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Gómez-Del Arco P, Isern J, Jimenez-Carretero D, López-Maderuelo D, Piñeiro-Sabarís R, El Abdellaoui-Soussi F, Torroja C, Vera-Pedrosa ML, Grima-Terrén M, Benguria A, Simón-Chica A, Queiro-Palou A, Dopazo A, Sánchez-Cabo F, Jalife J, de la Pompa JL, Filgueiras-Rama D, Muñoz-Cánoves P, Redondo JM. The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development. Nat Commun 2024; 15:8602. [PMID: 39366945 PMCID: PMC11452623 DOI: 10.1038/s41467-024-52809-1] [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: 05/03/2022] [Accepted: 09/19/2024] [Indexed: 10/06/2024] Open
Abstract
Extensive genetic studies have elucidated cardiomyocyte differentiation and associated gene networks using single-cell RNA-seq, yet the intricate transcriptional mechanisms governing cardiac conduction system (CCS) development and working cardiomyocyte differentiation remain largely unexplored. Here we show that mice deleted for Dhx36 (encoding the Dhx36 helicase) in the embryonic or neonatal heart develop overt dilated cardiomyopathy, surface ECG alterations related to cardiac impulse propagation, and (in the embryonic heart) a lack of a ventricular conduction system (VCS). Heart snRNA-seq and snATAC-seq reveal the role of Dhx36 in CCS development and in the differentiation of working cardiomyocytes. Dhx36 deficiency directly influences cardiomyocyte gene networks by disrupting the resolution of promoter G-quadruplexes in key cardiac genes, impacting cardiomyocyte differentiation and CCS morphogenesis, and ultimately leading to dilated cardiomyopathy and atrioventricular block. These findings further identify crucial genes and pathways that regulate the development and function of the VCS/Purkinje fiber (PF) network.
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Affiliation(s)
- Pablo Gómez-Del Arco
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain.
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
| | - Joan Isern
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Daniel Jimenez-Carretero
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Dolores López-Maderuelo
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Microscopy and Dynamic Imaging Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Rebeca Piñeiro-Sabarís
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Fadoua El Abdellaoui-Soussi
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Center for Stem Cells and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carlos Torroja
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - María Linarejos Vera-Pedrosa
- Cardiac Arrhythmia Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Mercedes Grima-Terrén
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Ana Simón-Chica
- Novel Arrhythmogenic Mechanisms Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Antonio Queiro-Palou
- Institute for Rare Diseases Research, Instituto de Salud Carlos III (ISCIII). Majadahonda, Madrid, Spain
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - José Jalife
- Cardiac Arrhythmia Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- University of Michigan, Ann Arbor, MI, USA
| | - José Luis de la Pompa
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Intercellular Signaling in Cardiovascular Development and Disease Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - David Filgueiras-Rama
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Novel Arrhythmogenic Mechanisms Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
- Cardiovascular Institute, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Pura Muñoz-Cánoves
- Altos Labs, Inc., San Diego Institute of Science, San Diego, CA, USA.
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Department of Experimental & Health Sciences, University Pompeu Fabra (UPF)/CIBERNED, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Juan Miguel Redondo
- Gene Regulation in Cardiovascular Remodelling and Inflammation Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
- Cell-Cell Communication & Inflammation Unit, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain.
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2
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Bolesani E, Bornhorst D, Iyer LM, Zawada D, Friese N, Morgan M, Lange L, Gonzalez DM, Schrode N, Leffler A, Wunder J, Franke A, Drakhlis L, Sebra R, Schambach A, Goedel A, Dubois NC, Dobreva G, Moretti A, Zelaráyan LC, Abdelilah-Seyfried S, Zweigerdt R. Transient stabilization of human cardiovascular progenitor cells from human pluripotent stem cells in vitro reflects stage-specific heart development in vivo. Cardiovasc Res 2024; 120:1295-1311. [PMID: 38836637 DOI: 10.1093/cvr/cvae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/11/2024] [Accepted: 04/06/2024] [Indexed: 06/06/2024] Open
Abstract
AIMS Understanding the molecular identity of human pluripotent stem cell (hPSC)-derived cardiac progenitors and mechanisms controlling their proliferation and differentiation is valuable for developmental biology and regenerative medicine. METHODS AND RESULTS Here, we show that chemical modulation of histone acetyl transferases (by IQ-1) and WNT (by CHIR99021) synergistically enables the transient and reversible block of directed cardiac differentiation progression on hPSCs. The resulting stabilized cardiovascular progenitors (SCPs) are characterized by ISL1pos/KI-67pos/NKX2-5neg expression. In the presence of the chemical inhibitors, SCPs maintain a proliferation quiescent state. Upon small molecules, removal SCPs resume proliferation and concomitant NKX2-5 up-regulation triggers cell-autonomous differentiation into cardiomyocytes. Directed differentiation of SCPs into the endothelial and smooth muscle lineages confirms their full developmental potential typical of bona fide cardiovascular progenitors. Single-cell RNA-sequencing-based transcriptional profiling of our in vitro generated human SCPs notably reflects the dynamic cellular composition of E8.25-E9.25 posterior second heart field of mouse hearts, hallmarked by nuclear receptor sub-family 2 group F member 2 expression. Investigating molecular mechanisms of SCP stabilization, we found that the cell-autonomously regulated retinoic acid and BMP signalling is governing SCP transition from quiescence towards proliferation and cell-autonomous differentiation, reminiscent of a niche-like behaviour. CONCLUSION The chemically defined and reversible nature of our stabilization approach provides an unprecedented opportunity to dissect mechanisms of cardiovascular progenitors' specification and reveal their cellular and molecular properties.
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Affiliation(s)
- Emiliano Bolesani
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Dorothee Bornhorst
- Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Lavanya M Iyer
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany
| | - Dorota Zawada
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nina Friese
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Lucas Lange
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - David M Gonzalez
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nadine Schrode
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Andreas Leffler
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, Germany
| | - Julian Wunder
- Department of Anesthesiology and Intensive Care Medicine, Hannover Medical School, Hannover, Germany
| | - Annika Franke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Lika Drakhlis
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Robert Sebra
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Alexander Goedel
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
| | - Nicole C Dubois
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Alessandra Moretti
- First Department of Medicine, Cardiology, Klinikum rechts der Isar, Technical University of Munich, School of Medicine and Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Munich Heart Alliance, Munich, Germany
| | - Laura C Zelaráyan
- Institute of Pharmacology and Toxicology, University Medical Center Göttingen, Göttingen, Germany
| | - Salim Abdelilah-Seyfried
- Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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3
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Simmons AD, Baumann C, Zhang X, Kamp TJ, De La Fuente R, Palecek SP. Integrated multi-omics analysis identifies features that predict human pluripotent stem cell-derived progenitor differentiation to cardiomyocytes. J Mol Cell Cardiol 2024; 196:52-70. [PMID: 39222876 DOI: 10.1016/j.yjmcc.2024.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/30/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are advancing cardiovascular development and disease modeling, drug testing, and regenerative therapies. However, hPSC-CM production is hindered by significant variability in the differentiation process. Establishment of early quality markers to monitor lineage progression and predict terminal differentiation outcomes would address this robustness and reproducibility roadblock in hPSC-CM production. An integrated transcriptomic and epigenomic analysis assesses how attributes of the cardiac progenitor cell (CPC) affect CM differentiation outcome. Resulting analysis identifies predictive markers of CPCs that give rise to high purity CM batches, including TTN, TRIM55, DGKI, MEF2C, MAB21L2, MYL7, LDB3, SLC7A11, and CALD1. Predictive models developed from these genes provide high accuracy in determining terminal CM purities at the CPC stage. Further, insights into mechanisms of batch failure and dominant non-CM cell types generated in failed batches are elucidated. Namely EMT, MAPK, and WNT signaling emerge as significant drivers of batch divergence, giving rise to off-target populations of fibroblasts/mural cells, skeletal myocytes, epicardial cells, and a non-CPC SLC7A11+ subpopulation. This study demonstrates how integrated multi-omic analysis of progenitor cells can identify quality attributes of that progenitor and predict differentiation outcomes, thereby improving differentiation protocols and increasing process robustness.
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Affiliation(s)
- Aaron D Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Claudia Baumann
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Xiangyu Zhang
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Timothy J Kamp
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, and Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA
| | - Sean P Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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4
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Zhu Z, Zou Q, Wang C, Li D, Yang Y, Xiao Y, Jin Y, Yan J, Luo L, Sun Y, Liang X. Isl Identifies the Extraembryonic Mesodermal/Allantois Progenitors and is Required for Placenta Morphogenesis and Vasculature Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400238. [PMID: 38923264 PMCID: PMC11348239 DOI: 10.1002/advs.202400238] [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] [Received: 01/08/2024] [Revised: 03/08/2024] [Indexed: 06/28/2024]
Abstract
The placenta links feto-maternal circulation for exchanges of nutrients, gases, and metabolic wastes between the fetus and mother, being essential for pregnancy process and maintenance. The allantois and mesodermal components of amnion, chorion, and yolk sac are derived from extraembryonic mesoderm (Ex-Mes), however, the mechanisms contributing to distinct components of the placenta and regulation the interactions between allantois and epithelium during chorioallantoic fusion and labyrinth formation remains unclear. Isl1 is expressed in progenitors of the Ex-Mes and allantois the Isl1 mut mouse line is analyzed to investigate contribution of Isl1+ Ex-Mes / allantoic progenitors to cells of the allantois and placenta. This study shows that Isl1 identifies the Ex-Mes progenitors for endothelial and vascular smooth muscle cells, and most of the mesenchymal cells of the placenta and umbilical cord. Deletion of Isl1 causes defects in allantois growth, chorioallantoic fusion, and placenta vessel morphogenesis. RNA-seq and CUT&Tag analyses revealed that Isl1 promotes allantoic endothelial, inhibits mesenchymal cell differentiation, and allantoic signals regulated by Isl1 mediating the inductive interactions between the allantois and chorion critical for chorionic epithelium differentiation, villous formation, and labyrinth angiogenesis. This study above reveals that Isl1 plays roles in regulating multiple genetic and epigenetic pathways of vascular morphogenesis, provides the insight into the mechanisms for placental formation, highlighting the necessity of Isl1 for placenta formation/pregnant maintenance.
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Affiliation(s)
- Zeyue Zhu
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Qicheng Zou
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Chunxiao Wang
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Dixi Li
- Department of Hematology, Tongji HospitalTongji University School of MedicineShanghai200120China
| | - Yan Yang
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Ying Xiao
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Yao Jin
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Jie Yan
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Lina Luo
- Key Laboratory of Arrhythmia of the Ministry of Education of ChinaEast HospitalTongji University School of MedicineShanghai200120China
| | - Yunfu Sun
- Shanghai East HospitalTongji University School of Medicine150 Jimo RoadShanghai200120China
| | - Xingqun Liang
- Shanghai East HospitalTongji University School of Medicine150 Jimo RoadShanghai200120China
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5
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Xia LX, Xiao YY, Jiang WJ, Yang XY, Tao H, Mandukhail SR, Qin JF, Pan QR, Zhu YG, Zhao LX, Huang LJ, Li Z, Yu XY. Exosomes derived from induced cardiopulmonary progenitor cells alleviate acute lung injury in mice. Acta Pharmacol Sin 2024; 45:1644-1659. [PMID: 38589686 PMCID: PMC11272782 DOI: 10.1038/s41401-024-01253-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/26/2024] [Indexed: 04/10/2024] Open
Abstract
Cardiopulmonary progenitor cells (CPPs) constitute a minor subpopulation of cells that are commonly associated with heart and lung morphogenesis during embryonic development but completely subside after birth. This fact offers the possibility for the treatment of pulmonary heart disease (PHD), in which the lung and heart are both damaged. A reliable source of CPPs is urgently needed. In this study, we reprogrammed human cardiac fibroblasts (HCFs) into CPP-like cells (or induced CPPs, iCPPs) and evaluated the therapeutic potential of iCPP-derived exosomes for acute lung injury (ALI). iCPPs were created in passage 3 primary HCFs by overexpressing GLI1, WNT2, ISL1 and TBX5 (GWIT). Exosomes were isolated from the culture medium of passage 6-8 GWIT-iCPPs. A mouse ALI model was established by intratracheal instillation of LPS. Four hours after LPS instillation, ALI mice were treated with GWIT-iCPP-derived exosomes (5 × 109, 5 × 1010 particles/mL) via intratracheal instillation. We showed that GWIT-iCPPs could differentiate into cell lineages, such as cardiomyocyte-like cells, endothelial cells, smooth muscle cells and alveolar epithelial cells, in vitro. Transcription analysis revealed that GWIT-iCPPs have potential for heart and lung development. Intratracheal instillation of iCPP-derived exosomes dose-dependently alleviated LPS-induced ALI in mice by attenuating lung inflammation, promoting endothelial function and restoring capillary endothelial cells and the epithelial cells barrier. This study provides a potential new method for the prevention and treatment of cardiopulmonary injury, especially lung injury, and provides a new cell model for drug screening.
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Affiliation(s)
- Luo-Xing Xia
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ying-Ying Xiao
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Wen-Jing Jiang
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xiang-Yu Yang
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Hua Tao
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Safur Rehman Mandukhail
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jian-Feng Qin
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Qian-Rong Pan
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yu-Guang Zhu
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Li-Xin Zhao
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Li-Juan Huang
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zhan Li
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Xi-Yong Yu
- The Fifth Affiliated Hospital, Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
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6
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Abubakar M, Hajjaj M, Naqvi ZEZ, Shanawaz H, Naeem A, Padakanti SSN, Bellitieri C, Ramar R, Gandhi F, Saleem A, Abdul Khader AHS, Faraz MA. Non-Coding RNA-Mediated Gene Regulation in Cardiovascular Disorders: Current Insights and Future Directions. J Cardiovasc Transl Res 2024; 17:739-767. [PMID: 38092987 DOI: 10.1007/s12265-023-10469-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/23/2023] [Indexed: 09/04/2024]
Abstract
Cardiovascular diseases (CVDs) pose a significant burden on global health. Developing effective diagnostic, therapeutic, and prognostic indicators for CVDs is critical. This narrative review explores the role of select non-coding RNAs (ncRNAs) and provides an in-depth exploration of the roles of miRNAs, lncRNAs, and circRNAs in different aspects of CVDs, offering insights into their mechanisms and potential clinical implications. The review also sheds light on the diverse functions of ncRNAs, including their modulation of gene expression, epigenetic modifications, and signaling pathways. It comprehensively analyzes the interplay between ncRNAs and cardiovascular health, paving the way for potential novel interventions. Finally, the review provides insights into the methodologies used to investigate ncRNA-mediated gene regulation in CVDs, as well as the implications and challenges associated with translating ncRNA research into clinical applications. Considering the broader implications, this research opens avenues for interdisciplinary collaborations, enhancing our understanding of CVDs across scientific disciplines.
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Affiliation(s)
- Muhammad Abubakar
- Department of Internal Medicine, Ameer-Ud-Din Medical College, Lahore General Hospital, Lahore, Punjab, Pakistan.
| | - Mohsin Hajjaj
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Zil E Zehra Naqvi
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | - Hameed Shanawaz
- Department of Internal Medicine, Windsor University School of Medicine, Cayon, Saint Kitts and Nevis
| | - Ammara Naeem
- Department of Cardiology, Heart & Vascular Institute, Dearborn, Michigan, USA
| | | | | | - Rajasekar Ramar
- Department of Internal Medicine, Rajah Muthiah Medical College, Chidambaram, Tamil Nadu, India
| | - Fenil Gandhi
- Department of Family Medicine, Lower Bucks Hospital, Bristol, PA, USA
| | - Ayesha Saleem
- Department of Internal Medicine, Jinnah Hospital, Lahore, Punjab, Pakistan
| | | | - Muhammad Ahmad Faraz
- Department of Forensic Medicine, Postgraduate Medical Institute, Lahore, Punjab, Pakistan
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7
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Mallaredy V, Roy R, Cheng Z, Gurrala CT, Benedict C, Truongcao M, Joladarashi D, Magadum A, Ibetti J, Cimini M, Gonzalez C, Garikipati VNS, Koch WJ, Kishore R. Tipifarnib Reduces Extracellular Vesicles and Protects From Heart Failure. Circ Res 2024; 135:280-297. [PMID: 38847080 PMCID: PMC11223950 DOI: 10.1161/circresaha.123.324110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/28/2024] [Indexed: 07/06/2024]
Abstract
BACKGROUND Heart failure (HF) is one of the leading causes of mortality worldwide. Extracellular vesicles, including small extracellular vesicles or exosomes, and their molecular cargo are known to modulate cell-to-cell communication during multiple cardiac diseases. However, the role of systemic extracellular vesicle biogenesis inhibition in HF models is not well documented and remains unclear. METHODS We investigated the role of circulating exosomes during cardiac dysfunction and remodeling in a mouse transverse aortic constriction (TAC) model of HF. Importantly, we investigate the efficacy of tipifarnib, a recently identified exosome biogenesis inhibitor that targets the critical proteins (Rab27a [Ras associated binding protein 27a], nSMase2 [neutral sphingomyelinase 2], and Alix [ALG-2-interacting protein X]) involved in exosome biogenesis for this mouse model of HF. In this study, 10-week-old male mice underwent TAC surgery were randomly assigned to groups with and without tipifarnib treatment (10 mg/kg 3 times/wk) and monitored for 8 weeks, and a comprehensive assessment was conducted through performed echocardiographic, histological, and biochemical studies. RESULTS TAC significantly elevated circulating plasma exosomes and markedly increased cardiac left ventricular dysfunction, cardiac hypertrophy, and fibrosis. Furthermore, injection of plasma exosomes from TAC mice induced left ventricular dysfunction and cardiomyocyte hypertrophy in uninjured mice without TAC. On the contrary, treatment of tipifarnib in TAC mice reduced circulating exosomes to baseline and remarkably improved left ventricular functions, hypertrophy, and fibrosis. Tipifarnib treatment also drastically altered the miRNA profile of circulating post-TAC exosomes, including miR 331-5p, which was highly downregulated both in TAC circulating exosomes and in TAC cardiac tissue. Mechanistically, miR 331-5p is crucial for inhibiting the fibroblast-to-myofibroblast transition by targeting HOXC8, a critical regulator of fibrosis. Tipifarnib treatment in TAC mice upregulated the expression of miR 331-5p that acts as a potent repressor for one of the fibrotic mechanisms mediated by HOXC8. CONCLUSIONS Our study underscores the pathological role of exosomes in HF and fibrosis in response to pressure overload. Tipifarnib-mediated inhibition of exosome biogenesis and cargo sorting may serve as a viable strategy to prevent progressive cardiac remodeling in HF.
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Affiliation(s)
- Vandana Mallaredy
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Rajika Roy
- Department of Surgery, Division of Cardiovascular and Thoracic Surgery, Duke University School of Medicine, Durham, NC 27710
| | - Zhongjian Cheng
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Charan Thej Gurrala
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Cindy Benedict
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - May Truongcao
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Darukeshwara Joladarashi
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Ajit Magadum
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Jessica Ibetti
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Maria Cimini
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Carolina Gonzalez
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
| | - Venkata Naga Srikanth Garikipati
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140
| | - Walter J. Koch
- Department of Surgery, Division of Cardiovascular and Thoracic Surgery, Duke University School of Medicine, Durham, NC 27710
| | - Raj Kishore
- Aging and Cardiovascular Discovery Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19140
- Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140
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8
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Choudhury S, Sivankutty I, Jung Y, Huang A, Araten S, Kenny C, An Z, Doan R, Foijer F, Matsu E, Rosen I, Marciano J, Jain A, Sun L, Hilal N, Lee E, Walsh C, Chen M. Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart. RESEARCH SQUARE 2024:rs.3.rs-4414468. [PMID: 38853931 PMCID: PMC11160865 DOI: 10.21203/rs.3.rs-4414468/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.
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9
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Zhang X, Zhu R, Yu D, Wang J, Yan Y, Xu K. Single-cell RNA sequencing to explore cancer-associated fibroblasts heterogeneity: "Single" vision for "heterogeneous" environment. Cell Prolif 2024; 57:e13592. [PMID: 38158643 PMCID: PMC11056715 DOI: 10.1111/cpr.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/24/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Cancer-associated fibroblasts (CAFs), a phenotypically and functionally heterogeneous stromal cell, are one of the most important components of the tumour microenvironment. Previous studies have consolidated it as a promising target against cancer. However, variable therapeutic efficacy-both protumor and antitumor effects have been observed not least owing to the strong heterogeneity of CAFs. Over the past 10 years, advances in single-cell RNA sequencing (scRNA-seq) technologies had a dramatic effect on biomedical research, enabling the analysis of single cell transcriptomes with unprecedented resolution and throughput. Specifically, scRNA-seq facilitates our understanding of the complexity and heterogeneity of diverse CAF subtypes. In this review, we discuss the up-to-date knowledge about CAF heterogeneity with a focus on scRNA-seq perspective to investigate the emerging strategies for integrating multimodal single-cell platforms. Furthermore, we summarized the clinical application of scRNA-seq on CAF research. We believe that the comprehensive understanding of the heterogeneity of CAFs form different visions will generate innovative solutions to cancer therapy and achieve clinical applications.
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Affiliation(s)
- Xiangjian Zhang
- The Dingli Clinical College of Wenzhou Medical UniversityWenzhouZhejiangChina
- Department of Surgical OncologyWenzhou Central HospitalWenzhouZhejiangChina
- The Second Affiliated Hospital of Shanghai UniversityWenzhouZhejiangChina
| | - Ruiqiu Zhu
- Interventional Cancer Institute of Chinese Integrative MedicinePutuo Hospital, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Die Yu
- Interventional Cancer Institute of Chinese Integrative MedicinePutuo Hospital, Shanghai University of Traditional Chinese MedicineShanghaiChina
| | - Juan Wang
- School of MedicineShanghai UniversityShanghaiChina
| | - Yuxiang Yan
- The Dingli Clinical College of Wenzhou Medical UniversityWenzhouZhejiangChina
- Department of Surgical OncologyWenzhou Central HospitalWenzhouZhejiangChina
- The Second Affiliated Hospital of Shanghai UniversityWenzhouZhejiangChina
| | - Ke Xu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Wenzhou Institute of Shanghai UniversityWenzhouChina
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10
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Khandibharad S, Singh S. Single-cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L. major infection. Microbiol Spectr 2024; 12:e0347823. [PMID: 38299832 PMCID: PMC10913457 DOI: 10.1128/spectrum.03478-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/31/2023] [Indexed: 02/02/2024] Open
Abstract
The hallmark characteristic of macrophages lies in their inherent plasticity, allowing them to adapt to dynamic microenvironments. Leishmania strategically modulates the phenotypic plasticity of macrophages, creating a favorable environment for intracellular survival and persistent infection through regulatory cytokine such as interleukin (IL)-10. Nevertheless, these effector cells can counteract infection by modulating crucial cytokines like IL-12 and key components involved in its production. Using sophisticated tool of single-cell assay for transposase accessible chromatin (ATAC) sequencing, we systematically examined the regulatory axis of IL-10 and IL-12 in a time-dependent manner during Leishmania major infection in macrophages Our analysis revealed the cellular heterogeneity post-infection with the regulators of IL-10 and IL-12, unveiling a reciprocal relationship between these cytokines. Notably, our significant findings highlighted the presence of sleepy macrophages and their pivotal role in mediating reciprocity between IL-10 and IL-12. To summarize, the roles of cytokine expression, transcription factors, cell cycle, and epigenetics of host cell machinery were vital in identification of sleepy macrophages, which is a transient state where transcription factors controlled the epigenetic remodeling and expression of genes involved in pro-inflammatory cytokine expression and recruitment of immune cells.IMPORTANCELeishmaniasis is an endemic affecting 99 countries and territories globally, as outlined in the 2022 World Health Organization report. The disease's severity is compounded by compromised host immune systems, emphasizing the pivotal role of the interplay between parasite and host immune factors in disease regulation. In instances of cutaneous leishmaniasis induced by L. major, macrophages function as sentinel cells. Our findings indicate that the plasticity and phenotype of macrophages can be modulated to express a cytokine profile involving IL-10 and IL-12, mediated by the regulation of transcription factors and their target genes post-L. major infection in macrophages. Employing sophisticated methodologies such as single-cell ATAC sequencing and computational genomics, we have identified a distinctive subset of macrophages termed "sleepy macrophages." These macrophages exhibit downregulated housekeeping genes while expressing a unique set of variable features. This data set constitutes a valuable resource for comprehending the intricate host-parasite interplay during L. major infection.
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Affiliation(s)
- Shweta Khandibharad
- Systems Medicine Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Shailza Singh
- Systems Medicine Lab, National Centre for Cell Science, SP Pune University Campus, Pune, India
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11
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Islam MT, Liu Y, Hassan MM, Abraham PE, Merlet J, Townsend A, Jacobson D, Buell CR, Tuskan GA, Yang X. Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0029. [PMID: 38435807 PMCID: PMC10905259 DOI: 10.34133/bdr.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/05/2024] Open
Abstract
Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings of complex plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type heterogeneity. Furthermore, scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology, which aims to modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational design for increasing crop yield and quality, promoting the bioeconomy and enhancing environmental sustainability. In particular, data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side effects. To date, scRNA-seq has been demonstrated in a limited number of plant species, including model plants (e.g., Arabidopsis thaliana), agricultural crops (e.g., Oryza sativa), and bioenergy crops (e.g., Populus spp.). It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in plants. In this review, we summarize current technical advancements in plant scRNA-seq, including sample preparation, sequencing, and data analysis, to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant samples. We then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology research. Finally, we discuss the challenges and opportunities for the application of scRNA-seq in plants.
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Affiliation(s)
- Md Torikul Islam
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md Mahmudul Hassan
- Department of Genetics and Plant Breeding,
Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jean Merlet
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Alice Townsend
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education,
University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - C. Robin Buell
- Center for Applied Genetic Technologies,
University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences,
University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics, and Genomics,
University of Georgia, Athens, GA 30602, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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12
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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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13
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Long X, Wei J, Fang Q, Yuan X, Du J. Single-cell RNA sequencing reveals the transcriptional heterogeneity of Tbx18-positive cardiac cells during heart development. Funct Integr Genomics 2024; 24:18. [PMID: 38265516 DOI: 10.1007/s10142-024-01290-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The T-box family transcription factor 18 (Tbx18) has been found to play a critical role in regulating the development of the mammalian heart during the primary stages of embryonic development while the cellular heterogeneity and landscape of Tbx18-positive (Tbx18+) cardiac cells remain incompletely characterized. Here, we analyzed prior published single-cell RNA sequencing (scRNA-seq) mouse heart data to explore the heterogeneity of Tbx18+ cardiac cell subpopulations and provide a comprehensive transcriptional landscape of Tbx18+ cardiac cells during their development. Bioinformatic analysis methods were utilized to identify the heterogeneity between cell groups. Based on the gene expression characteristics, Tbx18+ cardiac cells can be classified into a minimum of two distinct cell populations, namely fibroblast-like cells and cardiomyocytes. In terms of temporal heterogeneity, these cells exhibit three developmental stages, namely the MEM stage, ML_P0 stage, and P stage Tbx18+ cardiac cells. Furthermore, Tbx18+ cardiac cells encompass several cell types, including cardiac progenitor-like cells, cardiomyocytes, and epicardial/stromal cells, as determined by specific transcriptional regulatory networks. The scRNA-seq results revealed the involvement of extracellular matrix (ECM) signals and epicardial epithelial-to-mesenchymal transition (EMT) in the development of Tbx18+ cardiac cells. The utilization of a lineage-tracing model served to validate the crucial function of Tbx18 in the differentiation of cardiac cells. Consequently, these findings offer a comprehensive depiction of the cellular heterogeneity within Tbx18+ cardiac cells.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Jiangjun Wei
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Qinghua Fang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China.
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14
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Wei H, Zhong Z, Li Z, Zhang Y, Stukenbrock EH, Tang B, Yang N, Baroncelli R, Peng L, Liu Z, He X, Yang Y, Yuan Z. Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte. PLANT COMMUNICATIONS 2024; 5:100672. [PMID: 37563834 PMCID: PMC10811371 DOI: 10.1016/j.xplc.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.
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Affiliation(s)
- Huanshen Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118 Kiel, Germany; Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
| | - Ningning Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Long Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhuo Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuzhan Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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15
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Yekelchyk M, Li X, Guenther S, Braun T. Single-Nucleus ATAC-seq for Mapping Chromatin Accessibility in Individual Cells of Murine Hearts. Methods Mol Biol 2024; 2752:245-257. [PMID: 38194039 DOI: 10.1007/978-1-0716-3621-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
During the last decade a wide range of single-cell and single-nucleus next-generation sequencing techniques have been developed, which revolutionized detection of rare cell populations, enabling creation of comprehensive cell atlases of complex organs and tissues. State-of-the-art methods do not only allow classical transcriptomics of individual cells but also comprise a number of epigenetic approaches, including assessment of chromatin accessibility by single-nucleus Assay for Transposase Accessible Chromatin ATAC-seq (snATAC-seq). The snATAC-seq assay detects "open chromatin," a term for low nucleosome occupancy of genomic regions, which is a prerequisite for effective transcription factor binding. Information about open chromatin at the single-nucleus level helps to recognize epigenetic changes, sometimes before transcription of respective genes occurs. snATAC-seq detects cellular heterogeneity in otherwise still transcriptionally and/or morphologically homogeneous cell populations. Chromatin accessibility assays may be used to detect epigenetic changes in cardiac lineages during heart development, chromatin landscape changes during aging, and epigenetic alterations in heart diseases. Here, we provide an optimized protocol for snATAC-seq of murine hearts. We describe isolation of single nuclei from snap-frozen hearts, provide hints for preparation of libraries suitable for snATAC-seq next-generation sequencing (NGS) using the Chromium 10× platform, and give general recommendations for downstream analysis using conventional bioinformatic pipelines and packages. The protocol should serve as a beginner's guide to generate high-quality snATAC-seq datasets and to perform chromatin accessibility analysis of individual heart-derived cell nuclei.
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Affiliation(s)
- Michail Yekelchyk
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Xiang Li
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am Main, Germany.
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16
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Wei N, Lee C, Duan L, Galdos FX, Samad T, Raissadati A, Goodyer WR, Wu SM. Cardiac Development at a Single-Cell Resolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:253-268. [PMID: 38884716 DOI: 10.1007/978-3-031-44087-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Mammalian cardiac development is a complex, multistage process. Though traditional lineage tracing studies have characterized the broad trajectories of cardiac progenitors, the advent and rapid optimization of single-cell RNA sequencing methods have yielded an ever-expanding toolkit for characterizing heterogeneous cell populations in the developing heart. Importantly, they have allowed for a robust profiling of the spatiotemporal transcriptomic landscape of the human and mouse heart, revealing the diversity of cardiac cells-myocyte and non-myocyte-over the course of development. These studies have yielded insights into novel cardiac progenitor populations, chamber-specific developmental signatures, the gene regulatory networks governing cardiac development, and, thus, the etiologies of congenital heart diseases. Furthermore, single-cell RNA sequencing has allowed for the exquisite characterization of distinct cardiac populations such as the hard-to-capture cardiac conduction system and the intracardiac immune population. Therefore, single-cell profiling has also resulted in new insights into the regulation of cardiac regeneration and injury repair. Single-cell multiomics approaches combining transcriptomics, genomics, and epigenomics may uncover an even more comprehensive atlas of human cardiac biology. Single-cell analyses of the developing and adult mammalian heart offer an unprecedented look into the fundamental mechanisms of cardiac development and the complex diseases that may arise from it.
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Affiliation(s)
- Nicholas Wei
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Carissa Lee
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | - Lauren Duan
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | - Tahmina Samad
- Stanford University, Cardiovascular Institute, Stanford, CA, USA
| | | | | | - Sean M Wu
- Stanford University, Cardiovascular Institute, Stanford, CA, USA.
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17
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Buckingham M, Kelly RG. Cardiac Progenitor Cells of the First and Second Heart Fields. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:103-124. [PMID: 38884707 DOI: 10.1007/978-3-031-44087-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
The heart forms from the first and second heart fields, which contribute to distinct regions of the myocardium. This is supported by clonal analyses, which identify corresponding first and second cardiac cell lineages in the heart. Progenitor cells of the second heart field and its sub-domains are controlled by a gene regulatory network and signaling pathways, which determine their behavior. Multipotent cells in this field can also contribute cardiac endothelial and smooth muscle cells. Furthermore, the skeletal muscles of the head and neck are clonally related to myocardial cells that form the arterial and venous poles of the heart. These lineage relationships, together with the genes that regulate the heart fields, have major implications for congenital heart disease.
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Affiliation(s)
- Margaret Buckingham
- Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, Paris, France.
| | - Robert G Kelly
- Aix Marseille Université, Institut de Biologie du Dévelopment de Marseille, Marseille, France.
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18
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Xue H, Delbare SYN, Wells MT, Basu S, Clark AG. Integrative Analysis of Differentially Expressed Genes in Time-Course Multi-Omics Data with MINT-DE. RESEARCH SQUARE 2024:rs.3.rs-3806701. [PMID: 38260696 PMCID: PMC10802680 DOI: 10.21203/rs.3.rs-3806701/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Time-course multi-omics experiments have been highly informative for obtaining a comprehensive understanding of the dynamic relationships between molecules in a biological process, especially if the different profiles are obtained from the same samples. A fundamental step in analyzing time-course multi-omics data involves selecting a short list of genes or gene regions ("sites") that warrant further study. Two important criteria for site selection are the magnitude of change and the temporal dynamic consistency. However, existing methods only consider one of these criteria, while neglecting the other. Results In our study, we propose a framework called MINT-DE (Multi-omics INtegration of Time-course for Diffierential Expression analysis) to address this limitation. MINT-DE is capable of selecting sites based on summarized measures of both aforementioned aspects. We calculate evidence measures assessing the extent of differential expression for each assay and for the dynamical similarity across assays. Then based on the summary of the evidence assessment measures, sites are ranked. To evaluate the performance of MINT-DE, we apply it to analyze a time-course multi-omics dataset of Drosophila development. We compare the selection obtained from MINT-DE with those obtained from other existing methods. The analysis reveal that MINT-DE is able to identify differentially expressed time-course pairs with the highest correlations. Their corresponding genes are significantly enriched for known biological functions, as measured by gene-gene interaction networks and the Gene Ontology enrichment. Conclusions These findings suggest the effectiveness of MINT-DE in selecting sites that are both differentially expressed within at least one assay and temporally related across assays. This highlights the potential of MINT-DE to identify biologically important sites for downstream analysis and provide a complementarity of sites that is neglected by existing methods.
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Affiliation(s)
- Hao Xue
- Department of Computational Biology, Cornell University, 526 Campus Rd, Ithaca, 14853, NY, USA
| | - Sofie Y. N. Delbare
- Department of Statistics and Data Science, Cornell University, 129 Garden Ave, Itahca, 14853, NY, USA
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, 129 Garden Ave, Itahca, 14853, NY, USA
| | - Sumanta Basu
- Department of Statistics and Data Science, Cornell University, 129 Garden Ave, Itahca, 14853, NY, USA
| | - Andrew G. Clark
- Department of Computational Biology, Cornell University, 526 Campus Rd, Ithaca, 14853, NY, USA
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19
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Shen J, Ma L, Hu J, Li Y. Single-Cell Atlas of Neonatal Mouse Hearts Reveals an Unexpected Cardiomyocyte. J Am Heart Assoc 2023; 12:e028287. [PMID: 38014657 PMCID: PMC10727353 DOI: 10.1161/jaha.122.028287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Single-cell RNA sequencing is widely used in cancer research and organ development because of its powerful ability to analyze cellular heterogeneity. However, its application in cardiomyocytes is dissatisfactory mainly because the cardiomyocytes are too large and fragile to withstand traditional single-cell approaches. METHODS AND RESULTS Through designing the isolation procedure of neonatal mouse cardiac cells, we provide detailed cellular atlases of the heart at single-cell resolution across 4 different stages after birth. We have obtained 10 000 cardiomyocytes; to our knowledge, this is the most extensive reference framework to date. Moreover, we have discovered unexpected erythrocyte-like cardiomyocyte-terminal cardiomyocytes, comprising more than a third of all cardiomyocytes. Only a few genes are highly expressed in these cardiomyocytes. They are highly differentiated cardiomyocytes that function as contraction pumps. In addition, we have identified 2 cardiomyocyte-like conducting cells, lending support to the theory that the sinoatrial node pacemaker cells are specialized cardiomyocytes. Notably, we provide an initial blueprint for comprehensive interactions between cardiomyocytes and other cardiac cells. CONCLUSIONS This mouse cardiac cell atlas improves our understanding of cardiomyocyte heterogeneity and provides a valuable reference in response to varying physiological conditions and diseases.
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Affiliation(s)
- Junwei Shen
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu HospitalShanghaiChina
- Clinical Research Center for Mental DisordersShanghai Pudong New Area Mental Health Center, School of Medicine, Tongji UniversityShanghaiChina
| | - Linlin Ma
- School of Medical TechnologyShanghai University of Medicine and Health Sciences, ShanghaiShanghaiChina
| | - Jing Hu
- Shanghai First Maternity and Infant HospitalTongji University School of MedicineShanghaiChina
| | - Yanfei Li
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu HospitalShanghaiChina
- School of Medical TechnologyShanghai University of Medicine and Health Sciences, ShanghaiShanghaiChina
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20
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Wang Q, Zhang J, Liu Z, Duan Y, Li C. Integrative approaches based on genomic techniques in the functional studies on enhancers. Brief Bioinform 2023; 25:bbad442. [PMID: 38048082 PMCID: PMC10694556 DOI: 10.1093/bib/bbad442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/22/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
With the development of sequencing technology and the dramatic drop in sequencing cost, the functions of noncoding genes are being characterized in a wide variety of fields (e.g. biomedicine). Enhancers are noncoding DNA elements with vital transcription regulation functions. Tens of thousands of enhancers have been identified in the human genome; however, the location, function, target genes and regulatory mechanisms of most enhancers have not been elucidated thus far. As high-throughput sequencing techniques have leapt forwards, omics approaches have been extensively employed in enhancer research. Multidimensional genomic data integration enables the full exploration of the data and provides novel perspectives for screening, identification and characterization of the function and regulatory mechanisms of unknown enhancers. However, multidimensional genomic data are still difficult to integrate genome wide due to complex varieties, massive amounts, high rarity, etc. To facilitate the appropriate methods for studying enhancers with high efficacy, we delineate the principles, data processing modes and progress of various omics approaches to study enhancers and summarize the applications of traditional machine learning and deep learning in multi-omics integration in the enhancer field. In addition, the challenges encountered during the integration of multiple omics data are addressed. Overall, this review provides a comprehensive foundation for enhancer analysis.
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Affiliation(s)
- Qilin Wang
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Junyou Zhang
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Zhaoshuo Liu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yingying Duan
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chunyan Li
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, China
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21
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Zhong H, Zhang R, Li G, Huang P, Zhang Y, Zhu J, Kuang J, Hutchins AP, Qin D, Zhu P, Pei D, Li D. c-JUN is a barrier in hESC to cardiomyocyte transition. Life Sci Alliance 2023; 6:e202302121. [PMID: 37604584 PMCID: PMC10442936 DOI: 10.26508/lsa.202302121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
Loss of c-JUN leads to early mouse embryonic death, possibly because of a failure to develop a normal cardiac system. How c-JUN regulates human cardiomyocyte cell fate remains unknown. Here, we used the in vitro differentiation of human pluripotent stem cells into cardiomyocytes to study the role of c-JUN. Surprisingly, the knockout of c-JUN improved cardiomyocyte generation, as determined by the number of TNNT2+ cells. ATAC-seq data showed that the c-JUN defect led to increased chromatin accessibility on critical regulatory elements related to cardiomyocyte development. ChIP-seq data showed that the knockout c-JUN increased RBBP5 and SETD1B expression, leading to improved H3K4me3 deposition on key genes that regulate cardiogenesis. The c-JUN KO phenotype could be copied using the histone demethylase inhibitor CPI-455, which also up-regulated H3K4me3 levels and increased cardiomyocyte generation. Single-cell RNA-seq data defined three cell branches, and knockout c-JUN activated more regulons that are related to cardiogenesis. In summary, our data demonstrated that c-JUN could regulate cardiomyocyte cell fate by modulating H3K4me3 modification and chromatin accessibility and shed light on how c-JUN regulates heart development in humans.
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Affiliation(s)
- Hui Zhong
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ran Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Guihuan Li
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping Huang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Yudan Zhang
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jieying Zhu
- CAS Key Laboratory of Regenerative Biology, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Junqi Kuang
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Dajiang Qin
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Bioland Laboratory Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences; Hong Kong, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease and Guangzhou Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, Guangzhou, China
| | - Duanqing Pei
- Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Dongwei Li
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- https://ror.org/00zat6v61 Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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22
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Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023; 147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.
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Affiliation(s)
- Andrea Tangherloni
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy.
| | - Simone G Riva
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Brynelle Myers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Francesca M Buffa
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy; Bicocca Bioinformatics, Biostatistics, and Bioimaging Centre - B4, Via Follereau 3, Vedano al Lambro, 20854, Italy
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23
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Chen S, Jiang W, Du Y, Yang M, Pan Y, Li H, Cui M. Single-cell analysis technologies for cancer research: from tumor-specific single cell discovery to cancer therapy. Front Genet 2023; 14:1276959. [PMID: 37900181 PMCID: PMC10602688 DOI: 10.3389/fgene.2023.1276959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Single-cell sequencing (SCS) technology is changing our understanding of cellular components, functions, and interactions across organisms, because of its inherent advantage of avoiding noise resulting from genotypic and phenotypic heterogeneity across numerous samples. By directly and individually measuring multiple molecular characteristics of thousands to millions of single cells, SCS technology can characterize multiple cell types and uncover the mechanisms of gene regulatory networks, the dynamics of transcription, and the functional state of proteomic profiling. In this context, we conducted systematic research on SCS techniques, including the fundamental concepts, procedural steps, and applications of scDNA, scRNA, scATAC, scCITE, and scSNARE methods, focusing on the unique clinical advantages of SCS, particularly in cancer therapy. We have explored challenging but critical areas such as circulating tumor cells (CTCs), lineage tracing, tumor heterogeneity, drug resistance, and tumor immunotherapy. Despite challenges in managing and analyzing the large amounts of data that result from SCS, this technique is expected to reveal new horizons in cancer research. This review aims to emphasize the key role of SCS in cancer research and promote the application of single-cell technologies to cancer therapy.
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Affiliation(s)
- Siyuan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Weibo Jiang
- Department of Orthopaedic, The Second Hospital of Jilin University, Changchun, China
| | - Yanhui Du
- Department of Orthopaedics, Jilin Province People’s Hospital, Changchun, China
| | - Manshi Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yihan Pan
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Huan Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Mengying Cui
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
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24
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Hu P, Wang B, Jin D, Gu Y, He H, Meng X, Zhu W, Chiang DY, Li W, MacRae CA, Zu Y. Modeling of large-scale hoxbb cluster deletions in zebrafish uncovers a role for segmentation pathways in atrioventricular boundary specification. Cell Mol Life Sci 2023; 80:317. [PMID: 37801106 PMCID: PMC11072906 DOI: 10.1007/s00018-023-04933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/19/2023] [Indexed: 10/07/2023]
Abstract
Hox genes orchestrate the segmental specification of the muscular circulatory system in invertebrates but it has not proven straightforward to decipher segmental parallels in the vertebrate heart. Recently, patients with HOXB gene cluster deletion were found to exhibit abnormalities including atrioventricular canal defects. Using CRISPR, we established a mutant with the orthologous hoxbb cluster deletion in zebrafish. The mutant exhibited heart failure and atrioventricular regurgitation at 5 days. Analyzing the four genes in the hoxbb cluster, isolated deletion of hoxb1b-/- recapitulated the cardiac abnormalities, supporting hoxb1b as the causal gene. Both in situ and in vitro data indicated that hoxb1b regulates gata5 to inhibit hand2 expression and ultimately is required to pattern the vertebrate atrioventricular boundary. Together, these data reveal a role for segmental specification in vertebrate cardiac development and highlight the utility of CRISPR techniques for efficiently exploring the function of large structural genomic lesions.
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Affiliation(s)
- Peinan Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Bingqi Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Dongxu Jin
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Yedan Gu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hongyang He
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiangli Meng
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Wandi Zhu
- Cardiovascular Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - David Y Chiang
- Cardiovascular Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Calum A MacRae
- Cardiovascular Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA.
| | - Yao Zu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
- Cardiovascular Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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25
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Zhu M, Liang H, Zhang Z, Jiang H, Pu J, Hang X, Zhou Q, Xiang J, He X. Distinct mononuclear diploid cardiac subpopulation with minimal cell-cell communications persists in embryonic and adult mammalian heart. Front Med 2023; 17:939-956. [PMID: 37294383 DOI: 10.1007/s11684-023-0987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 01/31/2023] [Indexed: 06/10/2023]
Abstract
A small proportion of mononuclear diploid cardiomyocytes (MNDCMs), with regeneration potential, could persist in adult mammalian heart. However, the heterogeneity of MNDCMs and changes during development remains to be illuminated. To this end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cell RNA sequencing. Three cardiac developmental paths were identified: two switching to cardiomyocytes (CM) maturation with close CM-fibroblast (FB) communications and one maintaining MNDCM status with least CM-FB communications. Proliferative MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell-cell communications were identified in the third path. The non-pMNDCMs possessed distinct properties: the lowest mitochondrial metabolisms, the highest glycolysis, and high expression of Myl4 and Tnni1. Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4+Tnni1+ MNDCMs persisted in embryonic and adult hearts. These MNDCMs were mapped to the heart by integrating the spatial and single-cell transcriptomic data. In conclusion, a novel non-pMNDCM subpopulation with minimal cell-cell communications was unveiled, highlighting the importance of microenvironment contribution to CM fate during maturation. These findings could improve the understanding of MNDCM heterogeneity and cardiac development, thus providing new clues for approaches to effective cardiac regeneration.
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Affiliation(s)
- Miaomiao Zhu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huamin Liang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zhe Zhang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
| | - Hao Jiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingwen Pu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyi Hang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Zhou
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jiacheng Xiang
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, `, Wuhan, 430030, China.
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China.
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26
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Stathopoulou A, Wang P, Thellier C, Kelly RG, Zheng D, Scambler PJ. CHARGE syndrome-associated CHD7 acts at ISL1-regulated enhancers to modulate second heart field gene expression. Cardiovasc Res 2023; 119:2089-2105. [PMID: 37052590 PMCID: PMC10478754 DOI: 10.1093/cvr/cvad059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/20/2022] [Accepted: 04/12/2023] [Indexed: 04/14/2023] Open
Abstract
AIMS Haploinsufficiency of the chromo-domain protein CHD7 underlies most cases of CHARGE syndrome, a multisystem birth defect including congenital heart malformation. Context specific roles for CHD7 in various stem, progenitor, and differentiated cell lineages have been reported. Previously, we showed severe defects when Chd7 is absent from cardiopharyngeal mesoderm (CPM). Here, we investigate altered gene expression in the CPM and identify specific CHD7-bound target genes with known roles in the morphogenesis of affected structures. METHODS AND RESULTS We generated conditional KO of Chd7 in CPM and analysed cardiac progenitor cells using transcriptomic and epigenomic analyses, in vivo expression analysis, and bioinformatic comparisons with existing datasets. We show CHD7 is required for correct expression of several genes established as major players in cardiac development, especially within the second heart field (SHF). We identified CHD7 binding sites in cardiac progenitor cells and found strong association with histone marks suggestive of dynamically regulated enhancers during the mesodermal to cardiac progenitor transition of mESC differentiation. Moreover, CHD7 shares a subset of its target sites with ISL1, a pioneer transcription factor in the cardiogenic gene regulatory network, including one enhancer modulating Fgf10 expression in SHF progenitor cells vs. differentiating cardiomyocytes. CONCLUSION We show that CHD7 interacts with ISL1, binds ISL1-regulated cardiac enhancers, and modulates gene expression across the mesodermal heart fields during cardiac morphogenesis.
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Affiliation(s)
- Athanasia Stathopoulou
- Developmental Biology of Birth Defects, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- School of Medical Imaging, Tianjin Medical University, Tianjin, China
| | | | - Robert G Kelly
- Aix-Marseille University, CNRS UMR 7288, IBDM, Marseille, France
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Departments of Neurology and Neurosciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Peter J Scambler
- Developmental Biology of Birth Defects, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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27
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Alzamrooni A, Mendes Vieira P, Murciano N, Wolton M, Schubert FR, Robson SC, Dietrich S. Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme. Dev Biol 2023; 501:39-59. [PMID: 37301464 DOI: 10.1016/j.ydbio.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
The vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm has generic cardiac competence, how long this may last, and what happens as cardiac competence fades, is not clear. Bone morphogenetic proteins (Bmps) are known to promote cardiogenesis. Using 41 different marker genes in the chicken embryo, we show that the paraxial head mesoderm that normally does not engage in cardiogenesis has the ability to respond to Bmp for a long time. However, Bmp signals are interpreted differently at different time points. Up to early head fold stages, the paraxial head mesoderm is able to read Bmps as signal to engage in the cardiac programme; the ability to upregulate smooth muscle markers is retained slightly longer. Notably, as cardiac competence fades, Bmp promotes the head skeletal muscle programme instead. The switch from cardiac to skeletal muscle competence is Wnt-independent as Wnt caudalises the head mesoderm and also suppresses Msc-inducing Bmp provided by the prechordal plate, thus suppressing both the cardiac and the head skeletal muscle programmes. Our study for the first time suggests a specific transition state in the embryo when cardiac competence is replaced by skeletal muscle competence. It sets the stage to unravel the cardiac-skeletal muscle antagonism that is known to partially collapse in heart failure.
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Affiliation(s)
- Afnan Alzamrooni
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Petra Mendes Vieira
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Nicoletta Murciano
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK; Nanion Technologies GmbH, Ganghoferstr. 70A, DE - 80339, München, Germany; Saarland University, Theoretical Medicine and Biosciences, Kirrbergerstr. 100, DE - 66424, Homburg, Germany
| | - Matthew Wolton
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Frank R Schubert
- Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Samuel C Robson
- Institute of Biological and Biomedical Sciences, Faculty of Science & Health, University of Portsmouth, Portsmouth, UK
| | - Susanne Dietrich
- Institute of Biological and Biomedical Sciences, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK.
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28
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Mei Y, Wang X, Zhang J, Liu D, He J, Huang C, Liao J, Wang Y, Feng Y, Li H, Liu X, Chen L, Yi W, Chen X, Bai HM, Wang X, Li Y, Wang L, Liang Z, Ren X, Qiu L, Hui Y, Zhang Q, Leng Q, Chen J, Jia G. Siglec-9 acts as an immune-checkpoint molecule on macrophages in glioblastoma, restricting T-cell priming and immunotherapy response. NATURE CANCER 2023; 4:1273-1291. [PMID: 37460871 DOI: 10.1038/s43018-023-00598-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/14/2023] [Indexed: 07/27/2023]
Abstract
Neoadjuvant immune-checkpoint blockade therapy only benefits a limited fraction of patients with glioblastoma multiforme (GBM). Thus, targeting other immunomodulators on myeloid cells is an attractive therapeutic option. Here, we performed single-cell RNA sequencing and spatial transcriptomics of patients with GBM treated with neoadjuvant anti-PD-1 therapy. We identified unique monocyte-derived tumor-associated macrophage subpopulations with functional plasticity that highly expressed the immunosuppressive SIGLEC9 gene and preferentially accumulated in the nonresponders to anti-PD-1 treatment. Deletion of Siglece (murine homolog) resulted in dramatically restrained tumor development and prolonged survival in mouse models. Mechanistically, targeting Siglece directly activated both CD4+ T cells and CD8+ T cells through antigen presentation, secreted chemokines and co-stimulatory factor interactions. Furthermore, Siglece deletion synergized with anti-PD-1/PD-L1 treatment to improve antitumor efficacy. Our data demonstrated that Siglec-9 is an immune-checkpoint molecule on macrophages that can be targeted to enhance anti-PD-1/PD-L1 therapeutic efficacy for GBM treatment.
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Affiliation(s)
- Yan Mei
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xiumei Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ji Zhang
- Department of Neurosurgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Junjie He
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Chunliu Huang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jing Liao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yingzhao Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yongyi Feng
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongyu Li
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | | | - Lingdan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Hong-Min Bai
- Department of Neurosurgery, General Hospital of Southern Theater Command, Guangzhou, China
| | - Xinyu Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yiyi Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lixiang Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhigang Liang
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | | | - Li Qiu
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yuan Hui
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Qingling Zhang
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Qibin Leng
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China.
| | - Jun Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Guangdong Engineering & Technology Research Center for Disease-Model Animals, Laboratory Animal Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Guangshuai Jia
- GMU-GIBH Joint School of Life Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, Guangzhou, China.
- Cancer Institute, Xuzhou Medical University, Xuzhou, China.
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China.
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29
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Huang X, Fu Y, Lee H, Zhao Y, Yang W, van de Leemput J, Han Z. Single-cell profiling of the developing embryonic heart in Drosophila. Development 2023; 150:dev201936. [PMID: 37526610 PMCID: PMC10482008 DOI: 10.1242/dev.201936] [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: 05/01/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Drosophila is an important model for studying heart development and disease. Yet, single-cell transcriptomic data of its developing heart have not been performed. Here, we report single-cell profiling of the entire fly heart using ∼3000 Hand-GFP embryos collected at five consecutive developmental stages, ranging from bilateral migrating rows of cardiac progenitors to a fused heart tube. The data revealed six distinct cardiac cell types in the embryonic fly heart: cardioblasts, both Svp+ and Tin+ subtypes; and five types of pericardial cell (PC) that can be distinguished by four key transcription factors (Eve, Odd, Ct and Tin) and include the newly described end of the line PC. Notably, the embryonic fly heart combines transcriptional signatures of the mammalian first and second heart fields. Using unique markers for each heart cell type, we defined their number and location during heart development to build a comprehensive 3D cell map. These data provide a resource to track the expression of any gene in the developing fly heart, which can serve as a reference to study genetic perturbations and cardiac diseases.
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Affiliation(s)
- Xiaohu Huang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yulong Fu
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Hangnoh Lee
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Wendy Yang
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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30
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Abstract
Epigenetics has transformed our understanding of the molecular basis of complex diseases, including cardiovascular and metabolic disorders. This review offers a comprehensive overview of the current state of knowledge on epigenetic processes implicated in cardiovascular and metabolic diseases, highlighting the potential of DNA methylation as a precision medicine biomarker and examining the impact of social determinants of health, gut bacterial epigenomics, noncoding RNA, and epitranscriptomics on disease development and progression. We discuss challenges and barriers to advancing cardiometabolic epigenetics research, along with the opportunities for novel preventive strategies, targeted therapies, and personalized medicine approaches that may arise from a better understanding of epigenetic processes. Emerging technologies, such as single-cell sequencing and epigenetic editing, hold the potential to further enhance our ability to dissect the complex interplay between genetic, environmental, and lifestyle factors. To translate research findings into clinical practice, interdisciplinary collaborations, technical and ethical considerations, and accessibility of resources and knowledge are crucial. Ultimately, the field of epigenetics has the potential to revolutionize the way we approach cardiovascular and metabolic diseases, paving the way for precision medicine and personalized health care, and improving the lives of millions of individuals worldwide affected by these conditions.
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Affiliation(s)
- Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, New York (A.A.B.)
| | - José Ordovás
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging, at Tufts University, Boston, MA (J.O.)
- IMDEA Food Institute, CEI UAM + CSIC, Madrid, Spain (J.O.)
- Consortium CIBERObn, Instituto de Salud Carlos III (ISCIII), Madrid, Spain (J.O.)
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31
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Bryl R, Nawrocki MJ, Jopek K, Kaczmarek M, Bukowska D, Antosik P, Mozdziak P, Zabel M, Dzięgiel P, Kempisty B. Transcriptomic Characterization of Genes Regulating the Stemness in Porcine Atrial Cardiomyocytes during Primary In Vitro Culture. Genes (Basel) 2023; 14:1223. [PMID: 37372403 PMCID: PMC10297922 DOI: 10.3390/genes14061223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Heart failure remains a major cause of death worldwide. There is a need to establish new management options as current treatment is frequently suboptimal. Clinical approaches based on autologous stem cell transplant is potentially a good alternative. The heart was long considered an organ unable to regenerate and renew. However, several reports imply that it may possess modest intrinsic regenerative potential. To allow for detailed characterization of cell cultures, whole transcriptome profiling was performed after 0, 7, 15, and 30 days of in vitro cell cultures (IVC) from the right atrial appendage and right atrial wall utilizing microarray technology. In total, 4239 differentially expressed genes (DEGs) with ratio > abs |2| and adjusted p-value ≤ 0.05 for the right atrial wall and 4662 DEGs for the right atrial appendage were identified. It was shown that a subset of DEGs, which have demonstrated some regulation of expression levels with the duration of the cell culture, were enriched in the following GO BP (Gene Ontology Biological Process) terms: "stem cell population maintenance" and "stem cell proliferation". The results were validated by RT-qPCR. The establishment and detailed characterization of in vitro culture of myocardial cells may be important for future applications of these cells in heart regeneration processes.
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Affiliation(s)
- Rut Bryl
- Section of Regenerative Medicine and Cancer Research, Natural Sciences Club, Faculty of Biology, Adam Mickiewicz University, Poznań, 61-614 Poznan, Poland;
| | - Mariusz J. Nawrocki
- Department of Anatomy, Poznan University of Medical Sciences, 60-781 Poznan, Poland;
| | - Karol Jopek
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland;
| | - Mariusz Kaczmarek
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-866 Poznan, Poland;
- Gene Therapy Laboratory, Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Dorota Bukowska
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland;
| | - Paweł Antosik
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland;
| | - Paul Mozdziak
- Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC 27695, USA;
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC 27695, USA
| | - Maciej Zabel
- Department of Human Morphology and Embryology, Division of Histology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.Z.); (P.D.)
- Division of Anatomy and Histology, University of Zielona Góra, 65-046 Zielona Góra, Poland
| | - Piotr Dzięgiel
- Department of Human Morphology and Embryology, Division of Histology and Embryology, Wroclaw Medical University, 50-368 Wroclaw, Poland; (M.Z.); (P.D.)
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland;
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC 27695, USA
- Department of Human Morphology and Embryology, Division of Anatomy, Wroclaw Medical University, 50-367 Wroclaw, Poland
- Department of Obstetrics and Gynaecology, University Hospital and Masaryk University, 62500 Brno, Czech Republic
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32
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Lan M, Zhang S, Gao L. Efficient Generation of Paired Single-Cell Multiomics Profiles by Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2301169. [PMID: 37114830 PMCID: PMC10375161 DOI: 10.1002/advs.202301169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/08/2023] [Indexed: 06/19/2023]
Abstract
Recent advances in single-cell sequencing technology have made it possible to measure multiple paired omics simultaneously in a single cell such as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-nucleus chromatin accessibility and mRNA expression sequencing (SNARE-seq). However, the widespread application of these single-cell multiomics profiling technologies has been limited by their experimental complexity, noise in nature, and high cost. In addition, single-omics sequencing technologies have generated tremendous and high-quality single-cell datasets but have yet to be fully utilized. Here, single-cell multiomics generation (scMOG), a deep learning-based framework to generate single-cell assay for transposase-accessible chromatin (ATAC) data in silico is developed from experimentally available single-cell RNA-seq measurements and vice versa. The results demonstrate that scMOG can accurately perform cross-omics generation between RNA and ATAC, and generate paired multiomics data with biological meanings when one omics is experimentally unavailable and out of training datasets. The generated ATAC, either alone or in combination with measured RNA, exhibits equivalent or superior performance to that of the experimentally measured counterparts throughout multiple downstream analyses. scMOG is also applied to human lymphoma data, which proves to be more effective in identifying tumor samples than the experimentally measured ATAC data. Finally, the performance of scMOG is investigated in other omics such as proteomics and it still shows robust performance on surface protein generation.
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Affiliation(s)
- Meng Lan
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Shixiong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, 710071, China
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33
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Long X, Yuan X, Du J. Single-cell and spatial transcriptomics: Advances in heart development and disease applications. Comput Struct Biotechnol J 2023; 21:2717-2731. [PMID: 37181659 PMCID: PMC10173363 DOI: 10.1016/j.csbj.2023.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
Current transcriptomics technologies, including bulk RNA-seq, single-cell RNA sequencing (scRNA-seq), single-nucleus RNA-sequencing (snRNA-seq), and spatial transcriptomics (ST), provide novel insights into the spatial and temporal dynamics of gene expression during cardiac development and disease processes. Cardiac development is a highly sophisticated process involving the regulation of numerous key genes and signaling pathways at specific anatomical sites and developmental stages. Exploring the cell biological mechanisms involved in cardiogenesis also contributes to congenital heart disease research. Meanwhile, the severity of distinct heart diseases, such as coronary heart disease, valvular disease, cardiomyopathy, and heart failure, is associated with cellular transcriptional heterogeneity and phenotypic alteration. Integrating transcriptomic technologies in the clinical diagnosis and treatment of heart diseases will aid in advancing precision medicine. In this review, we summarize applications of scRNA-seq and ST in the cardiac field, including organogenesis and clinical diseases, and provide insights into the promise of single-cell and spatial transcriptomics in translational research and precision medicine.
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Affiliation(s)
- Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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34
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Zhao Y, van de Leemput J, Han Z. The opportunities and challenges of using Drosophila to model human cardiac diseases. Front Physiol 2023; 14:1182610. [PMID: 37123266 PMCID: PMC10130661 DOI: 10.3389/fphys.2023.1182610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
The Drosophila heart tube seems simple, yet it has notable anatomic complexity and contains highly specialized structures. In fact, the development of the fly heart tube much resembles that of the earliest stages of mammalian heart development, and the molecular-genetic mechanisms driving these processes are highly conserved between flies and humans. Combined with the fly's unmatched genetic tools and a wide variety of techniques to assay both structure and function in the living fly heart, these attributes have made Drosophila a valuable model system for studying human heart development and disease. This perspective focuses on the functional and physiological similarities between fly and human hearts. Further, it discusses current limitations in using the fly, as well as promising prospects to expand the capabilities of Drosophila as a research model for studying human cardiac diseases.
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Affiliation(s)
- Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
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35
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Gromova T, Gehred ND, Vondriska TM. Single-cell transcriptomes in the heart: when every epigenome counts. Cardiovasc Res 2023; 119:64-78. [PMID: 35325060 PMCID: PMC10233279 DOI: 10.1093/cvr/cvac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
The response of an organ to stimuli emerges from the actions of individual cells. Recent cardiac single-cell RNA-sequencing studies of development, injury, and reprogramming have uncovered heterogeneous populations even among previously well-defined cell types, raising questions about what level of experimental resolution corresponds to disease-relevant, tissue-level phenotypes. In this review, we explore the biological meaning behind this cellular heterogeneity by undertaking an exhaustive analysis of single-cell transcriptomics in the heart (including a comprehensive, annotated compendium of studies published to date) and evaluating new models for the cardiac function that have emerged from these studies (including discussion and schematics that depict new hypotheses in the field). We evaluate the evidence to support the biological actions of newly identified cell populations and debate questions related to the role of cell-to-cell variability in development and disease. Finally, we present emerging epigenomic approaches that, when combined with single-cell RNA-sequencing, can resolve basic mechanisms of gene regulation and variability in cell phenotype.
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Affiliation(s)
- Tatiana Gromova
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Natalie D Gehred
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Thomas M Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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36
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Bak ST, Harvald EB, Ellman DG, Mathiesen SB, Chen T, Fang S, Andersen KS, Fenger CD, Burton M, Thomassen M, Andersen DC. Ploidy-stratified single cardiomyocyte transcriptomics map Zinc Finger E-Box Binding Homeobox 1 to underly cardiomyocyte proliferation before birth. Basic Res Cardiol 2023; 118:8. [PMID: 36862248 PMCID: PMC9981540 DOI: 10.1007/s00395-023-00979-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/31/2022] [Accepted: 01/21/2023] [Indexed: 03/03/2023]
Abstract
Whereas cardiomyocytes (CMs) in the fetal heart divide, postnatal CMs fail to undergo karyokinesis and/or cytokinesis and therefore become polyploid or binucleated, a key process in terminal CM differentiation. This switch from a diploid proliferative CM to a terminally differentiated polyploid CM remains an enigma and seems an obstacle for heart regeneration. Here, we set out to identify the transcriptional landscape of CMs around birth using single cell RNA sequencing (scRNA-seq) to predict transcription factors (TFs) involved in CM proliferation and terminal differentiation. To this end, we established an approach combining fluorescence activated cell sorting (FACS) with scRNA-seq of fixed CMs from developing (E16.5, P1, and P5) mouse hearts, and generated high-resolution single-cell transcriptomic maps of in vivo diploid and tetraploid CMs, increasing the CM resolution. We identified TF-networks regulating the G2/M phases of developing CMs around birth. ZEB1 (Zinc Finger E-Box Binding Homeobox 1), a hereto unknown TF in CM cell cycling, was found to regulate the highest number of cell cycle genes in cycling CMs at E16.5 but was downregulated around birth. CM ZEB1-knockdown reduced proliferation of E16.5 CMs, while ZEB1 overexpression at P0 after birth resulted in CM endoreplication. These data thus provide a ploidy stratified transcriptomic map of developing CMs and bring new insight to CM proliferation and endoreplication identifying ZEB1 as a key player in these processes.
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Affiliation(s)
- Sara Thornby Bak
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Eva Bang Harvald
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Ditte Gry Ellman
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Sabrina Bech Mathiesen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Ting Chen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Shu Fang
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Kristian Skriver Andersen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
- Clinical Institute, University of Southern Denmark, Odense, Denmark
| | | | - Mark Burton
- Clinical Institute, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Mads Thomassen
- Clinical Institute, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Ditte Caroline Andersen
- Andersen Group, Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark.
- Clinical Institute, University of Southern Denmark, Odense, Denmark.
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37
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Li C, Virgilio MC, Collins KL, Welch JD. Multi-omic single-cell velocity models epigenome-transcriptome interactions and improves cell fate prediction. Nat Biotechnol 2023; 41:387-398. [PMID: 36229609 PMCID: PMC10246490 DOI: 10.1038/s41587-022-01476-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/16/2022] [Indexed: 12/13/2022]
Abstract
Multi-omic single-cell datasets, in which multiple molecular modalities are profiled within the same cell, offer an opportunity to understand the temporal relationship between epigenome and transcriptome. To realize this potential, we developed MultiVelo, a differential equation model of gene expression that extends the RNA velocity framework to incorporate epigenomic data. MultiVelo uses a probabilistic latent variable model to estimate the switch time and rate parameters of chromatin accessibility and gene expression and improves the accuracy of cell fate prediction compared to velocity estimates from RNA only. Application to multi-omic single-cell datasets from brain, skin and blood cells reveals two distinct classes of genes distinguished by whether chromatin closes before or after transcription ceases. We also find four types of cell states: two states in which epigenome and transcriptome are coupled and two distinct decoupled states. Finally, we identify time lags between transcription factor expression and binding site accessibility and between disease-associated SNP accessibility and expression of the linked genes. MultiVelo is available on PyPI, Bioconda and GitHub ( https://github.com/welch-lab/MultiVelo ).
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Affiliation(s)
- Chen Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Maria C Virgilio
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kathleen L Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
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38
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Kelly RG. The heart field transcriptional landscape at single-cell resolution. Dev Cell 2023; 58:257-266. [PMID: 36809764 DOI: 10.1016/j.devcel.2023.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/06/2022] [Accepted: 01/27/2023] [Indexed: 02/22/2023]
Abstract
Organogenesis requires the orchestrated development of multiple cell lineages that converge, interact, and specialize to generate coherent functional structures, exemplified by transformation of the cardiac crescent into a four-chambered heart. Cardiomyocytes originate from the first and second heart fields, which make different regional contributions to the definitive heart. In this review, a series of recent single-cell transcriptomic analyses, together with genetic tracing experiments, are discussed, providing a detailed panorama of the cardiac progenitor cell landscape. These studies reveal that first heart field cells originate in a juxtacardiac field adjacent to extraembryonic mesoderm and contribute to the ventrolateral side of the cardiac primordium. In contrast, second heart field cells are deployed dorsomedially from a multilineage-primed progenitor population via arterial and venous pole pathways. Refining our knowledge of the origin and developmental trajectories of cells that build the heart is essential to address outstanding challenges in cardiac biology and disease.
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Affiliation(s)
- Robert G Kelly
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille, France.
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39
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Kraus L, Beavens B. The Current Therapeutic Role of Chromatin Remodeling for the Prognosis and Treatment of Heart Failure. Biomedicines 2023; 11:biomedicines11020579. [PMID: 36831115 PMCID: PMC9953583 DOI: 10.3390/biomedicines11020579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Cardiovascular diseases are a major cause of death globally, with no cure to date. Many interventions have been studied and suggested, of which epigenetics and chromatin remodeling have been the most promising. Over the last decade, major advancements have been made in the field of chromatin remodeling, particularly for the treatment of heart failure, because of innovations in bioinformatics and gene therapy. Specifically, understanding changes to the chromatin architecture have been shown to alter cardiac disease progression via variations in genomic sequencing, targeting cardiac genes, using RNA molecules, and utilizing chromatin remodeler complexes. By understanding these chromatin remodeling mechanisms in an injured heart, treatments for heart failure have been suggested through individualized pharmaceutical interventions as well as biomarkers for major disease states. By understanding the current roles of chromatin remodeling in heart failure, a potential therapeutic approach may be discovered in the future.
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40
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Dominguez MH, Krup AL, Muncie JM, Bruneau BG. Graded mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart. Cell 2023; 186:479-496.e23. [PMID: 36736300 PMCID: PMC10091855 DOI: 10.1016/j.cell.2023.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/07/2022] [Accepted: 01/03/2023] [Indexed: 02/05/2023]
Abstract
Using four-dimensional whole-embryo light sheet imaging with improved and accessible computational tools, we longitudinally reconstruct early murine cardiac development at single-cell resolution. Nascent mesoderm progenitors form opposing density and motility gradients, converting the temporal birth sequence of gastrulation into a spatial anterolateral-to-posteromedial arrangement. Migrating precardiac mesoderm does not strictly preserve cellular neighbor relationships, and spatial patterns only become solidified as the cardiac crescent emerges. Progenitors undergo a mesenchymal-to-epithelial transition, with a first heart field (FHF) ridge apposing a motile juxta-cardiac field (JCF). Anchored along the ridge, the FHF epithelium rotates the JCF forward to form the initial heart tube, along with push-pull morphodynamics of the second heart field. In Mesp1 mutants that fail to make a cardiac crescent, mesoderm remains highly motile but directionally incoherent, resulting in density gradient inversion. Our practicable live embryo imaging approach defines spatial origins and behaviors of cardiac progenitors and identifies their unanticipated morphological transitions.
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Affiliation(s)
- Martin H Dominguez
- Gladstone Institutes, San Francisco, CA, USA; Department of Medicine, Division of Cardiology, University of California, San Francisco, San Francisco, CA, USA; Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, USA.
| | - Alexis Leigh Krup
- Gladstone Institutes, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | | | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA; Department of Pediatrics, Cardiovascular Research Institute, Institute for Human Genetics, and Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA.
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41
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Cai S, Hu B, Wang X, Liu T, Lin Z, Tong X, Xu R, Chen M, Duo T, Zhu Q, Liang Z, Li E, Chen Y, Li J, Liu X, Mo D. Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig. BMC Biol 2023; 21:19. [PMID: 36726129 PMCID: PMC9893630 DOI: 10.1186/s12915-023-01519-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/18/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Skeletal muscle development is a multistep process whose understanding is central in a broad range of fields and applications, from the potential medical value to human society, to its economic value associated with improvement of agricultural animals. Skeletal muscle initiates in the somites, with muscle precursor cells generated in the dermomyotome and dermomyotome-derived myotome before muscle differentiation ensues, a developmentally regulated process that is well characterized in model organisms. However, the regulation of skeletal muscle ontogeny during embryonic development remains poorly defined in farm animals, for instance in pig. Here, we profiled gene expression and chromatin accessibility in developing pig somites and myotomes at single-cell resolution. RESULTS We identified myogenic cells and other cell types and constructed a differentiation trajectory of pig skeletal muscle ontogeny. Along this trajectory, the dynamic changes in gene expression and chromatin accessibility coincided with the activities of distinct cell type-specific transcription factors. Some novel genes upregulated along the differentiation trajectory showed higher expression levels in muscular dystrophy mice than that in healthy mice, suggesting their involvement in myogenesis. Integrative analysis of chromatin accessibility, gene expression data, and in vitro experiments identified EGR1 and RHOB as critical regulators of pig embryonic myogenesis. CONCLUSIONS Collectively, our results enhance our understanding of the molecular and cellular dynamics in pig embryonic myogenesis and offer a high-quality resource for the further study of pig skeletal muscle development and human muscle disease.
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Affiliation(s)
- Shufang Cai
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Bin Hu
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaoyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tongni Liu
- Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Zhuhu Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Xian Tong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Rong Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Meilin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Tianqi Duo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Qi Zhu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Ziyun Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Enru Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Jianhao Li
- Guangdong Key Laboratory of Animal Breeding and Nutrition, State Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 Guangdong China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510006 Guangdong China
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42
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Zhang J, Ouyang Z, Xia L, Wang Q, Zheng F, Xu K, Xing Y, Wei K, Shi S, Li C, Yang J. Dynamic chromatin landscape encodes programs for perinatal transition of cardiomyocytes. Cell Death Dis 2023; 9:11. [PMID: 36653336 PMCID: PMC9849264 DOI: 10.1038/s41420-023-01322-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
The perinatal period occurring immediately before and after birth is critical for cardiomyocytes because they must change rapidly to accommodate the switch from fetal to neonatal circulation after birth. This transition is a well-orchestrated process, and any perturbation leads to unhealthy cardiomyocytes and heart disease. Despite its importance, little is known about how this transition is regulated and controlled. Here, by mapping the genome-wide chromatin accessibility, transcription-centered long-range chromatin interactions and gene expression in cardiomyocytes undergoing perinatal transition, we discovered two key transcription factors, MEF2 and AP1, that are crucial for driving the phenotypic changes within the perinatal window. Thousands of dynamic regulatory elements were found in perinatal cardiomyocytes and we show these elements mediated the transcriptional reprogramming through an elegant chromatin high-order architecture. We recompiled transcriptional program of induced stem cell-derived cardiomyocytes according to our discovered network, and they showed adult cardiomyocyte-like electrophysiological expression. Our work provides a comprehensive regulatory resource of cardiomyocytes perinatal reprogramming, and aids the gap-filling of cardiac translational research.
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Affiliation(s)
- Jing Zhang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Zhaohui Ouyang
- grid.24516.340000000123704535Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092 Shanghai, China
| | - Limei Xia
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Qi Wang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Feng Zheng
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Kun Xu
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Yuexian Xing
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Ke Wei
- grid.24516.340000000123704535Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092 Shanghai, China
| | - Shaolin Shi
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
| | - Chaojun Li
- grid.89957.3a0000 0000 9255 8984State Key Laboratory of Reproductive Medicine and China International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Gusu School, Nanjing Medical University, 211166 Nanjing, China
| | - Jingping Yang
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China ,grid.41156.370000 0001 2314 964XJiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, 210093 Nanjing, Jiangsu China
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43
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Yekelchyk M, Guenther S, Braun T. Assay for Transposase-Accessible Chromatin Using Sequencing of Freshly Isolated Muscle Stem Cells. Methods Mol Biol 2023; 2640:397-412. [PMID: 36995609 DOI: 10.1007/978-1-0716-3036-5_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Actively transcribed genes harbor cis-regulatory modules with comparatively low nucleosome occupancy and few high-order structures (="open chromatin"), whereas non-transcribed genes are characterized by high nucleosome density and extensive interactions between nucleosomes (="closed chromatin"), preventing transcription factor binding. Knowledge about chromatin accessibility is crucial to understand gene regulatory networks determining cellular decisions. Several techniques are available to map chromatin accessibility, among which the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is one of the most popular. ATAC-seq is based on a straightforward and robust protocol but requires adjustments for different cell types. Here, we describe an optimized protocol for ATAC-seq of freshly isolated murine muscle stem cells. We provide details for the isolation of MuSC, tagmentation, library amplification, double-sided SPRI bead cleanup, and library quality assessment and give recommendations for sequencing parameters and downstream analysis. The protocol should facilitate generation of high-quality data sets of chromatin accessibility in MuSCs, even for newcomers to the field.
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Affiliation(s)
- Michail Yekelchyk
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Stefan Guenther
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am Main, Germany.
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44
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Single-cell transcriptomic analysis identifies murine heart molecular features at embryonic and neonatal stages. Nat Commun 2022; 13:7960. [PMID: 36575170 PMCID: PMC9794824 DOI: 10.1038/s41467-022-35691-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Heart development is a continuous process involving significant remodeling during embryogenesis and neonatal stages. To date, several groups have used single-cell sequencing to characterize the heart transcriptomes but failed to capture the progression of heart development at most stages. This has left gaps in understanding the contribution of each cell type across cardiac development. Here, we report the transcriptional profile of the murine heart from early embryogenesis to late neonatal stages. Through further analysis of this dataset, we identify several transcriptional features. We identify gene expression modules enriched at early embryonic and neonatal stages; multiple cell types in the left and right atriums are transcriptionally distinct at neonatal stages; many congenital heart defect-associated genes have cell type-specific expression; stage-unique ligand-receptor interactions are mostly between epicardial cells and other cell types at neonatal stages; and mutants of epicardium-expressed genes Wt1 and Tbx18 have different heart defects. Assessment of this dataset serves as an invaluable source of information for studies of heart development.
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45
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Lopez LV, Camberos V, Bailey LL, Hasaniya N, Ramos C, Hughes L, Knox C, Kearns-Jonker MK. MicroRNA Expression in the Infarcted Heart Following Neonatal Cardiovascular Progenitor Cell Transplantation in a Sheep Model of Stem Cell-Based Repair. Cell Transplant 2022; 31:9636897221136787. [PMID: 36564913 PMCID: PMC9793054 DOI: 10.1177/09636897221136787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Myocardial infarctions affect approximately 735,000 people annually in the United States and have a substantial impact on quality of life. Neonates have an enhanced capability of repairing cardiovascular damage, while adults do not. The mechanistic basis for this age-dependent difference in regenerative capacity remains unknown. Recent studies have shown that microRNAs (miRNAs) play a significant role in regulating the regenerative ability of cardiovascular cells. This report defines the alterations in miRNA expression within the cardiovascular repair zone of infarcted sheep hearts following intracardiac injection of neonatal islet-1+ cardiovascular progenitor cells. Sheep were infarcted via left anterior descending coronary artery ligation. After 3 to 4 weeks of infarction, sheep neonatal islet-1+ cardiovascular progenitor cells were injected into the infarcted area for repair. Cell-treated sheep were euthanized 2 months following cell injection, and their hearts were harvested for the analysis of miRNA and gene expression within the cardiovascular repair zone. Ten miRNAs were differentially regulated in vivo, including miR-99, miR-100, miR-302a, miR-208a, miR-665, miR-1, miR-499a, miR-34a, miR-133a, and miR-199a. These miRNAs promote stemness, cell division, and survival. Several signaling pathways are regulated by these miRNAs, including Hippo, Wnt, and Erythroblastic Leukemia Viral Oncogene B (ERBB). Transcripts encoding Wnt, ERBB, and Neuregulin 1 (NRG1) were elevated in vivo in the infarct repair zone. Wnt5a signaling and ERBB/NRG1 transcripts contribute to activation of Yes-Associated Protein 1. MiRNAs that impact proliferation, cell survival, and signaling pathways that promote regeneration were induced during cardiovascular repair in the sheep model. This information can be used to design new approaches for the optimization of miRNA-based treatments for the heart.
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Affiliation(s)
- Larry V. Lopez
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Victor Camberos
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Leonard L. Bailey
- Department of Cardiovascular and
Thoracic Surgery, Loma Linda University School of Medicine, Loma Linda, CA,
USA
| | - Nahidh Hasaniya
- Department of Cardiovascular and
Thoracic Surgery, Loma Linda University School of Medicine, Loma Linda, CA,
USA
| | - Christopher Ramos
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Lorelei Hughes
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Cole Knox
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Mary K. Kearns-Jonker
- Department of Pathology and Human
Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA,Mary K. Kearns-Jonker, Department of
Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma
Linda, CA 92350, USA.
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46
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Wang Y, Sun X, Zhao H. Benchmarking automated cell type annotation tools for single-cell ATAC-seq data. Front Genet 2022; 13:1063233. [PMID: 36583014 PMCID: PMC9792779 DOI: 10.3389/fgene.2022.1063233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
As single-cell chromatin accessibility profiling methods advance, scATAC-seq has become ever more important in the study of candidate regulatory genomic regions and their roles underlying developmental, evolutionary, and disease processes. At the same time, cell type annotation is critical in understanding the cellular composition of complex tissues and identifying potential novel cell types. However, most existing methods that can perform automated cell type annotation are designed to transfer labels from an annotated scRNA-seq data set to another scRNA-seq data set, and it is not clear whether these methods are adaptable to annotate scATAC-seq data. Several methods have been recently proposed for label transfer from scRNA-seq data to scATAC-seq data, but there is a lack of benchmarking study on the performance of these methods. Here, we evaluated the performance of five scATAC-seq annotation methods on both their classification accuracy and scalability using publicly available single-cell datasets from mouse and human tissues including brain, lung, kidney, PBMC, and BMMC. Using the BMMC data as basis, we further investigated the performance of these methods across different data sizes, mislabeling rates, sequencing depths and the number of cell types unique to scATAC-seq. Bridge integration, which is the only method that requires additional multimodal data and does not need gene activity calculation, was overall the best method and robust to changes in data size, mislabeling rate and sequencing depth. Conos was the most time and memory efficient method but performed the worst in terms of prediction accuracy. scJoint tended to assign cells to similar cell types and performed relatively poorly for complex datasets with deep annotations but performed better for datasets only with major label annotations. The performance of scGCN and Seurat v3 was moderate, but scGCN was the most time-consuming method and had the most similar performance to random classifiers for cell types unique to scATAC-seq.
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Affiliation(s)
- Yuge Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Xingzhi Sun
- Department of Statistics and Data Science, Yale University, New Haven, CT, United States
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
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47
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Abplanalp WT, Tucker N, Dimmeler S. Single-cell technologies to decipher cardiovascular diseases. Eur Heart J 2022; 43:4536-4547. [PMID: 35265972 PMCID: PMC9659476 DOI: 10.1093/eurheartj/ehac095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/30/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiovascular disease remains the leading cause of death worldwide. A deeper understanding of the multicellular composition and molecular processes may help to identify novel therapeutic strategies. Single-cell technologies such as single-cell or single-nuclei RNA sequencing provide expression profiles of individual cells and allow for dissection of heterogeneity in tissue during health and disease. This review will summarize (i) how these novel technologies have become critical for delineating mechanistic drivers of cardiovascular disease, particularly, in humans and (ii) how they might serve as diagnostic tools for risk stratification or individualized therapy. The review will further discuss technical pitfalls and provide an overview of publicly available human and mouse data sets that can be used as a resource for research.
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Affiliation(s)
- Wesley Tyler Abplanalp
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany
- German Center for Cardiovascular Research DZHK, Partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Nathan Tucker
- Masonic Medical Research Institute, Utica, NY, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University Frankfurt, Theodor Stern Kai 7, 60590 Frankfurt, Germany
- German Center for Cardiovascular Research DZHK, Partner site Frankfurt Rhine-Main, Berlin, Germany
- Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany
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Ding S, Zhang X, Qiu H, Wo J, Zhang F, Na J. Non-cardiomyocytes in the heart in embryo development, health, and disease, a single-cell perspective. Front Cell Dev Biol 2022; 10:873264. [PMID: 36393852 PMCID: PMC9661523 DOI: 10.3389/fcell.2022.873264] [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: 02/10/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022] Open
Abstract
Recent single-cell atlases of the heart gave unprecedented details about the diversity of cell types and states during heart development in health and disease conditions. Beyond a profiling tool, researchers also use single-cell analyses to dissect the mechanism of diseases in animal models. The new knowledge from these studies revealed that beating cardiomyocytes account for less than 50% of the total heart cell population. In contrast, non-cardiomyocytes (NCMs), such as cardiac fibroblasts, endothelial cells, and immune cells, make up the remaining proportion and have indispensable roles in structural support, homeostasis maintenance, and injury repair of the heart. In this review, we categorize the composition and characteristics of NCMs from the latest single-cell studies of the heart in various contexts and compare the findings from both human samples and mouse models. This information will enrich our understanding of the cellular basis of heart development and diseases and provide insights into the potential therapeutic targets in NCMs to repair the heart.
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Affiliation(s)
- Shuangyuan Ding
- School of Medicine, Tsinghua University, Beijing, China
- Center for Life Sciences, Tsinghua University and Peking University, Beijing, China
- *Correspondence: Shuangyuan Ding, ; Jie Na,
| | - Xingwu Zhang
- School of Medicine, Tsinghua University, Beijing, China
| | - Hui Qiu
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaoyang Wo
- Center for Life Sciences, Tsinghua University and Peking University, Beijing, China
| | - Fengzhi Zhang
- Central Laboratory, First Hospital of Tsinghua University, Beijing, China
| | - Jie Na
- School of Medicine, Tsinghua University, Beijing, China
- *Correspondence: Shuangyuan Ding, ; Jie Na,
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Balasooriya GI, Spector DL. Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. Nat Commun 2022; 13:5984. [PMID: 36216821 PMCID: PMC9550772 DOI: 10.1038/s41467-022-33722-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/27/2022] [Indexed: 11/29/2022] Open
Abstract
Each mammalian autosomal gene is represented by two alleles in diploid cells. To our knowledge, no insights have been made in regard to allele-specific regulatory mechanisms of autosomes. Here we use allele-specific single cell transcriptomic analysis to elucidate the establishment of monoallelic gene expression in the cardiac lineage. We find that monoallelically expressed autosomal genes in mESCs and mouse blastocyst cells are differentially regulated based on the genetic background of the parental alleles. However, the genetic background of the allele does not affect the establishment of monoallelic genes in differentiated cardiomyocytes. Additionally, we observe epigenetic differences between deterministic and random autosomal monoallelic genes. Moreover, we also find a greater contribution of the maternal versus paternal allele to the development and homeostasis of cardiac tissue and in cardiac health, highlighting the importance of maternal influence in male cardiac tissue homeostasis. Our findings emphasize the significance of allele-specific insights into gene regulation in development, homeostasis and disease.
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Carangelo G, Magi A, Semeraro R. From multitude to singularity: An up-to-date overview of scRNA-seq data generation and analysis. Front Genet 2022; 13:994069. [PMID: 36263428 PMCID: PMC9575985 DOI: 10.3389/fgene.2022.994069] [Citation(s) in RCA: 7] [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: 07/14/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022] Open
Abstract
Single cell RNA sequencing (scRNA-seq) is today a common and powerful technology in biomedical research settings, allowing to profile the whole transcriptome of a very large number of individual cells and reveal the heterogeneity of complex clinical samples. Traditionally, cells have been classified by their morphology or by expression of certain proteins in functionally distinct settings. The advent of next generation sequencing (NGS) technologies paved the way for the detection and quantitative analysis of cellular content. In this context, transcriptome quantification techniques made their advent, starting from the bulk RNA sequencing, unable to dissect the heterogeneity of a sample, and moving to the first single cell techniques capable of analyzing a small number of cells (1-100), arriving at the current single cell techniques able to generate hundreds of thousands of cells. As experimental protocols have improved rapidly, computational workflows for processing the data have also been refined, opening up to novel methods capable of scaling computational times more favorably with the dataset size and making scRNA-seq much better suited for biomedical research. In this perspective, we will highlight the key technological and computational developments which have enabled the analysis of this growing data, making the scRNA-seq a handy tool in clinical applications.
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Affiliation(s)
- Giulia Carangelo
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Alberto Magi
- Department of Information Engineering, University of Florence, Florence, Italy
| | - Roberto Semeraro
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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