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Cano E, Schwarzkopf J, Kanda M, Lindberg EL, Hollfinger I, Pogontke C, Braeuning C, Fischer C, Hübner N, Gerhardt H. Intramyocardial Sprouting Tip Cells Specify Coronary Arterialization. Circ Res 2024; 135:671-684. [PMID: 39092506 PMCID: PMC11361357 DOI: 10.1161/circresaha.124.324868] [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: 05/13/2024] [Revised: 07/11/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND The elaborate patterning of coronary arteries critically supports the high metabolic activity of the beating heart. How coronary endothelial cells coordinate hierarchical vascular remodeling and achieve arteriovenous specification remains largely unknown. Understanding the molecular and cellular cues that pattern coronary arteries is crucial to develop innovative therapeutic strategies that restore functional perfusion within the ischemic heart. METHODS Single-cell transcriptomics and histological validation were used to delineate heterogeneous transcriptional states of the developing and mature coronary endothelium with a focus on sprouting endothelium and arterial cell specification. Genetic lineage tracing and high-resolution 3-dimensional imaging were used to characterize the origin and mechanisms of coronary angiogenic sprouting, as well as to fate-map selective endothelial lineages. Integration of single-cell transcriptomic data from ischemic adult mouse hearts and human embryonic data served to assess the conservation of transcriptional states across development, disease, and species. RESULTS We discover that coronary arteries originate from cells that have previously transitioned through a specific tip cell phenotype. We identify nonoverlapping intramyocardial and subepicardial tip cell populations with differential gene expression profiles and regulatory pathways. Esm1-lineage tracing confirmed that intramyocardial tip cells selectively contribute to coronary arteries and endocardial tunnels, but not veins. Notably, prearterial cells are detected from development stages to adulthood, increasingly in response to ischemic injury, and in human embryos, suggesting that tip cell-to-artery specification is a conserved mechanism. CONCLUSIONS A tip cell-to-artery specification mechanism drives arterialization of the intramyocardial plexus and endocardial tunnels throughout life and is reactivated upon ischemic injury. Differential sprouting programs govern the formation and specification of the venous and arterial coronary plexus.
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Affiliation(s)
- Elena Cano
- Integrative Vascular Biology Laboratory (E.C., J.S., I.H., H.G.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany (E.C., J.S., N.H., H.G.)
- Charité-Universitätsmedizin, Berlin, Germany (E.C., J.S., N.H., H.G.)
- Department of Animal Biology, University of Málaga, Spain (E.C., C.P.)
- Cardiovascular Development and Disease, Biomedical Research Institute of Malaga and Nanomedicine Platform (IBIMA - BIONAND Platform), Málaga, Spain (E.C., C.P.)
| | - Jennifer Schwarzkopf
- Integrative Vascular Biology Laboratory (E.C., J.S., I.H., H.G.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany (E.C., J.S., N.H., H.G.)
- Charité-Universitätsmedizin, Berlin, Germany (E.C., J.S., N.H., H.G.)
| | - Masatoshi Kanda
- Cardiovascular and Metabolic Sciences (M.K., E.L.L., N.H.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University, Japan (M.K.)
| | - Eric L. Lindberg
- Cardiovascular and Metabolic Sciences (M.K., E.L.L., N.H.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Medicine, Ludwig-Maximiliams-University Munich, Germany (E.L.L.)
| | - Irene Hollfinger
- Integrative Vascular Biology Laboratory (E.C., J.S., I.H., H.G.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Cristina Pogontke
- Department of Animal Biology, University of Málaga, Spain (E.C., C.P.)
- Cardiovascular Development and Disease, Biomedical Research Institute of Malaga and Nanomedicine Platform (IBIMA - BIONAND Platform), Málaga, Spain (E.C., C.P.)
| | | | | | - Norbert Hübner
- Cardiovascular and Metabolic Sciences (M.K., E.L.L., N.H.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany (E.C., J.S., N.H., H.G.)
- Charité-Universitätsmedizin, Berlin, Germany (E.C., J.S., N.H., H.G.)
| | - Holger Gerhardt
- Integrative Vascular Biology Laboratory (E.C., J.S., I.H., H.G.), Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), Berlin, Germany (E.C., J.S., N.H., H.G.)
- Charité-Universitätsmedizin, Berlin, Germany (E.C., J.S., N.H., H.G.)
- Berlin Institute of Health (BIH), Germany (H.G.)
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Arulsamy K, Xia B, Chen H, Zhang L, Chen K. Machine Learning Uncovers Vascular Endothelial Cell Identity Genes by Expression Regulation Features in Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609808. [PMID: 39253493 PMCID: PMC11383289 DOI: 10.1101/2024.08.27.609808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Deciphering cell identity genes is pivotal to understanding cell differentiation, development, and many diseases involving cell identity dysregulation. Here, we introduce SCIG, a machine-learning method to uncover cell identity genes in single cells. In alignment with recent reports that cell identity genes are regulated with unique epigenetic signatures, we found cell identity genes exhibit distinctive genetic sequence signatures, e.g., unique enrichment patterns of cis-regulatory elements. Using these genetic sequence signatures, along with gene expression information from single-cell RNA-seq data, enables SCIG to uncover the identity genes of a cell without a need for comparison to other cells. Cell identity gene score defined by SCIG surpassed expression value in network analysis to uncover master transcription factors regulating cell identity. Applying SCIG to the human endothelial cell atlas revealed that the tissue microenvironment is a critical supplement to master transcription factors for cell identity refinement. SCIG is publicly available at https://github.com/kaifuchenlab/SCIG , offering a valuable tool for advancing cell differentiation, development, and regenerative medicine research.
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3
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Limbu S, McCloskey KE. An Endothelial Cell Is Not Simply an Endothelial Cell. Stem Cells Dev 2024. [PMID: 39030822 DOI: 10.1089/scd.2024.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2024] Open
Abstract
Endothelial cells (ECs) are a multifaceted component of the vascular system with roles in immunity, maintaining tissue fluid balance, and vascular tone. Dysregulation or dysfunction of ECs can have far-reaching implications, leading pathologies ranging from cardiovascular diseases, such as hypertension and atherosclerosis, ischemia, chronic kidney disease, blood-brain barrier integrity, dementia, and tumor metastasis. Recent advancements in regenerative medicine have highlighted the potential of stem cell-derived ECs, particularly from induced pluripotent stem cells, to treat ischemic tissues, as well as models of vascular integrity. This review summarizes what is known in the generation of ECs with an emphasis on tissue-specific ECs and EC subphenotypes important in the development of targeted cell-based therapies for patient treatment.
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Affiliation(s)
- Shiwani Limbu
- Quantitative and System Biology Graduate Program, University of California, Merced, USA
| | - Kara E McCloskey
- Quantitative and System Biology Graduate Program, University of California, Merced, USA
- Materials Science and Engineering Department, University of California, Merced, USA
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4
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Huang D, Shang W, Xu M, Wan Q, Zhang J, Tang X, Shen Y, Wang Y, Yu Y. Genome-Wide Methylation Analysis Reveals a KCNK3-Prominent Causal Cascade on Hypertension. Circ Res 2024; 135:e76-e93. [PMID: 38841840 DOI: 10.1161/circresaha.124.324455] [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: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Despite advances in understanding hypertension's genetic structure, how noncoding genetic variants influence it remains unclear. Studying their interaction with DNA methylation is crucial to deciphering this complex disease's genetic mechanisms. METHODS We investigated the genetic and epigenetic interplay in hypertension using whole-genome bisulfite sequencing. Methylation profiling in 918 males revealed allele-specific methylation and methylation quantitative trait loci. We engineered rs1275988T/C mutant mice using CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), bred them for homozygosity, and subjected them to a high-salt diet. Telemetry captured their cardiovascular metrics. Protein-DNA interactions were elucidated using DNA pull-downs, mass spectrometry, and Western blots. A wire myograph assessed vascular function, and analysis of the Kcnk3 gene methylation highlighted the mutation's role in hypertension. RESULTS We discovered that DNA methylation-associated genetic effects, especially in non-cytosine-phosphate-guanine (non-CpG) island and noncoding distal regulatory regions, significantly contribute to hypertension predisposition. We identified distinct methylation quantitative trait locus patterns in the hypertensive population and observed that the onset of hypertension is influenced by the transmission of genetic effects through the demethylation process. By evidence-driven prioritization and in vivo experiments, we unearthed rs1275988 in a cell type-specific enhancer as a notable hypertension causal variant, intensifying hypertension through the modulation of local DNA methylation and consequential alterations in Kcnk3 gene expression and vascular remodeling. When exposed to a high-salt diet, mice with the rs1275988C/C genotype exhibited exacerbated hypertension and significant vascular remodeling, underscored by increased aortic wall thickness. The C allele of rs1275988 was associated with elevated DNA methylation levels, driving down the expression of the Kcnk3 gene by attenuating Nr2f2 (nuclear receptor subfamily 2 group F member 2) binding at the enhancer locus. CONCLUSIONS Our research reveals new insights into the complex interplay between genetic variations and DNA methylation in hypertension. We underscore hypomethylation's potential in hypertension onset and identify rs1275988 as a causal variant in vascular remodeling. This work advances our understanding of hypertension's molecular mechanisms and encourages personalized health care strategies.
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Affiliation(s)
- Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
- School of Food Science and Technology, Jiangnan University, Wuxi, China (D.H.)
| | - Wenlong Shang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Mengtong Xu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Qiangyou Wan
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine (Q.W.)
| | - Jin Zhang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Xiaofeng Tang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Yujun Shen
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
| | - Yan Wang
- Department of Cardiovascular Medicine, Research Center for Hypertension Management and Prevention in Community, State Key Laboratory of Medical Genomics, Shanghai Key Laboratory of Hypertension, Shanghai Institute of Hypertension, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, China (J.Z., X.T., Y.W.)
| | - Ying Yu
- Department of Pharmacology, Tianjin Key Laboratory of Inflammatory Biology, Center for Cardiovascular Diseases, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, School of Basic Medical Sciences, Tianjin Medical University, China (D.H., W.S., M.X., Y.S., Y.Y.)
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5
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Chen Q, Zheng J, Bian Q. Cell Fate Regulation During the Development of Infantile Hemangioma. J Invest Dermatol 2024:S0022-202X(24)01873-6. [PMID: 39023471 DOI: 10.1016/j.jid.2024.06.1275] [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: 02/29/2024] [Revised: 06/05/2024] [Accepted: 06/09/2024] [Indexed: 07/20/2024]
Abstract
As the most common benign vascular tumor in infants, infantile hemangioma (IH) is characterized by rapid growth and vasculogenesis early in infancy, followed by spontaneous involution into fibrofatty tissues over time. Extensive evidence suggests that IH originates from hemangioma stem cells (HemSCs), a group of stem cells with clonal expansion and multi-directional differentiation capacity. However, the intricate mechanisms governing the cell fate transition of HemSCs during IH development remain elusive. Here we comprehensively examine the cellular composition of IH, emphasizing the nuanced properties of various IH cell types and their correlation with the clinical features of the tumor. We also summarize the current understanding of the regulatory pathways directing HemSC differentiation into endothelial cells (ECs), pericytes, and adipocytes throughout the stages of IH progression and involution. Furthermore, we discuss recent advances in unraveling the transcriptional and epigenetic regulation of EC and adipocyte development under physiological conditions, which offer crucial perspectives for understanding IH pathogenesis.
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Affiliation(s)
- Qiming Chen
- Department of Oromaxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Jiawei Zheng
- Department of Oromaxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai, China; National Center for Stomatology, Shanghai, China; National Clinical Research Center for Oral Diseases, Shanghai, China; Shanghai Key Laboratory of Stomatology, Shanghai, China.
| | - Qian Bian
- Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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6
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Abraham E, Volmert B, Roule T, Huang L, Yu J, Williams AE, Cohen HM, Douglas A, Megill E, Morris A, Stronati E, Fueyo R, Zubillaga M, Elrod JW, Akizu N, Aguirre A, Estaras C. A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.602981. [PMID: 39026825 PMCID: PMC11257518 DOI: 10.1101/2024.07.11.602981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Vitamin A/Retinoic Acid (Vit A/RA) signaling is essential for heart development. In cardiac progenitor cells (CPCs), RA signaling induces the expression of atrial lineage genes while repressing ventricular genes, thereby promoting the acquisition of an atrial cardiomyocyte cell fate. To achieve this, RA coordinates a complex regulatory network of downstream effectors that is not fully identified. To address this gap, we applied a functional genomics approach (i.e scRNAseq and snATACseq) to untreated and RA-treated human embryonic stem cells (hESCs)-derived CPCs. Unbiased analysis revealed that the Hippo effectors YAP1 and TEAD4 are integrated with the atrial transcription factor enhancer network, and that YAP1 is necessary for activation of RA-enhancers in CPCs. Furthermore, in vivo analysis of control and conditionally YAP1 KO mouse embryos (Sox2-cre) revealed that the expression of atrial lineage genes, such as NR2F2, is compromised by YAP1 deletion in the CPCs of the second heart field. Accordingly, we found that YAP1 is required for the formation of an atrial chamber but is dispensable for the formation of a ventricle, in hESC-derived patterned cardiac organoids. Overall, our findings revealed that YAP1 is a non-canonical effector of RA signaling essential for the acquisition of atrial lineages during cardiogenesis.
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Affiliation(s)
- Elizabeth Abraham
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Brett Volmert
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, USA
| | - Thomas Roule
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ling Huang
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jingting Yu
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - April E Williams
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Henry M Cohen
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Aidan Douglas
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Emily Megill
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Alex Morris
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Eleonora Stronati
- Department of Child and Adolescence Psychiatry, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mikel Zubillaga
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - John W Elrod
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Aitor Aguirre
- Institute for Quantitative Health Science and Engineering, Division of Developmental and Stem Cell Biology, Michigan State University, East Lansing, MI, USA
| | - Conchi Estaras
- Department of Cardiovascular Sciences, Aging + Cardiovascular Discovery Center, Temple University, Lewis Katz School of Medicine, Philadelphia, PA, USA
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7
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Deng H, Zhang J, Wang Y, Joshi D, Pi X, De Val S, Schwartz MA. A KLF2-BMPER-Smad1/5 checkpoint regulates high fluid shear stress-mediated artery remodeling. NATURE CARDIOVASCULAR RESEARCH 2024; 3:785-798. [PMID: 39196179 DOI: 10.1038/s44161-024-00496-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/29/2024] [Indexed: 08/29/2024]
Abstract
Vascular remodeling to match arterial diameter to tissue requirements commonly fails in ischemic disease. Endothelial cells sense fluid shear stress (FSS) from blood flow to maintain FSS within a narrow range in healthy vessels. Thus, high FSS induces vessel outward remodeling, but mechanisms are poorly understood. We previously reported that Smad1/5 is maximally activated at physiological FSS. Smad1/5 limits Akt activation, suggesting that inhibiting Smad1/5 may facilitate outward remodeling. Here we report that high FSS suppresses Smad1/5 by elevating KLF2, which induces the bone morphogenetic protein (BMP) pathway inhibitor, BMP-binding endothelial regulator (BMPER), thereby de-inhibiting Akt. In mice, surgically induced high FSS elevated BMPER expression, inactivated Smad1/5 and induced vessel outward remodeling. Endothelial BMPER deletion impaired blood flow recovery and vascular remodeling. Blocking endothelial cell Smad1/5 activation with BMP9/10 blocking antibodies improved vascular remodeling in mouse models of type 1 and type 2 diabetes. Suppression of Smad1/5 is thus a potential therapeutic approach for ischemic disease.
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Affiliation(s)
- Hanqiang Deng
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jiasheng Zhang
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Yewei Wang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Divyesh Joshi
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA
| | - Xinchun Pi
- Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Sarah De Val
- Department of Physiology, Anatomy and Genetics, Institute of Developmental and Regenerative Medicine, University of Oxford, Oxford, UK
| | - Martin A Schwartz
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, USA.
- Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA.
- Department of Cell Biology, Yale School of Medicine, and Department of Biomedical Engineering, Yale School of Engineering, New Haven, CT, USA.
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8
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Liu Z, Tanke NT, Neal A, Yu T, Branch T, Sharma A, Cook JG, Bautch VL. Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis. Angiogenesis 2024:10.1007/s10456-024-09920-0. [PMID: 38795286 DOI: 10.1007/s10456-024-09920-0] [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: 12/21/2023] [Accepted: 04/15/2024] [Indexed: 05/27/2024]
Abstract
Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of S-phase proliferative tip cells relative to stalk cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip and stalk cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest and dynamics at the front. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.
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Affiliation(s)
- Ziqing Liu
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Natalie T Tanke
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC, USA
| | - Alexandra Neal
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tianji Yu
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tershona Branch
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Arya Sharma
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jean G Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, USA
| | - Victoria L Bautch
- Department of Biology, CB 3280, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC, USA.
- McAllister Heart Institute, The University of North Carolina, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC, USA.
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9
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Deng L, Pollmeier L, Bednarz R, Cao C, Laurette P, Wirth L, Mamazhakypov A, Bode C, Hein L, Gilsbach R, Lother A. Atlas of cardiac endothelial cell enhancer elements linking the mineralocorticoid receptor to pathological gene expression. SCIENCE ADVANCES 2024; 10:eadj5101. [PMID: 38446896 PMCID: PMC10917356 DOI: 10.1126/sciadv.adj5101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Endothelial cells play crucial roles in physiology and are increasingly recognized as therapeutic targets in cardiovascular disease. Here, we analyzed the regulatory landscape of cardiac endothelial cells by assessing chromatin accessibility, histone modifications, and 3D chromatin organization and confirmed the functional relevance of enhancer-promoter interactions by CRISPRi-mediated enhancer silencing. We used this dataset to explore mechanisms of transcriptional regulation in cardiovascular disease and compared six different experimental models of heart failure, hypertension, or diabetes. Enhancers that regulate gene expression in diseased endothelial cells were enriched with binding sites for a distinct set of transcription factors, including the mineralocorticoid receptor (MR), a known drug target in heart failure and hypertension. For proof of concept, we applied endothelial cell-specific MR deletion in mice to confirm MR-dependent gene expression and predicted direct MR target genes. Overall, we have compiled here a comprehensive atlas of cardiac endothelial cell enhancer elements that provides insight into the role of transcription factors in cardiovascular disease.
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Affiliation(s)
- Lisa Deng
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Cardiovascular Research Track, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Luisa Pollmeier
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Rebecca Bednarz
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Can Cao
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Patrick Laurette
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Luisa Wirth
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Argen Mamazhakypov
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christine Bode
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental Cardiology, Heidelberg University Hospital, Heidelberg, Germany
- DZHK (German Center of Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Achim Lother
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Interdisciplinary Medical Intensive Care, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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10
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Liu Z, Tanke NT, Neal A, Yu T, Branch T, Cook JG, Bautch VL. Differential endothelial cell cycle status in postnatal retinal vessels revealed using a novel PIP-FUCCI reporter and zonation analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574239. [PMID: 38249517 PMCID: PMC10798646 DOI: 10.1101/2024.01.04.574239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Cell cycle regulation is critical to blood vessel formation and function, but how the endothelial cell cycle integrates with vascular regulation is not well-understood, and available dynamic cell cycle reporters do not precisely distinguish all cell cycle stage transitions in vivo. Here we characterized a recently developed improved cell cycle reporter (PIP-FUCCI) that precisely delineates S phase and the S/G2 transition. Live image analysis of primary endothelial cells revealed predicted temporal changes and well-defined stage transitions. A new inducible mouse cell cycle reporter allele was selectively expressed in postnatal retinal endothelial cells upon Cre-mediated activation and predicted endothelial cell cycle status. We developed a semi-automated zonation program to define endothelial cell cycle status in spatially defined and developmentally distinct retinal areas and found predicted cell cycle stage differences in arteries, veins, and remodeled and angiogenic capillaries. Surprisingly, the predicted dearth of proliferative tip cells at the vascular front was accompanied by an unexpected enrichment for endothelial tip cells in G2, suggesting G2 stalling as a contribution to tip-cell arrest. Thus, this improved reporter precisely defines endothelial cell cycle status in vivo and reveals novel G2 regulation that may contribute to unique aspects of blood vessel network expansion.
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Affiliation(s)
- Ziqing Liu
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Natalie T Tanke
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC USA
| | - Alexandra Neal
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Tianji Yu
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Tershona Branch
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
| | - Jean G Cook
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC USA
| | - Victoria L Bautch
- Department of Biology, The University of North Carolina, Chapel Hill, NC USA
- Curriculum in Cell Biology and Physiology, The University of North Carolina, Chapel Hill, NC USA
- McAllister Heart Institute, The University of North Carolina, Chapel Hill, NC USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC USA
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11
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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: 3] [Impact Index Per Article: 3.0] [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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12
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McCracken IR, Baker AH, Smart N, De Val S. Transcriptional regulators of arterial and venous identity in the developing mammalian embryo. CURRENT OPINION IN PHYSIOLOGY 2023; 35:None. [PMID: 38328689 PMCID: PMC10844100 DOI: 10.1016/j.cophys.2023.100691] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The complex and hierarchical vascular network of arteries, veins, and capillaries features considerable endothelial heterogeneity, yet the regulatory pathways directing arteriovenous specification, differentiation, and identity are still not fully understood. Recent advances in analysis of endothelial-specific gene-regulatory elements, single-cell RNA sequencing, and cell lineage tracing have both emphasized the importance of transcriptional regulation in this process and shed considerable light on the mechanism and regulation of specification within the endothelium. In this review, we discuss recent advances in our understanding of how endothelial cells acquire arterial and venous identity and the role different transcription factors play in this process.
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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
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Andrew H Baker
- Centre for Cardiovascular Science, University of Edinburgh, Edinburgh EH16 4TJ, United Kingdom
| | - Nicola Smart
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
| | - Sarah De Val
- Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX3 7TY, United Kingdom
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13
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Michaeli JC, Albers S, de la Torre C, Schreiner Y, Faust S, Michaeli T, Michaeli DT, Liying A, Krämer BK, Stach K, Yard BA. Gene regulation for inflammation and inflammation resolution differs between umbilical arterial and venous endothelial cells. Sci Rep 2023; 13:16159. [PMID: 37758738 PMCID: PMC10533526 DOI: 10.1038/s41598-023-43142-6] [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: 05/27/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Systemic inflammation affects the whole vasculature, yet whether arterial and venous endothelial cells differ in their abilities to mediate inflammation and to return to homeostasis after an inflammatory stimulus has not been addressed thoroughly. We assessed gene-expression profiles in isolated endothelial cells from human umbilical arteries (HUAEC) or veins (HUVEC) under basal conditions, after TNF-α stimulation and various time points after TNF-α removal to allow reinstatement of homeostasis. TNF-α regulates the expression of different sets of transcripts that are significantly changed only in HUAEC, only in HUVEC or changed in both. We identified three types of gene regulation, i.e. genes that were significantly regulated after 24 h of TNF-α stimulation but no longer when TNF-α was removed (homeostatic regulation), genes that maintained significantly regulated after TNF-α removal (not homeostatic regulation) and genes that were only significantly regulated when TNF-α was removed (post-regulation). HUAEC and HUVEC quantitatively differed in these types of gene regulation, with relatively more genes being post-regulated in HUAEC. In conclusion our data demonstrate that HUAEC and HUVEC respond intrinsically different to an inflammatory insult. Whether this holds true for all endothelial cells and its relevance for inflammatory insults in different organs during systemic inflammation warrants further studies.
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Affiliation(s)
- Julia Caroline Michaeli
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- Department of Obstetrics and Gynecology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Sebastian Albers
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- Department of Orthopaedics and Sport Orthopaedics, School of Medicine, Klinikum Rechts Der Isar, Technical University of Munich, Munich, Germany
| | - Carolina de la Torre
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Yannick Schreiner
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Sara Faust
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Thomas Michaeli
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- DKFZ-Hector Cancer Institute, the University Medical Center Mannheim, Mannheim, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniel Tobias Michaeli
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - An Liying
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Bernhard K Krämer
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- European Center for Angioscience, Mannheim, Germany
| | - Ksenija Stach
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
- European Center for Angioscience, Mannheim, Germany
| | - Benito A Yard
- 5th Medical Department, University Hospital Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
- European Center for Angioscience, Mannheim, Germany.
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14
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Dougherty EJ, Chen LY, Awad KS, Ferreyra GA, Demirkale CY, Keshavarz A, Gairhe S, Johnston KA, Hicks ME, Sandler AB, Curran CS, Krack JM, Ding Y, Suffredini AF, Solomon MA, Elinoff JM, Danner RL. Inflammation and DKK1-induced AKT activation contribute to endothelial dysfunction following NR2F2 loss. Am J Physiol Lung Cell Mol Physiol 2023; 324:L783-L798. [PMID: 37039367 PMCID: PMC10202490 DOI: 10.1152/ajplung.00171.2022] [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: 06/02/2022] [Revised: 03/28/2023] [Accepted: 04/01/2023] [Indexed: 04/12/2023] Open
Abstract
NR2F2 is expressed in endothelial cells (ECs) and Nr2f2 knockout produces lethal cardiovascular defects. In humans, reduced NR2F2 expression is associated with cardiovascular diseases including congenital heart disease and atherosclerosis. Here, NR2F2 silencing in human primary ECs led to inflammation, endothelial-to-mesenchymal transition (EndMT), proliferation, hypermigration, apoptosis-resistance, and increased production of reactive oxygen species. These changes were associated with STAT and AKT activation along with increased production of DKK1. Co-silencing DKK1 and NR2F2 prevented NR2F2-loss-induced STAT and AKT activation and reversed EndMT. Serum DKK1 concentrations were elevated in patients with pulmonary arterial hypertension (PAH) and DKK1 was secreted by ECs in response to in vitro loss of either BMPR2 or CAV1, which are genetic defects associated with the development of PAH. In human primary ECs, NR2F2 suppressed DKK1, whereas its loss conversely induced DKK1 and disrupted endothelial homeostasis, promoting phenotypic abnormalities associated with pathologic vascular remodeling. Activating NR2F2 or blocking DKK1 may be useful therapeutic targets for treating chronic vascular diseases associated with EC dysfunction.NEW & NOTEWORTHY NR2F2 loss in the endothelial lining of blood vessels is associated with cardiovascular disease. Here, NR2F2-silenced human endothelial cells were inflammatory, proliferative, hypermigratory, and apoptosis-resistant with increased oxidant stress and endothelial-to-mesenchymal transition. DKK1 was induced in NR2F2-silenced endothelial cells, while co-silencing NR2F2 and DKK1 prevented NR2F2-loss-associated abnormalities in endothelial signaling and phenotype. Activating NR2F2 or blocking DKK1 may be useful therapeutic targets for treating vascular diseases associated with endothelial dysfunction.
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Affiliation(s)
- Edward J Dougherty
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Li-Yuan Chen
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Keytam S Awad
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Gabriela A Ferreyra
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Cumhur Y Demirkale
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Ali Keshavarz
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Salina Gairhe
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Kathryn A Johnston
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Madelyn E Hicks
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Alexis B Sandler
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Colleen S Curran
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Janell M Krack
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Yi Ding
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Anthony F Suffredini
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Michael A Solomon
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Jason M Elinoff
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert L Danner
- Clinical Center/Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland, United States
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15
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Parab S, Setten E, Astanina E, Bussolino F, Doronzo G. The tissue-specific transcriptional landscape underlines the involvement of endothelial cells in health and disease. Pharmacol Ther 2023; 246:108418. [PMID: 37088448 DOI: 10.1016/j.pharmthera.2023.108418] [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: 11/05/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023]
Abstract
Endothelial cells (ECs) that line vascular and lymphatic vessels are being increasingly recognized as important to organ function in health and disease. ECs participate not only in the trafficking of gases, metabolites, and cells between the bloodstream and tissues but also in the angiocrine-based induction of heterogeneous parenchymal cells, which are unique to their specific tissue functions. The molecular mechanisms regulating EC heterogeneity between and within different tissues are modeled during embryogenesis and become fully established in adults. Any changes in adult tissue homeostasis induced by aging, stress conditions, and various noxae may reshape EC heterogeneity and induce specific transcriptional features that condition a functional phenotype. Heterogeneity is sustained via specific genetic programs organized through the combinatory effects of a discrete number of transcription factors (TFs) that, at the single tissue-level, constitute dynamic networks that are post-transcriptionally and epigenetically regulated. This review is focused on outlining the TF-based networks involved in EC specialization and physiological and pathological stressors thought to modify their architecture.
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Affiliation(s)
- Sushant Parab
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elisa Setten
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Elena Astanina
- Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
| | - Federico Bussolino
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, IT, Italy; Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Torino, IT, Italy
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16
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Anderson JR, Morin EE, Brayer KJ, Salbato S, Gonzalez Bosc LV, Kanagy NL, Naik JS. Single-cell transcriptomic heterogeneity between conduit and resistance mesenteric arteries in rats. Physiol Genomics 2023; 55:179-193. [PMID: 36912534 PMCID: PMC10085562 DOI: 10.1152/physiolgenomics.00126.2022] [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: 08/11/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The endothelium contains morphologically similar cells throughout the vasculature, but individual cells along the length of a single vascular tree or in different regional circulations function dissimilarly. When observations made in large arteries are extrapolated to explain the function of endothelial cells (ECs) in the resistance vasculature, only a fraction of these observations are consistent between artery sizes. To what extent endothelial (EC) and vascular smooth muscle cells (VSMCs) from different arteriolar segments of the same tissue differ phenotypically at the single-cell level remains unknown. Therefore, single-cell RNA-seq (10x Genomics) was performed using a 10X Genomics Chromium system. Cells were enzymatically digested from large (>300 µm) and small (<150 µm) mesenteric arteries from nine adult male Sprague-Dawley rats, pooled to create six samples (3 rats/sample, 3 samples/group). After normalized integration, the dataset was scaled before unsupervised cell clustering and cluster visualization using UMAP plots. Differential gene expression analysis allowed us to infer the biological identity of different clusters. Our analysis revealed 630 and 641 differentially expressed genes (DEGs) between conduit and resistance arteries for ECs and VSMCs, respectively. Gene ontology analysis (GO-Biological Processes, GOBP) of scRNA-seq data discovered 562 and 270 pathways for ECs and VSMCs, respectively, that differed between large and small arteries. We identified eight and seven unique ECs and VSMCs subpopulations, respectively, with DEGs and pathways identified for each cluster. These results and this dataset allow the discovery and support of novel hypotheses needed to identify mechanisms that determine the phenotypic heterogeneity between conduit and resistance arteries.
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Affiliation(s)
- Jacob R Anderson
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Emily E Morin
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Kathryn J Brayer
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Sophia Salbato
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Laura V Gonzalez Bosc
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Nancy L Kanagy
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
| | - Jay S Naik
- Department of Cell Biology and Physiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States
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17
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Burr SP, Klimm F, Glynos A, Prater M, Sendon P, Nash P, Powell CA, Simard ML, Bonekamp NA, Charl J, Diaz H, Bozhilova LV, Nie Y, Zhang H, Frison M, Falkenberg M, Jones N, Minczuk M, Stewart JB, Chinnery PF. Cell lineage-specific mitochondrial resilience during mammalian organogenesis. Cell 2023; 186:1212-1229.e21. [PMID: 36827974 DOI: 10.1016/j.cell.2023.01.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/28/2022] [Accepted: 01/26/2023] [Indexed: 02/25/2023]
Abstract
Mitochondrial activity differs markedly between organs, but it is not known how and when this arises. Here we show that cell lineage-specific expression profiles involving essential mitochondrial genes emerge at an early stage in mouse development, including tissue-specific isoforms present before organ formation. However, the nuclear transcriptional signatures were not independent of organelle function. Genetically disrupting intra-mitochondrial protein synthesis with two different mtDNA mutations induced cell lineage-specific compensatory responses, including molecular pathways not previously implicated in organellar maintenance. We saw downregulation of genes whose expression is known to exacerbate the effects of exogenous mitochondrial toxins, indicating a transcriptional adaptation to mitochondrial dysfunction during embryonic development. The compensatory pathways were both tissue and mutation specific and under the control of transcription factors which promote organelle resilience. These are likely to contribute to the tissue specificity which characterizes human mitochondrial diseases and are potential targets for organ-directed treatments.
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Affiliation(s)
- Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Klimm
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Department of Mathematics, Imperial College London, London, UK; EPSRC Centre for Mathematics of Precision Healthcare, Imperial College, London, UK; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, D-14195 Berlin, Germany; Department of Computer Science, Freie Universität Berlin, Arnimallee 3, D-14195 Berlin, Germany
| | - Angelos Glynos
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Malwina Prater
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Pamella Sendon
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Pavel Nash
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Nina A Bonekamp
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Department of Neuroanatomy, Mannheim Centre for Translational Neuroscience (MCTN), Medical Faculty Mannheim/Heidelberg University, Heidelberg, Germany
| | - Julia Charl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, Germany
| | - Hector Diaz
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Lyuba V Bozhilova
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Yu Nie
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Haixin Zhang
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Michele Frison
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Nick Jones
- Department of Mathematics, Imperial College London, London, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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18
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Yan Y, Tian J, Wang Y, Li Y, Zhang C, Zhang S, Lin P, Peng R, Zhao C, Zhuang L, Lai B, Zhou L, Zhang G, Li H. Transcriptomic Heterogeneity of Skin Across Different Anatomic Sites. J Invest Dermatol 2023; 143:398-407.e5. [PMID: 36122800 DOI: 10.1016/j.jid.2022.08.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/05/2022] [Accepted: 08/26/2022] [Indexed: 02/05/2023]
Abstract
Multiomic studies, including RNA sequencing, single-cell RNA sequencing, and epigenomics, can provide insight into the connection between anatomically heterogeneous gene expression profile of the skin and dermatoses-predisposed sites, in which RNA sequencing is essential. Therefore, in this study, 159 skin samples collected mainly from discarded normal skin tissue during surgical treatment for benign skin tumors were used for RNA sequencing. On the basis of cluster analysis, the skin was divided into four regions, with each region showing specific physiological characteristics through differentially expressed gene analysis. The results showed that the head and neck region, perineum, and palmoplantar area were closely associated with lipid metabolism, hormone metabolism, blood circulation, and related neural regulation, respectively. Transcription factor enrichment indicated that different regions were associated with the development of adjacent tissues. Specifically, the head and neck region, trunk and extremities, perineum, and palmoplantar area were associated with the central nervous, axial, urogenital, and vascular systems, respectively. The results were imported into an open website (https://dermvis.github.io/) for retrieval. Our transcriptomic data elucidated that human skin exhibits transcriptomic heterogeneity reflecting physiological and developmental variation at different anatomic sites and provided guidance for further studies on skin development and dermatoses predisposed sites.
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Affiliation(s)
- Yicen Yan
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Jie Tian
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Yang Wang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Yurong Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Chong Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Shenxi Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Pingping Lin
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Rui Peng
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Chunxia Zhao
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China
| | - Le Zhuang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Department of Dermatology, Qilu Hospital of Shandong University, Jinan, China
| | - Binbin Lai
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Institute of Medical Technology, Peking University Health Science Center, Beijing, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Liang Zhou
- National Institute of Health Data Science, Peking University, Beijing, China
| | - Guohong Zhang
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; Pathology Department, Shantou University Medical College, Guangdong, China
| | - Hang Li
- Department of Dermatology and Venereology, Peking University First Hospital, Beijing, China; National Clinical Research Center for Skin and Immune Diseases, Beijing, China; Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China; NMPA Key Laboratory for Quality Control and Evaluation of Cosmetics, Beijing, China.
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19
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Abstract
Vascular endothelial cells form the inner layer of blood vessels where they have a key role in the development and maintenance of the functional circulatory system and provide paracrine support to surrounding non-vascular cells. Technical advances in the past 5 years in single-cell genomics and in in vivo genetic labelling have facilitated greater insights into endothelial cell development, plasticity and heterogeneity. These advances have also contributed to a new understanding of the timing of endothelial cell subtype differentiation and its relationship to the cell cycle. Identification of novel tissue-specific gene expression patterns in endothelial cells has led to the discovery of crucial signalling pathways and new interactions with other cell types that have key roles in both tissue maintenance and disease pathology. In this Review, we describe the latest findings in vascular endothelial cell development and diversity, which are often supported by large-scale, single-cell studies, and discuss the implications of these findings for vascular medicine. In addition, we highlight how techniques such as single-cell multimodal omics, which have become increasingly sophisticated over the past 2 years, are being utilized to study normal vascular physiology as well as functional perturbations in disease.
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Affiliation(s)
- Emily Trimm
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kristy Red-Horse
- Department of Biology, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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20
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Wang Y, Huang Z, Sun M, Huang W, Xia L. ETS transcription factors: Multifaceted players from cancer progression to tumor immunity. Biochim Biophys Acta Rev Cancer 2023; 1878:188872. [PMID: 36841365 DOI: 10.1016/j.bbcan.2023.188872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/18/2023] [Accepted: 01/28/2023] [Indexed: 02/26/2023]
Abstract
The E26 transformation specific (ETS) family comprises 28 transcription factors, the majority of which are involved in tumor initiation and development. Serving as a group of functionally heterogeneous gene regulators, ETS factors possess a structurally conserved DNA-binding domain. As one of the most prominent families of transcription factors that control diverse cellular functions, ETS activation is modulated by multiple intracellular signaling pathways and post-translational modifications. Disturbances in ETS activity often lead to abnormal changes in oncogenicity, including cancer cell survival, growth, proliferation, metastasis, genetic instability, cell metabolism, and tumor immunity. This review systematically addresses the basics and advances in studying ETS factors, from their tumor relevance to clinical translational utility, with a particular focus on elucidating the role of ETS family in tumor immunity, aiming to decipher the vital role and clinical potential of regulation of ETS factors in the cancer field.
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Affiliation(s)
- Yufei Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Zhao Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Wenjie Huang
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei 430030, China.
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China.
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21
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Ye S, Wang C, Xu Z, Lin H, Wan X, Yu Y, Adhicary S, Zhang JZ, Zhou Y, Liu C, Alonzo M, Bi J, Ramirez-Navarro A, Deschenes I, Ma Q, Garg V, Wu JC, Zhao MT. Impaired Human Cardiac Cell Development due to NOTCH1 Deficiency. Circ Res 2023; 132:187-204. [PMID: 36583388 PMCID: PMC9852089 DOI: 10.1161/circresaha.122.321398] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND NOTCH1 pathogenic variants are implicated in multiple types of congenital heart defects including hypoplastic left heart syndrome, where the left ventricle is underdeveloped. It is unknown how NOTCH1 regulates human cardiac cell lineage determination and cardiomyocyte proliferation. In addition, mechanisms by which NOTCH1 pathogenic variants lead to ventricular hypoplasia in hypoplastic left heart syndrome remain elusive. METHODS CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 genome editing was utilized to delete NOTCH1 in human induced pluripotent stem cells. Cardiac differentiation was carried out by sequential modulation of WNT signaling, and NOTCH1 knockout and wild-type differentiating cells were collected at day 0, 2, 5, 10, 14, and 30 for single-cell RNA-seq. RESULTS Human NOTCH1 knockout induced pluripotent stem cells are able to generate functional cardiomyocytes and endothelial cells, suggesting that NOTCH1 is not required for mesoderm differentiation and cardiovascular development in vitro. However, disruption of NOTCH1 blocks human ventricular-like cardiomyocyte differentiation but promotes atrial-like cardiomyocyte generation through shortening the action potential duration. NOTCH1 deficiency leads to defective proliferation of early human cardiomyocytes, and transcriptomic analysis indicates that pathways involved in cell cycle progression and mitosis are downregulated in NOTCH1 knockout cardiomyocytes. Single-cell transcriptomic analysis reveals abnormal cell lineage determination of cardiac mesoderm, which is manifested by the biased differentiation toward epicardial and second heart field progenitors at the expense of first heart field progenitors in NOTCH1 knockout cell populations. CONCLUSIONS NOTCH1 is essential for human ventricular-like cardiomyocyte differentiation and proliferation through balancing cell fate determination of cardiac mesoderm and modulating cell cycle progression. Because first heart field progenitors primarily contribute to the left ventricle, we speculate that pathogenic NOTCH1 variants lead to biased differentiation of first heart field progenitors, blocked ventricular-like cardiomyocyte differentiation, and defective cardiomyocyte proliferation, which collaboratively contribute to left ventricular hypoplasia in hypoplastic left heart syndrome.
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Affiliation(s)
- Shiqiao Ye
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Cankun Wang
- Department of Biomedical Informatics (C.W., Q.M.), The Ohio State University College of Medicine, Columbus, OH
| | - Zhaohui Xu
- Department of Pediatrics (Z.X., V.G., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH.,Center for Vaccines and Immunity, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (Z.X.)
| | - Hui Lin
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Xiaoping Wan
- Department of Physiology and Cell Biology (X.W., A.R.-N., I.D., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH
| | - Yang Yu
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Subhodip Adhicary
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Joe Z. Zhang
- Stanford Cardiovascular Institute (J.Z.Z., Y.Z., C.L., J.C.W.), Stanford University School of Medicine, Stanford, CA.,Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, China (J.Z.Z.)
| | - Yang Zhou
- Stanford Cardiovascular Institute (J.Z.Z., Y.Z., C.L., J.C.W.), Stanford University School of Medicine, Stanford, CA
| | - Chun Liu
- Stanford Cardiovascular Institute (J.Z.Z., Y.Z., C.L., J.C.W.), Stanford University School of Medicine, Stanford, CA
| | - Matthew Alonzo
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Jianli Bi
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.)
| | - Angelina Ramirez-Navarro
- Department of Physiology and Cell Biology (X.W., A.R.-N., I.D., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH
| | - Isabelle Deschenes
- Department of Physiology and Cell Biology (X.W., A.R.-N., I.D., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH
| | - Qin Ma
- Department of Biomedical Informatics (C.W., Q.M.), The Ohio State University College of Medicine, Columbus, OH
| | - Vidu Garg
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,Department of Pediatrics (Z.X., V.G., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH
| | - Joseph C. Wu
- Stanford Cardiovascular Institute (J.Z.Z., Y.Z., C.L., J.C.W.), Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Department of Medicine (J.C.W.), Stanford University School of Medicine, Stanford, CA.,Department of Radiology (J.C.W.), Stanford University School of Medicine, Stanford, CA
| | - Ming-Tao Zhao
- Center for Cardiovascular Research, The Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH (S.Y., H.L., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,The Heart Center, Nationwide Children’s Hospital, Columbus, OH (S.Y., Y.Y., S.A., M.A., J.B., V.G., M.-T.Z.).,Department of Pediatrics (Z.X., V.G., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH.,Department of Physiology and Cell Biology (X.W., A.R.-N., I.D., M.-T.Z.), The Ohio State University College of Medicine, Columbus, OH
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22
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Sun H, Wang H, Zhang W, Mao H, Li B. Single-cell RNA sequencing reveals resident progenitor and vascularization-associated cell subpopulations in rat annulus fibrosus. J Orthop Translat 2022; 38:256-267. [PMID: 36568849 PMCID: PMC9758498 DOI: 10.1016/j.jot.2022.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/08/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Abstract
Background One of the main causes of low back pain is intervertebral disc degeneration (IDD). Annulus fibrosus (AF) is important for the integrity and functions of the intervertebral disc (IVD). However, the resident functional cell components such as progenitors and vascularization-associated cells in AF are yet to be fully identified. Purpose Identification of functional AF cell subpopulations including resident progenitors and vascularization-associated cells. Methods In this study, the single-cell RNA sequencing data of rat IVDs from a public database were analyzed using Seurat for cell clustering, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for functional analysis, StemID for stem cell identification, Monocle and RNA velocity for pseudotime differentiation trajectory validation, single-cell regulatory network inference and clustering (SCENIC) for gene regulatory network (GRN) analysis, and CellChat for cell-cell interaction analysis. Immunostaining on normal and degenerated rat IVDs, as well as human AF, was used for validations. Results From the data analysis, seven AF cell clusters were identified, including two newly discovered functional clusters, the Grem1 + subpopulation and the Lum + subpopulation. The Grem1 + subpopulation had progenitor characteristics, while the Lum + subpopulation was associated with vascularization during IDD. The GRN analysis showed that Sox9 and Id1 were among the key regulators in the Grem1 + subpopulation, and Nr2f2 and Creb5 could be responsible for the vascularization function in the Lum + subpopulation. Cell-cell interaction analysis revealed highly regulated cellular communications between these cells, and multiple signaling networks including PDGF and MIF signaling pathways were involved in the interactions. Conclusions Our results revealed two new functional AF cell subpopulations, with stemness and vascularization induction potential, respectively. The Translational potential of this article These findings complement our knowledge about IVDs, especially the AF, and in return provide potential cell source and regulation targets for IDD treatment and tissue repair. The existence of the cell subpopulations was also validated in human AF, which strengthen the clinical relevance of the findings.
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Affiliation(s)
- Heng Sun
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Huan Wang
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Weidong Zhang
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China
| | - Haijiao Mao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang, China,Corresponding author.
| | - Bin Li
- Department of Orthopaedic Surgery, Orthopedic Institute, The First Affiliated Hospital, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, China,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, China,Corresponding author. 178 Ganjiang Rd, Rm 201 Bldg 18, Soochow University (North Campus), Suzhou, Jiangsu, 215007, China.
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23
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NR2F2 Regulates Cell Proliferation and Immunomodulation in Whartons’ Jelly Stem Cells. Genes (Basel) 2022; 13:genes13081458. [PMID: 36011369 PMCID: PMC9408747 DOI: 10.3390/genes13081458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/20/2022] Open
Abstract
(1) Background: Wharton’s Jelly stem cells (WJ-MSCs) are multipotent mesenchymal stem cells that can proliferate rapidly and have low immunogenicity. Therefore, WJ-MSCs have gained considerable attention in the fields of immunomodulation and disease treatment and have entered clinical trials for the treatment of various diseases. Therefore, it is crucial to study the underlying mechanisms of WJ-MSCs proliferation, immune regulation, and disease treatment. Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) is a transcription factor that is involved in the regulation of many different genes. However, it remains unknown how NR2F2 regulates stem cell identity in WJ-MSCs. (2) Methods: We used RNAi technology to knock down NR2F2 in WJ-MSCs, and studied the regulatory role of NR2F2 in WJ-MSCs by MTT, flow cytometry, RNA-seq, and other methods. We also utilized a co-culture system in which NR2F2-depleted WJ-MSCs with MH7A and HCT116/HepG2 were used to investigate the role of NR2F2 in immunomodulation and the inhibition of cancer cell growth. (3) Results: NR2F2 knockdown resulted in decreased expressions of Cyclin D1 and CDK4, slower cell proliferation, and increased expressions of IL6 and IL8. Furthermore, Cyclin D1, CDK4, and inflammatory factors were increased in human rheumatoid fibroblast-like synoviocyte line MH7A if co-cultured with NR2F2 depleted WJ-MSCs. In addition, we observed increased p53, decreased BCL-2, and increased cell apoptosis in liver cancer cell line HepG2 if co-cultured with NR2F2-depleted WJ-MSCs. (4) Conclusions: NR2F2 not only plays an important role in the cell cycle and immune regulation of WJ-MSCs but also has potential effects on the WJ-MSCs treatment of related diseases.
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24
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Do TH, Ma F, Andrade PR, Teles R, de Andrade Silva BJ, Hu C, Espinoza A, Hsu JE, Cho CS, Kim M, Xi J, Xing X, Plazyo O, Tsoi LC, Cheng C, Kim J, Bryson BD, O'Neill AM, Colonna M, Gudjonsson JE, Klechevsky E, Lee JH, Gallo RL, Bloom BR, Pellegrini M, Modlin RL. TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Sci Immunol 2022; 7:eabo2787. [PMID: 35867799 PMCID: PMC9400695 DOI: 10.1126/sciimmunol.abo2787] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Acne affects 1 in 10 people globally, often resulting in disfigurement. The disease involves excess production of lipids, particularly squalene, increased growth of Cutibacterium acnes, and a host inflammatory response with foamy macrophages. By combining single-cell and spatial RNA sequencing as well as ultrahigh-resolution Seq-Scope analyses of early acne lesions on back skin, we identified TREM2 macrophages expressing lipid metabolism and proinflammatory gene programs in proximity to hair follicle epithelium expressing squalene epoxidase. We established that the addition of squalene induced differentiation of TREM2 macrophages in vitro, which were unable to kill C. acnes. The addition of squalene to macrophages inhibited induction of oxidative enzymes and scavenged oxygen free radicals, providing an explanation for the efficacy of topical benzoyl peroxide in the clinical treatment of acne. The present work has elucidated the mechanisms by which TREM2 macrophages and unsaturated lipids, similar to their involvement in atherosclerosis, may contribute to the pathogenesis of acne.
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Affiliation(s)
- Tran H Do
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences-The Collaboratory, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Priscila R Andrade
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Rosane Teles
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Bruno J de Andrade Silva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Chanyue Hu
- Institute for Quantitative and Computational Biosciences-The Collaboratory, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alejandro Espinoza
- Institute for Quantitative and Computational Biosciences-The Collaboratory, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jer-En Hsu
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chun-Seok Cho
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Myungjin Kim
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jingyue Xi
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Xianying Xing
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olesya Plazyo
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol Cheng
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Jenny Kim
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA
| | - Bryan D Bryson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alan M O'Neill
- Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Eynav Klechevsky
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Richard L Gallo
- Department of Dermatology, University of California San Diego, La Jolla, CA 92093, USA
| | - Barry R Bloom
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matteo Pellegrini
- Institute for Quantitative and Computational Biosciences-The Collaboratory, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles,, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
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25
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Finding and Verifying Enhancers for Endothelial-Expressed Genes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2441:351-368. [PMID: 35099751 DOI: 10.1007/978-1-0716-2059-5_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Identification and analysis of enhancers for endothelial-expressed genes can provide crucial information regarding their upstream transcriptional regulators. However, enhancer identification can be challenging, particularly for people with limited access or experience of bioinformatics, and transgenic analysis of enhancer activity patterns can be prohibitively expensive. Here we describe how to use publicly available datasets displayed on the UCSC Genome Browser to identify putative endothelial enhancers for mammalian genes. Furthermore, we detail how to utilize mosaic Tol2-mediated transgenesis in zebrafish to verify whether a putative enhancer is capable of directing endothelial-specific patterns of gene expression.
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26
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Chen ZB, Liu X, Chen AT. "Enhancing" mechanosensing: Enhancers and enhancer-derived long non-coding RNAs in endothelial response to flow. CURRENT TOPICS IN MEMBRANES 2021; 87:153-169. [PMID: 34696884 DOI: 10.1016/bs.ctm.2021.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Endothelial cells (ECs), uniquely localized and strategically forming the inner lining of vascular wall, constitute the largest cell surface by area in the human body. The dynamic sensing and response of ECs to mechanical cues, especially shear stress, is crucial for maintenance of vascular homeostasis. It is well recognized that different flow patterns associated with atheroprotective vs atheroprone regions in the arterial tree, result in distinct EC functional phenotypes with differential transcriptome profiles. Mounting evidence has demonstrated an integrative and essential regulatory role of non-coding genome in EC biology. In particular, recent studies have begun to reveal the importance of enhancers and enhancer-derived transcripts in flow-regulated EC gene expression and function. In this minireview, we summarize studies in this area and discuss examples in support of the emerging importance of enhancers and enhancer(-derived) long non-coding RNAs (elncRNAs) in EC mechanosensing, with a focus on flow-responsive EC transcription. Finally, we will provide perspective and discuss standing questions to elucidate the role of these novel regulators in EC mechanobiology.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Duarte, CA, United States; Irell and Manella Graduate School of Biological Sciences, Duarte, CA, United States.
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, Duarte, CA, United States
| | - Aleysha T Chen
- Department of Bioengineering, University of California, Berkeley, CA, United States
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27
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Sissaoui S, Egginton S, Ting L, Ahmed A, Hewett PW. Hyperglycaemia up-regulates placental growth factor (PlGF) expression and secretion in endothelial cells via suppression of PI3 kinase-Akt signalling and activation of FOXO1. Sci Rep 2021; 11:16344. [PMID: 34381074 PMCID: PMC8357836 DOI: 10.1038/s41598-021-95511-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/13/2021] [Indexed: 01/13/2023] Open
Abstract
Placenta growth factor (PlGF) is a pro-inflammatory angiogenic mediator that promotes many pathologies including diabetic complications and atherosclerosis. Widespread endothelial dysfunction precedes the onset of these conditions. As very little is known of the mechanism(s) controlling PlGF expression in pathology we investigated the role of hyperglycaemia in the regulation of PlGF production in endothelial cells. Hyperglycaemia stimulated PlGF secretion in cultured primary endothelial cells, which was suppressed by IGF-1-mediated PI3K/Akt activation. Inhibition of PI3K activity resulted in significant PlGF mRNA up-regulation and protein secretion. Similarly, loss or inhibition of Akt activity significantly increased basal PlGF expression and prevented any further PlGF secretion in hyperglycaemia. Conversely, constitutive Akt activation blocked PlGF secretion irrespective of upstream PI3K activity demonstrating that Akt is a central regulator of PlGF expression. Knock-down of the Forkhead box O-1 (FOXO1) transcription factor, which is negatively regulated by Akt, suppressed both basal and hyperglycaemia-induced PlGF secretion, whilst FOXO1 gain-of-function up-regulated PlGF in vitro and in vivo. FOXO1 association to a FOXO binding sequence identified in the PlGF promoter also increased in hyperglycaemia. This study identifies the PI3K/Akt/FOXO1 signalling axis as a key regulator of PlGF expression and unifying pathway by which PlGF may contribute to common disorders characterised by endothelial dysfunction, providing a target for therapy.
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Affiliation(s)
- Samir Sissaoui
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Arima Genomics, 6404 Nancy Ridge Drive, San Diego, CA, 92121, USA
| | - Stuart Egginton
- Multidisciplinary Cardiovascular Research Centre, University of Leeds, Leeds, LS2 9JT, UK
| | - Ling Ting
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Asif Ahmed
- MyrZyme Therapeutics Ltd, Faraday Wharf, Innovation Birmingham Campus, Holt Street, Birmingham, B4 4BB, UK
- School of Health Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Peter W Hewett
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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28
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Harada Y, Tanaka T, Arai Y, Isomoto Y, Nakano A, Nakao S, Urasaki A, Watanabe Y, Kawamura T, Nakagawa O. ETS-dependent enhancers for endothelial-specific expression of serum/glucocorticoid-regulated kinase 1 during mouse embryo development. Genes Cells 2021; 26:611-626. [PMID: 34081835 DOI: 10.1111/gtc.12874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/23/2022]
Abstract
Serum/glucocorticoid-regulated kinase 1 (SGK1) is predominantly expressed in endothelial cells of mouse embryos, and Sgk1 null mice show embryonic lethality due to impaired vascular formation. However, how the SGK1 expression is controlled in developing vasculature remains unknown. In this study, we first identified a proximal endothelial enhancer through lacZ reporter mouse analyses. The mouse Sgk1 proximal enhancer was narrowed down to the 5' region of the major transcription initiation site, while a human corresponding region possessed relatively weak activity. We then searched for distal enhancer candidates using in silico analyses of publicly available databases for DNase accessibility, RNA polymerase association and chromatin modification. A region approximately 500 kb distant from the human SGK1 gene was conserved in the mouse, and the mouse and human genomic fragments drove transcription restricted to embryonic endothelial cells. Minimal fragments of both proximal and distal enhancers had consensus binding elements for the ETS transcription factors, which were essential for the responsiveness to ERG, FLI1 and ETS1 proteins in luciferase assays and the endothelial lacZ reporter expression in mouse embryos. These results suggest that endothelial SGK1 expression in embryonic vasculature is maintained through at least two ETS-regulated enhancers located in the proximal and distal regions.
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Affiliation(s)
- Yukihiro Harada
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Toru Tanaka
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yuji Arai
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan.,Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yoshie Isomoto
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Atsushi Nakano
- Laboratory of Animal Experiment and Medical Management, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Shu Nakao
- Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Akihiro Urasaki
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Yusuke Watanabe
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | - Teruhisa Kawamura
- Laboratory of Stem Cell & Regenerative Medicine, Department of Biomedical Sciences, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
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29
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Krause BJ. Novel insights for the role of nitric oxide in placental vascular function during and beyond pregnancy. J Cell Physiol 2021; 236:7984-7999. [PMID: 34121195 DOI: 10.1002/jcp.30470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 01/02/2023]
Abstract
More than 30 years have passed since endothelial nitric oxide synthesis was described using the umbilical artery and vein endothelium. That seminal report set the cornerstone for unveiling the molecular aspects of endothelial function. In parallel, the understanding of placental physiology has gained growing interest, due to its crucial role in intrauterine development, with considerable long-term health consequences. This review discusses the evidence for nitric oxide (NO) as a critical player of placental development and function, with a special focus on endothelial nitric oxide synthase (eNOS) vascular effects. Also, the regulation of eNOS-dependent vascular responses in normal pregnancy and pregnancy-related diseases and their impact on prenatal and postnatal vascular health are discussed. Recent and compelling evidence has reinforced that eNOS regulation results from a complex network of processes, with novel data concerning mechanisms such as mechano-sensing, epigenetic, posttranslational modifications, and the expression of NO- and l-arginine-related pathways. In this regard, most of these mechanisms are expressed in an arterial-venous-specific manner and reflect traits of the fetal systemic circulation. Several studies using umbilical endothelial cells are not aimed to understand placental function but general endothelial function, reinforcing the influence of the placenta on general knowledge in physiology.
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Affiliation(s)
- Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
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30
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Vega-Tapia F, Peñaloza E, Krause BJ. Specific arterio-venous transcriptomic and ncRNA-RNA interactions in human umbilical endothelial cells: A meta-analysis. iScience 2021; 24:102675. [PMID: 34222842 PMCID: PMC8243012 DOI: 10.1016/j.isci.2021.102675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 01/06/2023] Open
Abstract
Whether arterial-venous differences of primary endothelial cells commonly used for vascular research are preserved in vitro remains under debate. To address this issue, a meta-analysis of Affymetrix transcriptomic data sets from human umbilical artery (HUAECs) and vein (HUVEC) endothelial cells was performed. The meta-analysis showed 2,742 transcripts differentially expressed (false discovery rate <0.05), of which 78% were downregulated in HUVECs. Comparisons with RNA-seq data sets showed high levels of agreement and correlation (p < 0.0001), identifying 84 arterial-venous identity markers. Functional analysis revealed enrichment of key vascular processes in HUAECs/HUVECs, including nitric oxide- (NO) and hypoxia-related genes, as well as differences in miRNA- and ncRNA-mRNA interaction profiles. A proof of concept of these findings in primary cells exposed to hypoxia in vitro and in vivo confirmed the arterial-venous differences in NO-related genes and miRNAs. Altogether, these data defined a cross-platform arterial-venous transcript profile for cultured HUAEC-HUVEC and support a preserved identity involving key vascular pathways post-transcriptionally regulated in vitro. Transcriptional differences among HUAEC and HUVEC are preserved in culture These differences occur even after correcting for experimental conditions The heterogenous regulation affects NO- and hypoxia-related genes Cell-specific ncRNA/mRNA interactions are found
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Affiliation(s)
- Fabian Vega-Tapia
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
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31
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Neal A, Nornes S, Louphrasitthiphol P, Sacilotto N, Preston MD, Fleisinger L, Payne S, De Val S. ETS factors are required but not sufficient for specific patterns of enhancer activity in different endothelial subtypes. Dev Biol 2021; 473:1-14. [PMID: 33453264 PMCID: PMC8026812 DOI: 10.1016/j.ydbio.2021.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/16/2020] [Accepted: 01/08/2021] [Indexed: 12/11/2022]
Abstract
Correct vascular differentiation requires distinct patterns of gene expression in different subtypes of endothelial cells. Members of the ETS transcription factor family are essential for the transcriptional activation of arterial and angiogenesis-specific gene regulatory elements, leading to the hypothesis that they play lineage-defining roles in arterial and angiogenic differentiation directly downstream of VEGFA signalling. However, an alternative explanation is that ETS binding at enhancers and promoters is a general requirement for activation of many endothelial genes regardless of expression pattern, with subtype-specificity provided by additional factors. Here we use analysis of Ephb4 and Coup-TFII (Nr2f2) vein-specific enhancers to demonstrate that ETS factors are equally essential for vein, arterial and angiogenic-specific enhancer activity patterns. Further, we show that ETS factor binding at these vein-specific enhancers is enriched by VEGFA signalling, similar to that seen at arterial and angiogenic enhancers. However, while arterial and angiogenic enhancers can be activated by VEGFA in vivo, the Ephb4 and Coup-TFII venous enhancers are not, suggesting that the specificity of VEGFA-induced arterial and angiogenic enhancer activity occurs via non-ETS transcription factors. These results support a model in which ETS factors are not the primary regulators of specific patterns of gene expression in different endothelial subtypes. Vein-specific enhancers can contain essential ETS motifs. VEGFA induced an increase in ETS binding at vein, arterial and angiogenic enhancers. VEGFA stimulation cannot induce vein-specific enhancer activity.
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Affiliation(s)
- Alice Neal
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
| | - Svanhild Nornes
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Natalia Sacilotto
- Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Mark D Preston
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, EN6 3QG, United Kingdom
| | - Lucija Fleisinger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Sophie Payne
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Sarah De Val
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom; Ludwig Institute for Cancer Research Ltd, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom.
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32
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Zhao ZH, Li CY, Meng TG, Wang Y, Liu WB, Li A, Cai YJ, Hou Y, Schatten H, Wang ZB, Sun QY, Sun Q. Single-cell RNA sequencing reveals regulation of fetal ovary development in the monkey (Macaca fascicularis). Cell Discov 2020; 6:97. [PMID: 33372178 PMCID: PMC7769980 DOI: 10.1038/s41421-020-00219-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
Germ cells are vital for reproduction and heredity. However, the mechanisms underlying female germ cell development in primates, especially in late embryonic stages, remain elusive. Here, we performed single-cell RNA sequencing of 12,471 cells from whole fetal ovaries, and explored the communications between germ cells and niche cells. We depicted the two waves of oogenesis at single-cell resolution and demonstrated that progenitor theca cells exhibit similar characteristics to Leydig cells in fetal monkey ovaries. Notably, we found that ZGLP1 displays differentially expressed patterns between mouse and monkey, which is not overlapped with NANOG in monkey germ cells, suggesting its role in meiosis entry but not in activating oogenic program in primates. Furthermore, the majority of germ cell clusters that sharply express PRDM9 and SPO11 might undergo apoptosis after cyst breakdown, leading to germ cell attrition. Overall, our work provides new insights into the molecular and cellular basis of primate fetal ovary development at single-cell resolution.
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Affiliation(s)
- Zheng-Hui Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chun-Yang Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Tie-Gang Meng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, Guangdong, China
| | - Yan Wang
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Wen-Bo Liu
- Department of Reproductive Medicine Center, Third Affiliated Hospital of Guangzhou Medical University, 510150, Guangzhou, Guangdong, China
| | - Ang Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yi-Jun Cai
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yi Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, Guangdong, China.
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, CAS Key Laboratory of Primate Neurobiology, Chinese Academy of Sciences, 200031, Shanghai, China.
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33
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Luo W, Garcia-Gonzalez I, Fernández-Chacón M, Casquero-Garcia V, Sanchez-Muñoz MS, Mühleder S, Garcia-Ortega L, Andrade J, Potente M, Benedito R. Arterialization requires the timely suppression of cell growth. Nature 2020; 589:437-441. [PMID: 33299176 PMCID: PMC7116692 DOI: 10.1038/s41586-020-3018-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/15/2020] [Indexed: 01/09/2023]
Abstract
The formation of arteries is thought to occur by the induction of a highly conserved arterial genetic programme in a subset of vessels that will later experience an increase in oxygenated blood flow1,2. The initial steps of arterial specification require both the VEGF and Notch signalling pathways3–5. Here, we combine inducible genetic mosaics and transcriptomics to modulate and define the function of these signalling pathways in cell proliferation, arteriovenous differentiation and mobilization. We show that endothelial cells with high levels of VEGF or Notch signalling are intrinsically biased to mobilize and form arteries; however, they are not genetically pre-determined, and can also form veins. Mechanistically, we found that increased levels of VEGF and Notch signalling in pre-arterial capillaries suppresses MYC-dependent metabolic and cell-cycle activities, and promotes the incorporation of endothelial cells into arteries. Mosaic lineage-tracing studies showed that endothelial cells that lack the Notch–RBPJ transcriptional activator complex rarely form arteries; however, these cells regained the ability to form arteries when the function of MYC was suppressed. Thus, the development of arteries does not require the direct induction of a Notch-dependent arterial differentiation programme, but instead depends on the timely suppression of endothelial cell-cycle progression and metabolism, a process that precedes arterial mobilization and complete differentiation.
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Affiliation(s)
- Wen Luo
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Irene Garcia-Gonzalez
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Macarena Fernández-Chacón
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Verónica Casquero-Garcia
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Maria S Sanchez-Muñoz
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Severin Mühleder
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Lourdes Garcia-Ortega
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jorge Andrade
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michael Potente
- Angiogenesis & Metabolism Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Max Delbrück Center for Molecular Medicine (MDC), Berlin, Germany
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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34
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Peñaloza E, Soto-Carrasco G, Krause BJ. MiR-21-5p directly contributes to regulating eNOS expression in human artery endothelial cells under normoxia and hypoxia. Biochem Pharmacol 2020; 182:114288. [PMID: 33075314 DOI: 10.1016/j.bcp.2020.114288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Clinical conditions associated with hypoxia and oxidative stress, such as fetal growth restriction (FGR), results in endothelial dysfunction. Previous reports show that changes in eNOS expression under these conditions are tightly controlled by DNA methylation and histone posttranslational modifications. However, the contribution of an orchestrating epigenetic mechanism, such as miRNAs, on the NO-related genes expression has not been addressed. We aimed to determine the levels of miRNAs highly expressed in normal endothelial cells (EC), miR-21 and miR-126, in FGR human umbilical artery EC (HUAEC), and their effects on hypoxia-dependent regulation of both, NO-related and oxidative stress-related genes. Results were validated by transcriptome analysis of HUAEC cultured under chronic low oxygen conditions. Cultured FGR-HUAEC showed decreased hsa-miR-21, DDAH1, SOD1, and NRF2, but increased miR-126, NOX4, and eNOS levels, compared with controls. MiR-21-5p levels in FGR were associated with increased hg-miR-21 gene promoter methylation, with no changes in hg-miR-126 gene promoter methylation. HUAEC exposed to hypoxia showed a transient increase in eNOS and DDAH11, paralleled by decrease miR-21-5p levels, but no changes in miR-126-3p and the other genes under study. Transcriptome profiling showed an inverse relationship among miR-21 and several transcripts targeted by miR-21 in HUAEC exposed to hypoxia, meanwhile miR-21-5p-mimic decreased eNOS and DDAH1 transcripts stability, blocking their induction by hypoxia. Consequently, FGR programs a hypoxia-related miRNA that contributes to the regulation of the NO pathway, involving a direct effect of miR-21-5p on eNOS transcript stability, not previously reported. Moreover, hypoxia downregulates miR-21-5p, contributing to increasing the expression of NO-related genes in arterial endothelial cells.
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Affiliation(s)
- Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | | | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile.
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35
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Yukselen O, Turkyilmaz O, Ozturk AR, Garber M, Kucukural A. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 2020; 21:310. [PMID: 32306927 PMCID: PMC7168977 DOI: 10.1186/s12864-020-6714-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/01/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to maintain pipelines for large organizations. RESULTS To simplify development, maintenance, and execution of complex pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful Nextflow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis. CONCLUSION DolphinNext is a flexible, intuitive, web-based data processing and analysis platform that enables creating, deploying, sharing, and executing complex Nextflow pipelines with extensive revisioning and interactive reporting to enhance reproducible results.
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Affiliation(s)
- Onur Yukselen
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Osman Turkyilmaz
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ahmet Rasit Ozturk
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Manuel Garber
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Alper Kucukural
- Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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