cells compared with primary heart valve cells were characterized. Longitudinal single-cell RNA sequencing was used to uncover the trajectory, switch genes, pathways, and transcription factors of the differentiation. RESULTS An efficient protocol was developed to induce hiPSCs to differentiate into functional hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells. After 6-day differentiation and CD144 magnetic bead sorting, ≈70% CD144+ cells and 30% CD144- cells were obtained. On the basis of single-cell RNA sequencing data, the CD144+ cells and CD144- cells were found to be highly similar to primary heart valve endothelial cells and primary heart valve interstitial cells in gene expression profile. Furthermore, CD144+ cells had the typical function of primary heart valve endothelial cells, including tube formation, uptake of low-density lipoprotein, generation of endothelial nitric oxide synthase, and response to shear stress. Meanwhile, CD144- cells could secret collagen and matrix metalloproteinases, and differentiate into osteogenic or adipogenic lineages like primary heart valve interstitial cells. Therefore, we identified CD144+ cells and CD144- cells as hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells, respectively. Using single-cell RNA sequencing analysis, we demonstrated that the trajectory of heart valve cell differentiation was consistent with embryonic valve development. We identified the main switch genes (NOTCH1, HEY1, and MEF2C), signaling pathways (TGF-β, Wnt, and NOTCH), and transcription factors (MSX1, SP5, and MECOM) that mediated the differentiation. Finally, we found that hiPSC-derived valve interstitial-like cells might derive from hiPSC-derived valve endothelial-like cells undergoing endocardial-mesenchymal transition. CONCLUSIONS In summary, this is the first study to report an efficient strategy to generate functional hiPSC-derived valve endothelial-like cells and hiPSC-derived valve interstitial-like cells from hiPSCs, as well as to elucidate the differentiation trajectory and transcriptional dynamics of hiPSCs differentiated into heart valve cells.
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Affiliation(s)
- Ziwen Cai
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, China (Z.C.)
| | - Miaomiao Zhu
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, China (Z.C.)
- Institute of Maternal and Children Health, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji medical College, Huazhong University of Science & Technology, Hubei, China (M.Z.)
| | - Li Xu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Yue Wang
- Department of Anesthesiology, Union Hospital, Fujian Medical University, Fuzhou, China (Y.W.)
| | - Yin Xu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Wai Yen Yim
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Hong Cao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Ruikang Guo
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Xiang Qiu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (M.Z., X.H.)
| | - Jiawei Shi
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Weihua Qiao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
| | - Nianguo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China (Z.C., L.X., Y.X., W.Y.Y., H.C., R.G., X.Q, J.S., W.Q., N.D.)
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3
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Xie M, Cao H, Qiao W, Yan G, Qian X, Zhang Y, Xu L, Wen S, Shi J, Cheng M, Dong N. Shear stress activates the Piezo1 channel to facilitate valvular endothelium-oriented differentiation and maturation of human induced pluripotent stem cells. Acta Biomater 2024; 178:181-195. [PMID: 38447808 DOI: 10.1016/j.actbio.2024.02.043] [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] [Received: 07/27/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Valvular endothelial cells (VECs) derived from human induced pluripotent stem cells (hiPSCs) provide an unlimited cell source for tissue engineering heart valves (TEHVs); however, they are limited by their low differentiation efficiency and immature function. In our study, we applied unidirectional shear stress to promote hiPSCs differentiation into valvular endothelial-like cells (VELs). Compared to the static group, shear stress efficiently promoted the differentiation and functional maturation of hiPSC-VELs, as demonstrated by the efficiency of endothelial differentiation reaching 98.3% in the high shear stress group (45 dyn/cm2). Furthermore, we found that Piezo1 served as a crucial mechanosensor for the differentiation and maturation of VELs. Mechanistically, the activation of Piezo1 by shear stress resulted in the influx of calcium ions, which in turn initiated the Akt signaling pathway and promoted the differentiation of hiPSCs into mature VELs. Moreover, VELs cultured on decellularized heart valves (DHVs) exhibited a notable propensity for proliferation, robust adhesion properties, and antithrombotic characteristics, which were dependent on the activation of the Piezo1 channel. Overall, our study demonstrated that proper shear stress activated the Piezo1 channel to facilitate the differentiation and maturation of hiPSC-VELs via the Akt pathway, providing a potential cell source for regenerative medicine, drug screening, pathogenesis, and disease modeling. STATEMENT OF SIGNIFICANCE: This is the first research that systematically analyzes the effect of shear stress on valvular endothelial-like cells (VELs) derived from human induced pluripotent stem cells (hiPSCs). Mechanistically, unidirectional shear stress activates Piezo1, resulting in an elevation of calcium levels, which triggers the Akt signaling pathway and then facilitates the differentiation of functional maturation VELs. After exposure to shear stress, the VELs exhibited enhanced proliferation, robust adhesion capabilities, and antithrombotic characteristics while being cultured on decellularized heart valves. Thus, it is of interest to develop hiPSCs-VELs using shear stress and the Piezo1 channel provides insights into the functional maturation of valvular endothelial cells, thereby serving as a catalyst for potential applications in the development of therapeutic and tissue-engineered heart valves in the future.
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Affiliation(s)
- Minghui Xie
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hong Cao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Weihua Qiao
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ge Yan
- Department of Cardiovascular Surgery, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430014, China
| | - Xingyu Qian
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yecen Zhang
- Department of Cardiovascular Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Li Xu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shuyu Wen
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jiawei Shi
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Min Cheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Nianguo Dong
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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4
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McCracken IR, Smart N. Control of coronary vascular cell fate in development and regeneration. Semin Cell Dev Biol 2024; 155:50-61. [PMID: 37714806 DOI: 10.1016/j.semcdb.2023.08.005] [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: 07/04/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/17/2023]
Abstract
The coronary vasculature consists of a complex hierarchal network of arteries, veins, and capillaries which collectively function to perfuse the myocardium. However, the pathways controlling the temporally and spatially restricted mechanisms underlying the formation of this vascular network remain poorly understood. In recent years, the increasing use and refinement of transgenic mouse models has played an instrumental role in offering new insights into the cellular origins of the coronary vasculature, as well as identifying a continuum of transitioning cell states preceding the full maturation of the coronary vasculature. Coupled with the emergence of single cell RNA sequencing platforms, these technologies have begun to uncover the key regulatory factors mediating the convergence of distinct cellular origins to ensure the formation of a collectively functional, yet phenotypically diverse, vascular network. Furthermore, improved understanding of the key regulatory factors governing coronary vessel formation in the embryo may provide crucial clues into future therapeutic strategies to reactivate these developmentally functional mechanisms to drive the revascularisation of the ischaemic adult heart.
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Affiliation(s)
- Ian R McCracken
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
| | - Nicola Smart
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom.
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5
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Kesidou D, Bennett M, Monteiro JP, McCracken IR, Klimi E, Rodor J, Condie A, Cowan S, Caporali A, Wit JBM, Mountford JC, Brittan M, Beqqali A, Baker AH. Extracellular vesicles from differentiated stem cells contain novel proangiogenic miRNAs and induce angiogenic responses at low doses. Mol Ther 2024; 32:185-203. [PMID: 38096818 PMCID: PMC10787168 DOI: 10.1016/j.ymthe.2023.11.023] [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: 05/16/2023] [Revised: 10/10/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Extracellular vesicles (EVs) released from healthy endothelial cells (ECs) have shown potential for promoting angiogenesis, but their therapeutic efficacy remains poorly understood. We have previously shown that transplantation of a human embryonic stem cell-derived endothelial cell product (hESC-ECP), promotes new vessel formation in acute ischemic disease in mice, likely via paracrine mechanism(s). Here, we demonstrated that EVs from hESC-ECPs (hESC-eEVs) significantly increased EC tube formation and wound closure in vitro at ultralow doses, whereas higher doses were ineffective. More important, EVs isolated from the mesodermal stage of the differentiation (hESC-mEVs) had no effect. Small RNA sequencing revealed that hESC-eEVs have a unique transcriptomic profile and are enriched in known proangiogenic microRNAs (miRNAs, miRs). Moreover, an in silico analysis identified three novel hESC-eEV-miRNAs with potential proangiogenic function. Differential expression analysis suggested that two of those, miR-4496 and miR-4691-5p, are highly enriched in hESC-eEVs. Overexpression of miR-4496 or miR-4691-5p resulted in increased EC tube formation and wound closure in vitro, validating the novel proangiogenic function of these miRNAs. In summary, we demonstrated that hESC-eEVs are potent inducers of EC angiogenic response at ultralow doses and contain a unique EV-associated miRNA repertoire, including miR-4496 and miR-4691-5p, with novel proangiogenic function.
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Affiliation(s)
- Despoina Kesidou
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Matthew Bennett
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - João P Monteiro
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian R McCracken
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX3 7TY, UK
| | - Eftychia Klimi
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Alison Condie
- Scottish National Blood Transfusion Service, Edinburgh EH14 4BE, UK
| | - Scott Cowan
- Scottish National Blood Transfusion Service, Edinburgh EH14 4BE, UK
| | - Andrea Caporali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Jan B M Wit
- Mirabilis Therapeutics BV, Maastricht, the Netherlands
| | | | - Mairi Brittan
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Abdelaziz Beqqali
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK.
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, UK; CARIM Institute, University of Maastricht, Maastricht 6229HX, the Netherlands.
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6
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Payne S, Neal A, De Val S. Transcription factors regulating vasculogenesis and angiogenesis. Dev Dyn 2024; 253:28-58. [PMID: 36795082 PMCID: PMC10952167 DOI: 10.1002/dvdy.575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Transcription factors (TFs) play a crucial role in regulating the dynamic and precise patterns of gene expression required for the initial specification of endothelial cells (ECs), and during endothelial growth and differentiation. While sharing many core features, ECs can be highly heterogeneous. Differential gene expression between ECs is essential to pattern the hierarchical vascular network into arteries, veins and capillaries, to drive angiogenic growth of new vessels, and to direct specialization in response to local signals. Unlike many other cell types, ECs have no single master regulator, instead relying on differing combinations of a necessarily limited repertoire of TFs to achieve tight spatial and temporal activation and repression of gene expression. Here, we will discuss the cohort of TFs known to be involved in directing gene expression during different stages of mammalian vasculogenesis and angiogenesis, with a primary focus on development.
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Affiliation(s)
- Sophie Payne
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Alice Neal
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
| | - Sarah De Val
- Department of Physiology, Anatomy and GeneticsInstitute of Developmental and Regenerative Medicine, University of OxfordOxfordUK
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Rosowski S, Remmert C, Marder M, Akishiba M, Bushe J, Feuchtinger A, Platen A, Ussar S, Theis F, Wiedenmann S, Meier M. Single-cell characterization of neovascularization using hiPSC-derived endothelial cells in a 3D microenvironment. Stem Cell Reports 2023; 18:1972-1986. [PMID: 37714147 PMCID: PMC10656300 DOI: 10.1016/j.stemcr.2023.08.008] [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] [Received: 10/21/2022] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/17/2023] Open
Abstract
The formation of vascular structures is fundamental for in vitro tissue engineering. Vascularization can enable the nutrient supply within larger structures and increase transplantation efficiency. We differentiated human induced pluripotent stem cells toward endothelial cells in 3D suspension culture. To investigate in vitro neovascularization and various 3D microenvironmental approaches, we designed a comprehensive single-cell transcriptomic study. Time-resolved single-cell transcriptomics of the endothelial and co-evolving mural cells gave insights into cell type development, stability, and plasticity. Transfer to a 3D hydrogel microenvironment induced neovascularization and facilitated tracing of migrating, coalescing, and tubulogenic endothelial cell states. During maturation, we monitored two pericyte subtypes evolving mural cells. Profiling cell-cell interactions between pericytes and endothelial cells revealed angiogenic signals during tubulogenesis. In silico discovered ligands were tested for their capability to attract endothelial cells. Our data, analyses, and results provide an in vitro roadmap to guide vascularization in future tissue engineering.
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Affiliation(s)
- Simon Rosowski
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Caroline Remmert
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maren Marder
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Misao Akishiba
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Judith Bushe
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz München, 85764 Neuherberg, Germany
| | - Alina Platen
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Siegfried Ussar
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany; Department of Mathematics, Technical University of Munich, 85748 Garching bei München, Germany
| | - Sandra Wiedenmann
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Matthias Meier
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany; University Leipzig, Center for Biotechnology and Biomedicine, Institute of Biochemistry, Leipzig, Germany.
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8
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Xu X, Chen J, Zhao H, Pi Y, Lin G, Hu L. Single-Cell RNA-seq Analysis of a Human Embryonic Stem Cell to Endothelial Cell System Based on Transcription Factor Overexpression. Stem Cell Rev Rep 2023; 19:2497-2509. [PMID: 37537495 DOI: 10.1007/s12015-023-10598-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Human embryonic stem cell (hESC)-derived endothelial cells (ECs) possess therapeutic potential in many diseases. Cytokine supplementation induction and transcription factor overexpression have become two mainstream methods of hESC-EC induction. Single-cell RNA-seq technology has been widely used to analyse dynamic processes during hESC-EC induction and components of induced endothelial cells. However, studies that used single-cell RNA-seq are mainly based on cytokine supplementation methods. In this study, we used a high-efficiency human embryonic stem cell-endothelial cell line (hESC-EC) called the "FLI1-PKC system" as a research model and employed single-cell RNA sequencing (scRNA-seq) to investigate the transcriptional landscape and cellular dynamics. METHODS The high-efficiency hESC-EC induction (FLI1-PKC) system was established in our previous study. We applied single-cell RNA sequencing (scRNA-seq) of the differentiated cells at different time points and investigated the gene expression profiles. RESULTS The FLI1-PKC induction system can directionally differentiate hESCs into mature endothelial cells with all the requisite functions. Unlike other hES-EC induction protocols, the FLI1-PKC method follows a different induction route; nonetheless, the transcriptome of induced endothelial cells (iECs) remains the same. The elevated number of activated transcription factors may explain why the FLI1-PKC system is more effective than other hES-EC protocols. CONCLUSION Our study has presented a single-cell transcriptional overview of a high-efficiency hESC-EC induction system, which can be used as a model and reference for further improvement in other hESC induction systems.
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Affiliation(s)
- XiangWang Xu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
| | - JunRu Chen
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China
| | - Hao Zhao
- Xiangya Hospital of Central South University, Changsha, Human, China
| | - YuZe Pi
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, National Engineering and Research Center of Human Stem Cell, Changsha, 410008, Hunan, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Xiangya Road 88#, Changsha, 410008, Hunan, People's Republic of China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Hunan, 410008, Changsha, China.
- Hunan International Scientific and Technological Cooperation Base of Development and Carcinogenesis, National Engineering and Research Center of Human Stem Cell, Changsha, 410008, Hunan, China.
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9
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Theodoris CV, Xiao L, Chopra A, Chaffin MD, Al Sayed ZR, Hill MC, Mantineo H, Brydon EM, Zeng Z, Liu XS, Ellinor PT. Transfer learning enables predictions in network biology. Nature 2023; 618:616-624. [PMID: 37258680 PMCID: PMC10949956 DOI: 10.1038/s41586-023-06139-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Mapping gene networks requires large amounts of transcriptomic data to learn the connections between genes, which impedes discoveries in settings with limited data, including rare diseases and diseases affecting clinically inaccessible tissues. Recently, transfer learning has revolutionized fields such as natural language understanding1,2 and computer vision3 by leveraging deep learning models pretrained on large-scale general datasets that can then be fine-tuned towards a vast array of downstream tasks with limited task-specific data. Here, we developed a context-aware, attention-based deep learning model, Geneformer, pretrained on a large-scale corpus of about 30 million single-cell transcriptomes to enable context-specific predictions in settings with limited data in network biology. During pretraining, Geneformer gained a fundamental understanding of network dynamics, encoding network hierarchy in the attention weights of the model in a completely self-supervised manner. Fine-tuning towards a diverse panel of downstream tasks relevant to chromatin and network dynamics using limited task-specific data demonstrated that Geneformer consistently boosted predictive accuracy. Applied to disease modelling with limited patient data, Geneformer identified candidate therapeutic targets for cardiomyopathy. Overall, Geneformer represents a pretrained deep learning model from which fine-tuning towards a broad range of downstream applications can be pursued to accelerate discovery of key network regulators and candidate therapeutic targets.
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Affiliation(s)
- Christina V Theodoris
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School Genetics Training Program, Boston, USA.
| | - Ling Xiao
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Anant Chopra
- Precision Cardiology Laboratory, Bayer US LLC, Cambridge, MA, USA
| | - Mark D Chaffin
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zeina R Al Sayed
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew C Hill
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Helene Mantineo
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative and Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
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10
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Chen Z, Li Y, Yuan Y, Lai K, Ye K, Lin Y, Lan R, Chen H, Xu Y. Single-cell sequencing reveals homogeneity and heterogeneity of the cytopathological mechanisms in different etiology-induced AKI. Cell Death Dis 2023; 14:318. [PMID: 37169762 PMCID: PMC10175265 DOI: 10.1038/s41419-023-05830-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/13/2023]
Abstract
Homogeneity and heterogeneity of the cytopathological mechanisms in different etiology-induced acute kidney injury (AKI) are poorly understood. Here, we performed single-cell sequencing (scRNA) on mouse kidneys with five common AKI etiologies (CP-Cisplatin, IRI-Ischemia-reperfusion injury, UUO-Unilateral ureteral obstruction, FA-Folic acid, and SO-Sodium oxalate). We constructed a potent multi-model AKI scRNA atlas containing 20 celltypes with 80,689 high-quality cells. The data suggest that compared to IRI and CP-AKI, FA- and SO-AKI exhibit injury characteristics more similar to UUO-AKI, which may due to tiny crystal-induced intrarenal obstruction. Through scRNA atlas, 7 different functional proximal tubular cell (PTC) subtypes were identified, we found that Maladaptive PTCs and classical Havcr1 PTCs but not novel Krt20 PTCs affect the pro-inflammatory and pro-fibrotic levels in different AKI models. And cell death and cytoskeletal remodeling events are widespread patterns of injury in PTCs. Moreover, we found that programmed cell death predominated in PTCs, whereas apoptosis and autophagy prevailed in the remaining renal tubules. We also identified S100a6 as a novel AKI-endothelial injury biomarker. Furthermore, we revealed that the dynamic and active immune (especially Arg1 Macro_2 cells) -parenchymal cell interactions are important features of AKI. Taken together, our study provides a potent resource for understanding the pathogenesis of AKI and early intervention in AKI progression at single-cell resolution.
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Affiliation(s)
- Zhimin Chen
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yinshuang Li
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ying Yuan
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Kunmei Lai
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Keng Ye
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yujiao Lin
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ruilong Lan
- Central laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Hong Chen
- Department of Pathology, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Yanfang Xu
- Department of Nephrology, Blood Purification Research Center, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Research Center for Metabolic Chronic Kidney Disease, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
- Department of Nephrology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Central laboratory, the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
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11
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Lv J, Meng S, Gu Q, Zheng R, Gao X, Kim JD, Chen M, Xia B, Zuo Y, Zhu S, Zhao D, Li Y, Wang G, Wang X, Meng Q, Cao Q, Cooke JP, Fang L, Chen K, Zhang L. Epigenetic landscape reveals MECOM as an endothelial lineage regulator. Nat Commun 2023; 14:2390. [PMID: 37185814 PMCID: PMC10130150 DOI: 10.1038/s41467-023-38002-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
A comprehensive understanding of endothelial cell lineage specification will advance cardiovascular regenerative medicine. Recent studies found that unique epigenetic signatures preferentially regulate cell identity genes. We thus systematically investigate the epigenetic landscape of endothelial cell lineage and identify MECOM to be the leading candidate as an endothelial cell lineage regulator. Single-cell RNA-Seq analysis verifies that MECOM-positive cells are exclusively enriched in the cell cluster of bona fide endothelial cells derived from induced pluripotent stem cells. Our experiments demonstrate that MECOM depletion impairs human endothelial cell differentiation, functions, and Zebrafish angiogenesis. Through integrative analysis of Hi-C, DNase-Seq, ChIP-Seq, and RNA-Seq data, we find MECOM binds enhancers that form chromatin loops to regulate endothelial cell identity genes. Further, we identify and verify the VEGF signaling pathway to be a key target of MECOM. Our work provides important insights into epigenetic regulation of cell identity and uncovered MECOM as an endothelial cell lineage regulator.
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Affiliation(s)
- Jie Lv
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Shu Meng
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Qilin Gu
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Rongbin Zheng
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xinlei Gao
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jun-Dae Kim
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Min Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bo Xia
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Yihan Zuo
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sen Zhu
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Dongyu Zhao
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Yanqiang Li
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Guangyu Wang
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Xin Wang
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Qingshu Meng
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qi Cao
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John P Cooke
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
| | - Longhou Fang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
| | - Kaifu Chen
- Center for Bioinformatics and Computational Biology, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Lili Zhang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA.
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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12
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De Kleijn KMA, Zuure WA, Straasheijm KR, Martens MB, Avramut MC, Koning RI, Martens GJM. Human cortical spheroids with a high diversity of innately developing brain cell types. Stem Cell Res Ther 2023; 14:50. [PMID: 36959625 PMCID: PMC10035191 DOI: 10.1186/s13287-023-03261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/28/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)function. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated exploration of CNS (disease) mechanisms. METHODS Here we report a 5-month culture protocol that reproducibly generates H9 embryonic stem cell-derived human cortical spheroids (hCSs) with a large cell-type variety. RESULTS We established the presence of not only neuroectoderm-derived neural progenitor populations, mature excitatory and inhibitory neurons, astrocytes and oligodendrocyte (precursor) cells, but also mesoderm-derived microglia and endothelial cell populations in the hCSs via RNA-sequencing, qPCR, immunocytochemistry and transmission electron microscopy. Transcriptomic analysis revealed resemblance between the 5-months-old hCSs and dorsal frontal rather than inferior regions of human fetal brains of 19-26 weeks of gestational age. Pro-inflammatory stimulation of the generated hCSs induced a neuroinflammatory response, offering a proof-of-principle of the applicability of the spheroids. CONCLUSIONS Our protocol provides a 3D human brain cell model containing a wide variety of innately developing neuroectoderm- as well as mesoderm-derived cell types, furnishing a versatile platform for comprehensive examination of intercellular CNS communication and neurological disease mechanisms.
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Affiliation(s)
- Kim M A De Kleijn
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands.
| | - Wieteke A Zuure
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
| | | | | | - M Cristina Avramut
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands
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13
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Liu Q, Song Y, Cui Y, Hu C, Luo Y, Hu D, Wang H, Li K, Chen J, Xiao H. Heterogeneity of fibroblasts is a hallmark of age-associated erectile dysfunction. Int J Biochem Cell Biol 2023; 156:106343. [PMID: 36503049 DOI: 10.1016/j.biocel.2022.106343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND The prevalence of age-associated erectile dysfunction (ED) increases pronouncedly with age. However, the cellular composition and transcriptomic changes of aging penile corpus cavernosum remain largely unclear. METHODS Herein, we performed single cell sequencing penile corpus cavernosum from five young with normal erectile response and five old rats with ED. RESULTS Clustering analysis identified 19 cell types, such as fibroblasts, myofibroblasts and immune cells. We next revealed their transcriptomic alterations and investigated novel subpopulations of major cell types. Among them, fibroblasts possessed the largest cell number and showed apparent heterogeneity. By performing single-cell entropy analysis on fibroblasts, we observed the age-associated decrease of entropy, and aged fibroblasts were found to adopt senescent secretory phenotype, as evidenced by the high expression of genes associated with the senescence-associated secretory phenotype (SASP). Finally, we constructed a comprehensive intercellular communication network and highlighted key mediators of crosstalk between fibroblasts and other cell types. CONCLUSIONS We plotted a cellular atlas of aging cells within penile corpus cavernosum, especially fibroblasts. Our work will deepen the understanding of the heterogeneity among certain cell types within aged penile corpus cavernosum, which will generate positive effects on the future treatment of age-associated ED.
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Affiliation(s)
- Qiwei Liu
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China; Plastic Surgery Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100040, China
| | - Yulong Song
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yubin Cui
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Cheng Hu
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Yun Luo
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Daoyuan Hu
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Hua Wang
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Ke Li
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
| | - Jun Chen
- Department of Infertility and Sexual Medicine, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
| | - Hengjun Xiao
- Department of Urology, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China.
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14
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Yasui R, Matsui A, Sekine K, Okamoto S, Taniguchi H. Highly Sensitive Detection of Human Pluripotent Stem Cells by Loop-Mediated Isothermal Amplification. Stem Cell Rev Rep 2022; 18:2995-3007. [PMID: 35661077 PMCID: PMC9622575 DOI: 10.1007/s12015-022-10402-3] [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] [Subscribe] [Scholar Register] [Accepted: 05/20/2022] [Indexed: 11/24/2022]
Abstract
For safe regenerative medicines, contaminated or remaining tumorigenic undifferentiated cells in cell-derived products must be rigorously assessed through sensitive assays. Although in vitro nucleic acid tests offer particularly sensitive tumorigenicity-associated assays, the human pluripotent stem cell (hPSC) detectability is partly constrained by the small input amount of RNA per test. To overcome this limitation, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays that are highly gene specific and robust against interfering materials. LAMP could readily assay microgram order of input sample per test and detected an equivalent model of 0.00002% hiPSC contamination in a simple one-pot reaction. For the evaluation of cell-derived total RNA, RT-LAMP detected spiked-in hPSCs among hPSC-derived trilineage cells utilizing multiple pluripotency RNAs. We also developed multiplex RT-LAMP assays and further applied for in situ cell imaging, achieving specific co-staining of pluripotency proteins and RNAs. Our attempts uncovered the utility of RT-LAMP approaches for tumorigenicity-associated assays, supporting practical applications of regenerative medicine.
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Affiliation(s)
- Ryota Yasui
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Fundamental Research Laboratory, Eiken Chemical Co., Ltd., Nogi, Tochigi, 329-0114, Japan
| | - Atsuka Matsui
- Biochemical Research Laboratory, Eiken Chemical Co., Ltd., Ohtawara, Tochigi, 324-0036, Japan
| | - Keisuke Sekine
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Satoshi Okamoto
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hideki Taniguchi
- Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, 236-0004, Japan.
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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15
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Vargas R, Egurbide-Sifre A, Medina L. Organ-on-a-Chip systems for new drugs development. ADMET AND DMPK 2022; 9:111-141. [PMID: 35299767 PMCID: PMC8920106 DOI: 10.5599/admet.942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/04/2021] [Indexed: 11/18/2022] Open
Abstract
Research on alternatives to the use of animal models and cell cultures has led to the creation of organ-on-a-chip systems, in which organs and their physiological reactions to the presence of external stimuli are simulated. These systems could even replace the use of human beings as subjects for the study of drugs in clinical phases and have an impact on personalized therapies. Organ-on-a-chip technology present higher potential than traditional cell cultures for an appropriate prediction of functional impairments, appearance of adverse effects, the pharmacokinetic and toxicological profile and the efficacy of a drug. This potential is given by the possibility of placing different cell lines in a three-dimensional-arranged polymer piece and simulating and controlling specific conditions. Thus, the normal functioning of an organ, tissue, barrier, or physiological phenomenon can be simulated, as well as the interrelation between different systems. Furthermore, this alternative allows the study of physiological and pathophysiological processes. Its design combines different disciplines such as materials engineering, cell cultures, microfluidics and physiology, among others. This work presents the main considerations of OoC systems, the materials, methods and cell lines used for their design, and the conditions required for their proper functioning. Examples of applications and main challenges for the development of more robust systems are shown. This non-systematic review is intended to be a reference framework that facilitates research focused on the development of new OoC systems, as well as their use as alternatives in pharmacological, pharmacokinetic and toxicological studies.
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Affiliation(s)
- Ronny Vargas
- Industrial Pharmacy Department, Faculty of Pharmacy, University of Costa Rica 11501-2060, San José, Costa Rica.,Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-1, 08028, Barcelona, Spain
| | - Andrea Egurbide-Sifre
- Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-1, 08028, Barcelona, Spain
| | - Laura Medina
- Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-1, 08028, Barcelona, Spain
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16
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Spiroski AM, McCracken IR, Thomson A, Magalhaes-Pinto M, Lalwani MK, Newton KJ, Miller E, Bénézech C, Hadoke P, Brittan M, Mountford JC, Beqqali A, Gray GA, Baker AH. Human embryonic stem cell-derived endothelial cell product injection attenuates cardiac remodeling in myocardial infarction. Front Cardiovasc Med 2022; 9:953211. [PMID: 36299872 PMCID: PMC9588936 DOI: 10.3389/fcvm.2022.953211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Mechanisms contributing to tissue remodeling of the infarcted heart following cell-based therapy remain elusive. While cell-based interventions have the potential to influence the cardiac healing process, there is little direct evidence of preservation of functional myocardium. Aim The aim of the study was to investigate tissue remodeling in the infarcted heart following human embryonic stem cell-derived endothelial cell product (hESC-ECP) therapy. Materials and methods Following coronary artery ligation (CAL) to induce cardiac ischemia, we investigated infarct size at 1 day post-injection in media-injected controls (CALM, n = 11), hESC-ECP-injected mice (CALC, n = 10), and dead hESC-ECP-injected mice (CALD, n = 6); echocardiography-based functional outcomes 14 days post-injection in experimental (CALM, n = 13; CALC, n = 17) and SHAM surgical mice (n = 4); and mature infarct size (CALM and CALC, both n = 6). We investigated ligand-receptor interactions (LRIs) in hESC-ECP cell populations, incorporating a publicly available C57BL/6J mouse cardiomyocyte-free scRNAseq dataset with naive, 1 day, and 3 days post-CAL hearts. Results Human embryonic stem cell-derived endothelial cell product injection reduces the infarct area (CALM: 54.5 ± 5.0%, CALC: 21.3 ± 4.9%), and end-diastolic (CALM: 87.8 ± 8.9 uL, CALC: 63.3 ± 2.7 uL) and end-systolic ventricular volume (CALM: 56.4 ± 9.3 uL, CALC: 33.7 ± 2.6 uL). LRI analyses indicate an alternative immunomodulatory effect mediated via viable hESC-ECP-resident signaling. Conclusion Delivery of the live hESC-ECP following CAL modulates the wound healing response during acute pathological remodeling, reducing infarct area, and preserving functional myocardium in this relatively acute model. Potential intrinsic myocardial cellular/hESC-ECP interactions indicate that discreet immunomodulation could provide novel therapeutic avenues to improve cardiac outcomes following myocardial infarction.
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Affiliation(s)
- Ana-Mishel Spiroski
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- BHF Centre for Vascular Regeneration, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian R. McCracken
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Thomson
- Edinburgh Preclinical Imaging, University of Edinburgh, Edinburgh, United Kingdom
| | - Marlene Magalhaes-Pinto
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- BHF Centre for Vascular Regeneration, University of Edinburgh, Edinburgh, United Kingdom
| | - Mukesh K. Lalwani
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kathryn J. Newton
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Eileen Miller
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Cecile Bénézech
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Patrick Hadoke
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mairi Brittan
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- BHF Centre for Vascular Regeneration, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Abdelaziz Beqqali
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Gillian A. Gray
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew H. Baker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- BHF Centre for Vascular Regeneration, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Andrew H. Baker,
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17
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Han JK, Shin Y, Kim HS. Direct Conversion of Cell Fate and Induced Endothelial Cells. Circ J 2021; 86:1925-1933. [PMID: 34732599 DOI: 10.1253/circj.cj-21-0703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in nuclear reprogramming technology have enabled the dedifferentiation and transdifferentiation of mammalian cells. Forced induction of the key transcription factors constituting a transcriptional network can convert cells back to their pluripotent status or directly to another cell fate without inducing pluripotency. To date, direct conversion to several cell types, including cardiomyocytes, various types of neurons, and pancreatic β-cells, has been reported. We previously demonstrated direct lineage reprogramming of adult fibroblasts into induced endothelial cells (iECs) in mice and humans. In contrast to induced pluripotent stem cells, for which there is consensus on the criteria defining pluripotency, such criteria have not yet been established in the field of direct conversion. We thus suggest that careful assessment of the status of converted cells using genetic and epigenetic profiling, various functional assays, and the use of multiple readouts is essential to determine successful conversion. As direct conversion does not go through pluripotent status, this technique can be utilized for therapeutic purposes without the risk of tumorigenesis. Further, direct conversion can be induced in vivo by gene delivery to the target tissue or organ in situ. Thus, direct conversion technology can be developed into cell therapy or gene therapy for regenerative purposes. Here, we review the potential and future directions of direct cell fate conversion and iECs.
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Affiliation(s)
- Jung-Kyu Han
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
| | - Youngchul Shin
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
| | - Hyo-Soo Kim
- Department of Internal Medicine, and Strategic Center of Cell and Bio Therapy for Heart, Diabetes and Cancer, Seoul National University Hospital
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18
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Chen Z, Wei L, Duru F, Chen L. Single-cell RNA Sequencing: In-depth Decoding of Heart Biology and Cardiovascular Diseases. Curr Genomics 2020; 21:585-601. [PMID: 33414680 PMCID: PMC7770632 DOI: 10.2174/1389202921999200604123914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 04/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background The cardiac system is a combination of a complex structure, various cells, and versatile specified functions and sophisticated regulatory mechanisms. Moreover, cardiac diseases that encompass a wide range of endogenous conditions, remain a serious health burden worldwide. Recent genome-wide profiling techniques have taken the lead in uncovering a new realm of cell types and molecular programs driving physiological and pathological processes in various organs and diseases. In particular, the emerging technique single-cell RNA sequencing dominates a breakthrough in decoding the cell heterogeneity, phenotype transition, and developmental dynamics in cardiovascular science. Conclusion Herein, we review recent advances in single cellular studies of cardiovascular system and summarize new insights provided by single-cell RNA sequencing in heart developmental sciences, stem-cell researches as well as normal or disease-related working mechanisms.
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Affiliation(s)
- Zhongli Chen
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Liang Wei
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Firat Duru
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Liang Chen
- 1Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China; 2State Key Laboratory of Cardiovascular Disease, Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3University Heart Center Zurich, University Heart Center, Zurich, Switzerland; 4Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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19
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Pinto AR, Bobik A. Mapping human pluripotent stem cell-endothelial cell differentiation using scRNA-seq: a step towards therapeutic angiogenesis. Eur Heart J 2020; 41:1037-1039. [PMID: 31263875 DOI: 10.1093/eurheartj/ehz464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Alexander R Pinto
- Baker Heart and Diabetes Institute, Melbourne, Australia.,Centre for Cardiovascular Biology and Disease Research, La Trobe University, Melbourne, Australia
| | - Alex Bobik
- Baker Heart and Diabetes Institute, Melbourne, Australia.,Department of Immunology, Monash University, Melbourne, Australia
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20
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Spencer HL, Sanders R, Boulberdaa M, Meloni M, Cochrane A, Spiroski AM, Mountford J, Emanueli C, Caporali A, Brittan M, Rodor J, Baker AH. The LINC00961 transcript and its encoded micropeptide, small regulatory polypeptide of amino acid response, regulate endothelial cell function. Cardiovasc Res 2020; 116:1981-1994. [PMID: 31990292 PMCID: PMC8216332 DOI: 10.1093/cvr/cvaa008] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 09/10/2019] [Accepted: 02/11/2020] [Indexed: 12/18/2022] Open
Abstract
AIMS Long non-coding RNAs (lncRNAs) play functional roles in physiology and disease, yet understanding of their contribution to endothelial cell (EC) function is incomplete. We identified lncRNAs regulated during EC differentiation and investigated the role of LINC00961 and its encoded micropeptide, small regulatory polypeptide of amino acid response (SPAAR), in EC function. METHODS AND RESULTS Deep sequencing of human embryonic stem cell differentiation to ECs was combined with Encyclopedia of DNA Elements (ENCODE) RNA-seq data from vascular cells, identifying 278 endothelial enriched genes, including 6 lncRNAs. Expression of LINC00961, first annotated as an lncRNA but reassigned as a protein-coding gene for the SPAAR micropeptide, was increased during the differentiation and was EC enriched. LINC00961 transcript depletion significantly reduced EC adhesion, tube formation, migration, proliferation, and barrier integrity in primary ECs. Overexpression of the SPAAR open reading frame increased tubule formation; however, overexpression of the full-length transcript did not, despite production of SPAAR. Furthermore, overexpression of an ATG mutant of the full-length transcript reduced network formation, suggesting a bona fide non-coding RNA function of the transcript with opposing effects to SPAAR. As the LINC00961 locus is conserved in mouse, we generated an LINC00961 locus knockout (KO) mouse that underwent hind limb ischaemia (HLI) to investigate the angiogenic role of this locus in vivo. In agreement with in vitro data, KO animals had a reduced capillary density in the ischaemic adductor muscle after 7 days. Finally, to characterize LINC00961 and SPAAR independent functions in ECs, we performed pull-downs of both molecules and identified protein-binding partners. LINC00961 RNA binds the G-actin sequestering protein thymosin beta-4x (Tβ4) and Tβ4 depletion phenocopied the overexpression of the ATG mutant. SPAAR binding partners included the actin-binding protein, SYNE1. CONCLUSION The LINC00961 locus regulates EC function in vitro and in vivo. The gene produces two molecules with opposing effects on angiogenesis: SPAAR and LINC00961.
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Affiliation(s)
- Helen L Spencer
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Rachel Sanders
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Mounia Boulberdaa
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Marco Meloni
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Amy Cochrane
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Ana-Mishel Spiroski
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Joanne Mountford
- Institute of Cardiovascular and Medical Sciences, University of
Glasgow, 126 University Pl, Glasgow G12 8TA, UK
| | - Costanza Emanueli
- National Heart and Lung Institute, Vascular Sciences and Cardiac Function,
Imperial Centre for Translational and Experimental Medicine, Imperial College
London, London W12 0NN, UK
| | - Andrea Caporali
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Mairi Brittan
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Julie Rodor
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
| | - Andrew H Baker
- University/BHF Centre for Cardiovascular Science, Queens Medical Research
Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh
EH16 4TJ, UK
- Institute of Cardiovascular and Medical Sciences, University of
Glasgow, 126 University Pl, Glasgow G12 8TA, UK
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21
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Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. Proc Natl Acad Sci U S A 2020; 117:19854-19865. [PMID: 32759214 DOI: 10.1073/pnas.1911532117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The blood-retina barrier and blood-brain barrier (BRB/BBB) are selective and semipermeable and are critical for supporting and protecting central nervous system (CNS)-resident cells. Endothelial cells (ECs) within the BRB/BBB are tightly coupled, express high levels of Claudin-5 (CLDN5), a junctional protein that stabilizes ECs, and are important for proper neuronal function. To identify novel CLDN5 regulators (and ultimately EC stabilizers), we generated a CLDN5-P2A-GFP stable cell line from human pluripotent stem cells (hPSCs), directed their differentiation to ECs (CLDN5-GFP hPSC-ECs), and performed flow cytometry-based chemogenomic library screening to measure GFP expression as a surrogate reporter of barrier integrity. Using this approach, we identified 62 unique compounds that activated CLDN5-GFP. Among them were TGF-β pathway inhibitors, including RepSox. When applied to hPSC-ECs, primary brain ECs, and retinal ECs, RepSox strongly elevated barrier resistance (transendothelial electrical resistance), reduced paracellular permeability (fluorescein isothiocyanate-dextran), and prevented vascular endothelial growth factor A (VEGFA)-induced barrier breakdown in vitro. RepSox also altered vascular patterning in the mouse retina during development when delivered exogenously. To determine the mechanism of action of RepSox, we performed kinome-, transcriptome-, and proteome-profiling and discovered that RepSox inhibited TGF-β, VEGFA, and inflammatory gene networks. In addition, RepSox not only activated vascular-stabilizing and barrier-establishing Notch and Wnt pathways, but also induced expression of important tight junctions and transporters. Taken together, our data suggest that inhibiting multiple pathways by selected individual small molecules, such as RepSox, may be an effective strategy for the development of better BRB/BBB models and novel EC barrier-inducing therapeutics.
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22
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Paik DT, Cho S, Tian L, Chang HY, Wu JC. Single-cell RNA sequencing in cardiovascular development, disease and medicine. Nat Rev Cardiol 2020; 17:457-473. [PMID: 32231331 PMCID: PMC7528042 DOI: 10.1038/s41569-020-0359-y] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/24/2020] [Indexed: 02/08/2023]
Abstract
Advances in single-cell RNA sequencing (scRNA-seq) technologies in the past 10 years have had a transformative effect on biomedical research, enabling the profiling and analysis of the transcriptomes of single cells at unprecedented resolution and throughput. Specifically, scRNA-seq has facilitated the identification of novel or rare cell types, the analysis of single-cell trajectory construction and stem or progenitor cell differentiation, and the comparison of healthy and disease-related tissues at single-cell resolution. These applications have been critical in advances in cardiovascular research in the past decade as evidenced by the generation of cell atlases of mammalian heart and blood vessels and the elucidation of mechanisms involved in cardiovascular development and stem or progenitor cell differentiation. In this Review, we summarize the currently available scRNA-seq technologies and analytical tools and discuss the latest findings using scRNA-seq that have substantially improved our knowledge on the development of the cardiovascular system and the mechanisms underlying cardiovascular diseases. Furthermore, we examine emerging strategies that integrate multimodal single-cell platforms, focusing on future applications in cardiovascular precision medicine that use single-cell omics approaches to characterize cell-specific responses to drugs or environmental stimuli and to develop effective patient-specific therapeutics.
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Affiliation(s)
- David T Paik
- Stanford Cardiovascular Institute, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Sangkyun Cho
- Stanford Cardiovascular Institute, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Lei Tian
- Stanford Cardiovascular Institute, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford, CA, USA.
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA.
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Von Willebrand Disease: From In Vivo to In Vitro Disease Models. Hemasphere 2020; 3:e297. [PMID: 31942548 PMCID: PMC6919471 DOI: 10.1097/hs9.0000000000000297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/04/2019] [Indexed: 01/28/2023] Open
Abstract
Von Willebrand factor (VWF) plays an essential role in primary hemostasis and is exclusively synthesized and stored in endothelial cells and megakaryocytes. Upon vascular injury, VWF is released into the circulation where this multimeric protein is required for platelet adhesion. Defects of VWF lead to the most common inherited bleeding disorder von Willebrand disease (VWD). Three different types of VWD exist, presenting with varying degrees of bleeding tendencies. The pathophysiology of VWD can be investigated by examining the synthesis, storage and secretion in VWF producing cells. These cells can either be primary VWF producing cells or transfected heterologous cell models. For many years transfected heterologous cells have been used successfully to elucidate many aspects of VWF synthesis. However, those cells do not fully reflect the characteristics of primary cells. Obtaining primary endothelial cells or megakaryocytes with a VWD phenotype, requires invasive procedures, such as vessel collection or a bone marrow biopsy. A more recent and promising development is the isolation of endothelial colony forming cells (ECFCs) from peripheral blood as a true-to-nature cell model. Alternatively, various animal models are available but limiting, therefore, new approaches are needed to study VWD and other bleeding disorders. A potential versatile source of endothelial cells and megakaryocytes could be induced pluripotent stem cells (iPSCs). This review gives an overview of models that are available to study VWD and VWF and will discuss novel approaches that can be considered to improve the understanding of the structural and functional mechanisms underlying this disease.
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