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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [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: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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2
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Benard EL, Küçükaylak I, Hatzold J, Berendes KU, Carney TJ, Beleggia F, Hammerschmidt M. wnt10a is required for zebrafish median fin fold maintenance and adult unpaired fin metamorphosis. Dev Dyn 2024; 253:566-592. [PMID: 37870737 PMCID: PMC11035493 DOI: 10.1002/dvdy.672] [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: 08/24/2023] [Revised: 10/03/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Mutations of human WNT10A are associated with odonto-ectodermal dysplasia syndromes. Here, we present analyses of wnt10a loss-of-function mutants in the zebrafish. RESULTS wnt10a mutant zebrafish embryos display impaired tooth development and a collapsing median fin fold (MFF). Rescue experiments show that wnt10a is essential for MFF maintenance both during embryogenesis and later metamorphosis. The MFF collapse could not be attributed to increased cell death or altered proliferation rates of MFF cell types. Rather, wnt10a mutants show reduced expression levels of dlx2a in distal-most MFF cells, followed by compromised expression of col1a1a and other extracellular matrix proteins encoding genes. Transmission electron microscopy analysis shows that although dermal MFF compartments of wnt10a mutants initially are of normal morphology, with regular collagenous actinotrichia, positioning of actinotrichia within the cleft of distal MFF cells becomes compromised, coinciding with actinotrichia shrinkage and MFF collapse. CONCLUSIONS MFF collapse of wnt10a mutant zebrafish is likely caused by the loss of distal properties in the developing MFF, strikingly similar to the proposed molecular pathomechanisms underlying the teeth defects caused by the loss of Wnt10 in fish and mammals. In addition, it points to thus fur unknown mechanisms controlling the linear growth and stability of actinotrichia and their collagen fibrils.
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Affiliation(s)
- Erica L. Benard
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Ismail Küçükaylak
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Julia Hatzold
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Kilian U.W. Berendes
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
| | - Thomas J. Carney
- Discovery Research Division, Institute of Molecular and
Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research),
Singapore, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological
University, Singapore, Republic of Singapore
| | - Filippo Beleggia
- Department I of Internal Medicine, Faculty of Medicine and
University Hospital Cologne, University of Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine
and University Hospital Cologne, University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne
Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital Cologne,
University of Cologne, Cologne, Germany
| | - Matthias Hammerschmidt
- Institute of Zoology, Developmental Biology Unit,
University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of
Cologne, Cologne, Germany
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3
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Kinget L, Naulaerts S, Govaerts J, Vanmeerbeek I, Sprooten J, Laureano RS, Dubroja N, Shankar G, Bosisio FM, Roussel E, Verbiest A, Finotello F, Ausserhofer M, Lambrechts D, Boeckx B, Wozniak A, Boon L, Kerkhofs J, Zucman-Rossi J, Albersen M, Baldewijns M, Beuselinck B, Garg AD. A spatial architecture-embedding HLA signature to predict clinical response to immunotherapy in renal cell carcinoma. Nat Med 2024; 30:1667-1679. [PMID: 38773341 DOI: 10.1038/s41591-024-02978-9] [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: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 05/23/2024]
Abstract
An important challenge in the real-world management of patients with advanced clear-cell renal cell carcinoma (aRCC) is determining who might benefit from immune checkpoint blockade (ICB). Here we performed a comprehensive multiomics mapping of aRCC in the context of ICB treatment, involving discovery analyses in a real-world data cohort followed by validation in independent cohorts. We cross-connected bulk-tumor transcriptomes across >1,000 patients with validations at single-cell and spatial resolutions, revealing a patient-specific crosstalk between proinflammatory tumor-associated macrophages and (pre-)exhausted CD8+ T cells that was distinguished by a human leukocyte antigen repertoire with higher preference for tumoral neoantigens. A cross-omics machine learning pipeline helped derive a new tumor transcriptomic footprint of neoantigen-favoring human leukocyte antigen alleles. This machine learning signature correlated with positive outcome following ICB treatment in both real-world data and independent clinical cohorts. In experiments using the RENCA-tumor mouse model, CD40 agonism combined with PD1 blockade potentiated both proinflammatory tumor-associated macrophages and CD8+ T cells, thereby achieving maximal antitumor efficacy relative to other tested regimens. Thus, we present a new multiomics and spatial map of the immune-community architecture that drives ICB response in patients with aRCC.
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Affiliation(s)
- Lisa Kinget
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Stefan Naulaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Isaure Vanmeerbeek
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Raquel S Laureano
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolina Dubroja
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Gautam Shankar
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Francesca M Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Eduard Roussel
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Francesca Finotello
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Markus Ausserhofer
- Department of Molecular Biology, Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | - Johan Kerkhofs
- Histocompatibility and Immunogenetics Laboratory, Belgian Red Cross-Flanders, Mechelen, Belgium
| | - Jessica Zucman-Rossi
- Inserm, UMRS-1138, Génomique fonctionnelle des tumeurs solides, Centre de recherche des Cordeliers, Paris, France
| | - Maarten Albersen
- Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | | | - Benoit Beuselinck
- Laboratory of Experimental Oncology, KU Leuven, Leuven, Belgium.
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.
| | - Abhishek D Garg
- Laboratory of Cell Stress and Immunity (CSI), Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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4
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Wilson CA, Batzel P, Postlethwait JH. Direct male development in chromosomally ZZ zebrafish. Front Cell Dev Biol 2024; 12:1362228. [PMID: 38529407 PMCID: PMC10961373 DOI: 10.3389/fcell.2024.1362228] [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: 12/27/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish (Danio rerio), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome, or fewer than two Z chromosomes, is essential to initiate oocyte development; and without the W factor, or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
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5
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Gurung S, Restrepo NK, Sumanas S. Endocardium gives rise to blood cells in zebrafish embryos. Cell Rep 2024; 43:113736. [PMID: 38308842 PMCID: PMC10993658 DOI: 10.1016/j.celrep.2024.113736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 11/14/2023] [Accepted: 01/17/2024] [Indexed: 02/05/2024] Open
Abstract
Previous studies have suggested that the endocardium contributes to hematopoiesis in murine embryos, although definitive evidence to demonstrate the hematopoietic potential of the endocardium is still missing. Here, we use a zebrafish embryonic model to test the emergence of hematopoietic progenitors from the endocardium. By using a combination of expression analysis, time-lapse imaging, and lineage-tracing approaches, we demonstrate that myeloid cells emerge from the endocardium in zebrafish embryos. Inhibition of Etv2/Etsrp or Scl/Tal1, two known master regulators of hematopoiesis and vasculogenesis, does not affect the emergence of endocardial-derived myeloid cells, while inhibition of Hedgehog signaling results in their reduction. Single-cell RNA sequencing analysis followed by experimental validation suggests that the endocardium is the major source of neutrophilic granulocytes. These findings will promote our understanding of alternative mechanisms involved in hematopoiesis, which are likely to be conserved between zebrafish and mammalian embryos.
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Affiliation(s)
- Suman Gurung
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL 33602, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pathology, Advanced Diagnostics Laboratories, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Nicole K Restrepo
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL 33602, USA
| | - Saulius Sumanas
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL 33602, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; University of Cincinnati College of Medicine, Department of Pediatrics, Cincinnati, OH 45229, USA.
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6
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Zhu L, Gou W, Ou L, Liu B, Liu M, Feng H. Role and new insights of microfibrillar-associated protein 4 in fibrotic diseases. APMIS 2024; 132:55-67. [PMID: 37957836 DOI: 10.1111/apm.13358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023]
Abstract
Fibrosis is one of the most worrisome complications of chronic inflammatory diseases, leading to tissue damage, organ failure, and ultimately, death. The most notable pathological characteristic of fibrosis is the excessive accumulation of extracellular matrix (ECM) components such as collagen and fibronectin adjacent to foci of inflammation or damage. The human microfibrillar-associated protein 4 (MFAP4), an important member of the superfamily of fibrinogen-related proteins, is considered to have an extremely important role in ECM transformation of fibrogenesis. This review summarizes the structure, characteristics, and physiological functions of MFAP4 and the importance of MFAP4 in various fibrotic diseases. Meanwhile, we elaborated the underlying actions and mechanisms of MFAP4 in the development of fibrosis, suggesting that a better understand of MFAP4 broadens novel perspective for early screening, diagnosis, prognostic risk assessment, and treatment of fibrotic diseases.
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Affiliation(s)
- Long Zhu
- Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Changsha, China
- Xiangya Stomatological Hospital, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Wenqun Gou
- Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Changsha, China
- Xiangya Stomatological Hospital, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
- Changsha Stomatological Hospital, Changsha, China
| | - Lijia Ou
- Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Changsha, China
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Binjie Liu
- Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Changsha, China
- Xiangya Stomatological Hospital, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Manyi Liu
- Xiangya Stomatological Hospital, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Hui Feng
- Hunan Clinical Research Center of Oral Major Diseases and Oral Health, Changsha, China
- Xiangya Stomatological Hospital, Changsha, China
- Xiangya School of Stomatology, Central South University, Changsha, China
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7
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Duan S, Li H, Wang Z, Li J, Huang W, Fang Z, Li C, Zeng Z, Sun B, Liu Y. Tibetan tea consumption prevents obesity by modulating the cellular composition and metabolic reprogramming of white adipose tissue. Food Funct 2024; 15:208-222. [PMID: 38047533 DOI: 10.1039/d3fo03506a] [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: 12/05/2023]
Abstract
Obesity, a global health concern, is linked with numerous metabolic and inflammatory disorders. Tibetan tea, a traditional Chinese beverage rich in theabrownin, is investigated in this study for its potential anti-obesity effects. Our work demonstrates that Tibetan tea consumption in C57BL/6J mice significantly mitigates obesity-related phenotypic changes without altering energy intake. Computational prediction revealed that Tibetan tea consumption reconstructs gene expression in white adipose tissue (WAT), promoting lipid catabolism and thereby increasing energy expenditure. We also note that Tibetan tea suppresses inflammation in WAT, reducing adipocyte hyperplasia and immune cell infiltration. Furthermore, Tibetan tea induces profound metabolic reprogramming, influencing amino acid metabolic pathways, specifically enhancing glutamine synthesis, which in turn suppresses pro-inflammatory chemokine production. These findings highlight Tibetan tea as a potential candidate in obesity prevention, providing a nuanced understanding of its capacity to modulate the cellular composition and metabolic landscape of WAT.
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Affiliation(s)
- Songqi Duan
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Hongyu Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Ziqi Wang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Junqi Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Weimin Huang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Zhengfeng Fang
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Cheng Li
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Zhen Zeng
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
| | - Baofa Sun
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuntao Liu
- College of Food Science, Sichuan Agricultural University, Yaan, 625014, China.
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8
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Zhang G, Lu J, Zheng J, Mei S, Li H, Zhang X, Ping A, Gao S, Fang Y, Yu J. Spi1 regulates the microglial/macrophage inflammatory response via the PI3K/AKT/mTOR signaling pathway after intracerebral hemorrhage. Neural Regen Res 2024; 19:161-170. [PMID: 37488863 PMCID: PMC10479839 DOI: 10.4103/1673-5374.375343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 07/26/2023] Open
Abstract
Preclinical and clinical studies have shown that microglia and macrophages participate in a multiphasic brain damage repair process following intracerebral hemorrhage. The E26 transformation-specific sequence-related transcription factor Spi1 regulates microglial/macrophage commitment and maturation. However, the effect of Spi1 on intracerebral hemorrhage remains unclear. In this study, we found that Spi1 may regulate recovery from the neuroinflammation and neurofunctional damage caused by intracerebral hemorrhage by modulating the microglial/macrophage transcriptome. We showed that high Spi1 expression in microglia/macrophages after intracerebral hemorrhage is associated with the activation of many pathways that promote phagocytosis, glycolysis, and autophagy, as well as debris clearance and sustained remyelination. Notably, microglia with higher levels of Spi1 expression were characterized by activation of pathways associated with a variety of hemorrhage-related cellular processes, such as complement activation, angiogenesis, and coagulation. In conclusion, our results suggest that Spi1 plays a vital role in the microglial/macrophage inflammatory response following intracerebral hemorrhage. This new insight into the regulation of Spi1 and its target genes may advance our understanding of neuroinflammation in intracerebral hemorrhage and provide therapeutic targets for patients with intracerebral hemorrhage.
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Affiliation(s)
- Guoqiang Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jianan Lu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingwei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Shuhao Mei
- Department of Neurosurgery, Huashan Hospital of Fudan University School of Medicine, Shanghai, China
| | - Huaming Li
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Xiaotao Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - An Ping
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Shiqi Gao
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Yuanjian Fang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jun Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
- Clinical Research Center for Neurological Diseases of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou, Zhejiang Province, China
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9
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Wilson CA, Batzel P, Postlethwait JH. Direct Male Development in Chromosomally ZZ Zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573483. [PMID: 38234788 PMCID: PMC10793451 DOI: 10.1101/2023.12.27.573483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish ( Danio rerio ), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB strain fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome or fewer than two Z chromosomes is essential to initiate oocyte development; and without the W factor or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
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10
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Ninomiya I, Koyama A, Otsu Y, Onodera O, Kanazawa M. Regeneration of the cerebral cortex by direct chemical reprogramming of macrophages into neuronal cells in acute ischemic stroke. Front Cell Neurosci 2023; 17:1225504. [PMID: 37636590 PMCID: PMC10457112 DOI: 10.3389/fncel.2023.1225504] [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: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Theoretically, direct chemical reprogramming of somatic cells into neurons in the infarct area represents a promising regenerative therapy for ischemic stroke. Previous studies have reported that human fibroblasts and astrocytes transdifferentiate into neuronal cells in the presence of small molecules without introducing ectopic transgenes. However, the optimal combination of small molecules for the transdifferentiation of macrophages into neurons has not yet been determined. The authors hypothesized that a combination of small molecules could induce the transdifferentiation of monocyte-derived macrophages into neurons and that the administration of this combination may be a regenerative therapy for ischemic stroke because monocytes and macrophages are directly involved in the ischemic area. Transcriptomes and morphologies of the cells were compared before and after stimulation using RNA sequencing and immunofluorescence staining. Microscopic analyses were also performed to identify cell markers and evaluate functional recovery by blinded examination following the administration of small molecules after ischemic stroke in CB-17 mice. In this study, an essential combination of six small molecules [CHIR99021, Dorsomorphin, Forskolin, isoxazole-9 (ISX-9), Y27632, and DB2313] that transdifferentiated monocyte-derived macrophages into neurons in vitro was identified. Moreover, administration of six small molecules after cerebral ischemia in model animals generated a new neuronal layer in the infarct cortex by converting macrophages into neuronal cells, ultimately improving neurological function. These results suggest that altering the transdifferentiation of monocyte-derived macrophages by the small molecules to adjust their adaptive response will facilitate the development of regenerative therapies for ischemic stroke.
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Affiliation(s)
- Itaru Ninomiya
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akihide Koyama
- Department of Legal Medicine, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Yutaka Otsu
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Osamu Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masato Kanazawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
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11
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Zhao C, Li Y, Tang J, Zhou Q, Lin X, Wen Z. Metaphocytes are IL-22BP-producing cells regulated by ETS transcription factor Spic and essential for zebrafish barrier immunity. Cell Rep 2023; 42:112483. [PMID: 37148242 DOI: 10.1016/j.celrep.2023.112483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/03/2023] [Accepted: 04/20/2023] [Indexed: 05/08/2023] Open
Abstract
Metaphocytes are tissue-resident macrophage (TRM)/dendritic cell (DC)-like cells of non-hematopoietic origin in zebrafish barrier tissues. One remarkable property of metaphocytes is their ability to capture soluble antigens from the external environment via transepithelial protrusions, a unique function manifested by specialized subpopulations of the TRMs/DCs in mammal barrier tissues. Yet, how metaphocytes acquire myeloid-like cell properties from non-hematopoietic precursors and how they regulate barrier immunity remains unknown. Here, we show that metaphocytes are in situ generated from local progenitors guided by the ETS transcription factor Spic, the deficiency of which results in the absence of metaphocytes. We further document that metaphocytes are the major IL-22BP-producing cells, and the depletion of metaphocytes causes dysregulated barrier immunity that resembles the phenotype of IL-22BP-deficient mice. These findings reveal the ontogeny, development, and function of metaphocytes in zebrafish, which facilitates our understanding of the nature and function of the mammalian TRM/DC counterparts.
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Affiliation(s)
- Changlong Zhao
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yunbo Li
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jinlin Tang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qiuxia Zhou
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xi Lin
- Brigham and Women's Hospital, Harvard Medical School, Boston, MS 02115, USA
| | - Zilong Wen
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518055, China; Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China; Department of Immunology and Microbiology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China.
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12
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Single-cell sequencing reveals that endothelial cells, EndMT cells and mural cells contribute to the pathogenesis of cavernous malformations. Exp Mol Med 2023; 55:628-642. [PMID: 36914857 PMCID: PMC10073145 DOI: 10.1038/s12276-023-00962-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/13/2022] [Accepted: 01/01/2023] [Indexed: 03/14/2023] Open
Abstract
Cavernous malformations (CMs) invading the central nervous system occur in ~0.16-0.4% of the general population, often resulting in hemorrhages and focal neurological deficits. Further understanding of disease mechanisms and therapeutic strategies requires a deeper knowledge of CMs in humans. Herein, we performed single-cell RNA sequencing (scRNA-seq) analysis on unselected viable cells from twelve human CM samples and three control samples. A total of 112,670 high-quality cells were clustered into 11 major cell types, which shared a number of common features in CMs harboring different genetic mutations. A new EC subpopulation marked with PLVAP was uniquely identified in lesions. The cellular ligand‒receptor network revealed that the PLVAP-positive EC subcluster was the strongest contributor to the ANGPT and VEGF signaling pathways in all cell types. The PI3K/AKT/mTOR pathway was strongly activated in the PLVAP-positive subcluster even in non-PIK3CA mutation carriers. Moreover, endothelial-to-mesenchymal transition (EndMT) cells were identified for the first time in CMs at the single-cell level, which was accompanied by strong immune activation. The transcription factor SPI1 was predicted to be a novel key driver of EndMT, which was confirmed by in vitro and in vivo studies. A specific fibroblast-like phenotype was more prevalent in lesion smooth muscle cells, hinting at the role of vessel reconstructions and repairs in CMs, and we also confirmed that TWIST1 could induce SMC phenotypic switching in vitro and in vivo. Our results provide novel insights into the pathomechanism decryption and further precise therapy of CMs.
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13
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Single-Cell RNA-Seq Analysis Reveals Macrophages Are Involved in the Pathogenesis of Human Sporadic Acute Type A Aortic Dissection. Biomolecules 2023; 13:biom13020399. [PMID: 36830768 PMCID: PMC9952989 DOI: 10.3390/biom13020399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023] Open
Abstract
Macrophages play an important role in the progression of sporadic acute type A aortic dissection (ATAAD). The aim of this study was to characterize the cellular heterogeneity of macrophages in ATAAD tissues by scRNA-seq. Ascending aortic wall tissue from six ATAAD patients and three heart transplant donors was assessed by scRNA-seq and then analyzed and validated by various bioinformatic algorithms and histopathology experiments. The results revealed that the proportion of macrophages in ATAAD tissues (24.51%) was significantly higher than that in normal tissues (13.69%). Among the six macrophage subclusters, pro-inflammatory macrophages accounted for 14.96% of macrophages in the AD group and 0.18% in the normal group. Chemokine- and inflammation-related genes (CCL2, CCL20, S100A8, and S100A9) were expressed more intensively in macrophages in ATAAD tissue than in those in normal tissue. Additionally, intercellular communication analysis and transcription factor analysis indicated the activation of inflammation and degradation of the extracellular matrix in ATAAD tissue. Finally, immunohistochemistry, immunofluorescence, and Western blot experiments confirmed the overexpression of macrophage marker genes (CD68 and CD163) and matrix metalloproteinases (MMP9 and MMP2) in ATAAD tissue. Collectively, our study provides a preliminary evaluation of the role of macrophages in ATAAD, and the results could aid in the development of therapeutic options in the future.
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14
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Liu X, Ni G, Zhang P, Li H, Li J, Cavallazzi Sebold B, Wu X, Chen G, Yuan S, Wang T. Single-nucleus RNA sequencing and deep tissue proteomics reveal distinct tumour microenvironment in stage-I and II cervical cancer. J Exp Clin Cancer Res 2023; 42:28. [PMID: 36683048 PMCID: PMC9869594 DOI: 10.1186/s13046-023-02598-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Cervical cancer (CC) is the 3rd most common cancer in women and the 4th leading cause of deaths in gynaecological malignancies, yet the exact progression of CC is inconclusive, mainly due to the high complexity of the changing tumour microenvironment (TME) at different stages of tumorigenesis. Importantly, a detailed comparative single-nucleus transcriptomic analysis of tumour microenvironment (TME) of CC patients at different stages is lacking. METHODS In this study, a total of 42,928 and 29,200 nuclei isolated from the tumour tissues of stage-I and II CC patients and subjected to single-nucleus RNA sequencing (snRNA-seq) analysis. The cell heterogeneity and functions were comparatively investigated using bioinformatic tools. In addition, label-free quantitative mass spectrometry based proteomic analysis was carried out. The proteome profiles of stage-I and II CC patients were compared, and an integrative analysis with the snRNA-seq was performed. RESULTS Compared with the stage-I CC (CCI) patients, the immune response relevant signalling pathways were largely suppressed in various immune cells of the stage-II CC (CCII) patients, yet the signalling associated with cell and tissue development was enriched, as well as metabolism for energy production suggested by the upregulation of genes associated with mitochondria. This was consistent with the quantitative proteomic analysis that showed the dominance of proteins promoting cell growth and intercellular matrix development in the TME of CCII group. The interferon-α and γ responses appeared the most activated pathways in many cell populations of the CCI patients. Several collagens, such as COL12A1, COL5A1, COL4A1 and COL4A2, were found significantly upregulated in the CCII group, suggesting their roles in diagnosing CC progression. A novel transcript AC244205.1 was detected as the most upregulated gene in CCII patients, and its possible mechanistic role in CC may be investigated further. CONCLUSIONS Our study provides important resources for decoding the progression of CC and set the foundation for developing novel approaches for diagnosing CC and tackling the immunosuppressive TME.
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Affiliation(s)
- Xiaosong Liu
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | - Guoying Ni
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Pingping Zhang
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Hejie Li
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia
| | - Junjie Li
- The First Affiliated Hospital/School of Clinical Medicineof, Guangdong Pharmaceutical University, Guangzhou, 510080, Guangdong, China
| | | | - Xiaolian Wu
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Guoqiang Chen
- Cancer Research Institute, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China.
| | - Songhua Yuan
- Department of Gynaecology, First People's Hospital of Foshan, Foshan, 528000, Guangdong, China.
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore BC, QLD, 4558, Australia.
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15
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Leiba J, Özbilgiç R, Hernández L, Demou M, Lutfalla G, Yatime L, Nguyen-Chi M. Molecular Actors of Inflammation and Their Signaling Pathways: Mechanistic Insights from Zebrafish. BIOLOGY 2023; 12:biology12020153. [PMID: 36829432 PMCID: PMC9952950 DOI: 10.3390/biology12020153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Inflammation is a hallmark of the physiological response to aggressions. It is orchestrated by a plethora of molecules that detect the danger, signal intracellularly, and activate immune mechanisms to fight the threat. Understanding these processes at a level that allows to modulate their fate in a pathological context strongly relies on in vivo studies, as these can capture the complexity of the whole process and integrate the intricate interplay between the cellular and molecular actors of inflammation. Over the years, zebrafish has proven to be a well-recognized model to study immune responses linked to human physiopathology. We here provide a systematic review of the molecular effectors of inflammation known in this vertebrate and recapitulate their modes of action, as inferred from sterile or infection-based inflammatory models. We present a comprehensive analysis of their sequence, expression, and tissue distribution and summarize the tools that have been developed to study their function. We further highlight how these tools helped gain insights into the mechanisms of immune cell activation, induction, or resolution of inflammation, by uncovering downstream receptors and signaling pathways. These progresses pave the way for more refined models of inflammation, mimicking human diseases and enabling drug development using zebrafish models.
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16
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Robertson TF, Hou Y, Shen S, Rindy J, Sauer JD, Dinh HQ, Huttenlocher A. A tessellated lymphoid network provides whole-body T cell surveillance in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524414. [PMID: 36711463 PMCID: PMC9882119 DOI: 10.1101/2023.01.17.524414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Homeostatic trafficking to lymph nodes allows T cells to efficiently survey the host for cognate antigen. Non-mammalian jawed vertebrates lack lymph nodes but maintain similarly diverse T cell pools. Here, we exploit in vivo imaging of transparent zebrafish to investigate how T cells organize and survey for antigen in an animal devoid of lymph nodes. We find that naïve-like T cells in zebrafish organize into a previously undescribed whole-body lymphoid network that supports streaming migration and coordinated trafficking through the host. This network has the cellular hallmarks of a mammalian lymph node, including naïve T cells and CCR7-ligand expressing non-hematopoietic cells, and facilitates rapid collective migration. During infection, T cells transition to a random walk that supports antigen presenting cell interactions and subsequent activation. Our results reveal that T cells can toggle between collective migration and individual random walks to prioritize either large-scale trafficking or antigen search in situ . This novel lymphoid network thus facilitates whole-body T cell trafficking and antigen surveillance in the absence of a lymph node system. Significance Statement In mammals, lymph nodes play a critical role in the initiation of adaptive immune responses by providing a dedicated place for T cells to scan antigen-presenting cells. Birds, reptiles, amphibians, and fish all maintain diverse repertoires of T cells but lack lymph nodes, raising questions about how adaptive immunity functions in lower jawed vertebrates. Here, we describe a novel network of lymphocytes in zebrafish that supports whole-body T cell trafficking and provides a site for antigen search, mirroring the function of mammalian lymph nodes. Within this network, T cells can prioritize large-scale trafficking or antigen scanning by toggling between two distinct modes of migration. This network provides valuable insights into the evolution of adaptive immunity.
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17
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Oderberg IM, Goessling W. Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish. JCI Insight 2023; 8:163929. [PMID: 36625346 PMCID: PMC9870093 DOI: 10.1172/jci.insight.163929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 01/11/2023] Open
Abstract
The liver is a highly regenerative organ, yet the presence of a dedicated stem cell population remains controversial. Here, we interrogate a severe hepatocyte injury model in adult zebrafish to define that regeneration involves a stem cell population. After near-total hepatocyte ablation, single-cell transcriptomic and high-resolution imaging analyses throughout the entire regenerative timeline reveal that biliary epithelial cells undergo transcriptional and morphological changes to become hepatocytes. As a population, biliary epithelial cells give rise to both hepatocytes and biliary epithelial cells. Biliary epithelial cells proliferate and dedifferentiate to express hepatoblast transcription factors prior to hepatocyte differentiation. This process is characterized by increased MAPK, PI3K, and mTOR signaling, and chemical inhibition of these pathways impairs biliary epithelial cell proliferation and fate conversion. We conclude that, upon severe hepatocyte ablation in the adult liver, biliary epithelial cells act as facultative liver stem cells in an EGFR-PI3K-mTOR-dependent manner.
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Affiliation(s)
- Isaac M. Oderberg
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wolfram Goessling
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts USA.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA.,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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18
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Sobah ML, Scott AC, Laird M, Koole C, Liongue C, Ward AC. Socs3b regulates the development and function of innate immune cells in zebrafish. Front Immunol 2023; 14:1119727. [PMID: 36969252 PMCID: PMC10030509 DOI: 10.3389/fimmu.2023.1119727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Abstract
Introduction Suppressor of cytokine signaling 3 (SOCS3) is a critical component of the negative feedback regulation that controls signaling by cytokines and other factors thereby ensuring that important processes such as hematopoiesis and inflammation occur at appropriate levels. Methods To gain further insights into SOCS3 function, the zebrafish socs3b gene was investigated through analysis of a knockout line generated using CRISPR/Cas9-mediated genome editing. Results Zebrafish socs3b knockout embryos displayed elevated numbers of neutrophils during primitive and definitive hematopoiesis but macrophage numbers were not altered. However, the absence of socs3b reduced neutrophil functionality but enhanced macrophage responses. Adult socs3b knockout zebrafish displayed reduced survival that correlated with an eye pathology involving extensive infiltration of neutrophils and macrophages along with immune cell dysregulation in other tissues. Discussion These findings identify a conserved role for Socs3b in the regulation of neutrophil production and macrophage activation.
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Affiliation(s)
| | - Aimee C. Scott
- Institue for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
| | - Miranda Laird
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Cassandra Koole
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institue for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institue for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
- *Correspondence: Alister C. Ward,
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19
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Wang T, Xu C, Xu D, Yang X, Liu Y, Li X, Li Z, Dang N, Lv Y, Zhang Z, Li L, Ye K. Integrating cell interaction with transcription factors to obtain a robust gene panel for prognostic prediction and therapies in cholangiocarcinoma. Front Genet 2022; 13:981145. [DOI: 10.3389/fgene.2022.981145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/24/2022] [Indexed: 12/05/2022] Open
Abstract
Objective: The efficacy of immunotherapy for cholangiocarcinoma (CCA) is blocked by a high degree of tumor heterogeneity. Cell communication contributes to heterogeneity in the tumor microenvironment. This study aimed to explore critical cell signaling and biomarkers induced via cell communication during immune exhaustion in CCA.Methods: We constructed empirical Bayes and Markov random field models eLBP to determine transcription factors, interacting genes, and associated signaling pathways involved in cell-cell communication using single-cell RNAseq data. We then analyzed the mechanism of immune exhaustion during CCA progression.Results: We found that VEGFA-positive macrophages with high levels of LGALS9 could interact with HAVCR2 to promote the exhaustion of CD8+ T cells in CCA. Transcription factors SPI1 and IRF1 can upregulate the expression of LGALS9 in VEGFA-positive macrophages. Subsequently, we obtained a panel containing 54 genes through the model, which identified subtype S2 with high expression of immune checkpoint genes that are suitable for immunotherapy. Moreover, we found that patients with subtype S2 with a higher mutation ratio of MUC16 had immune-exhausted genes, such as HAVCR2 and TIGIT. Finally, we constructed a nine-gene eLBP-LASSO-COX risk model, which was designated the tumor microenvironment risk score (TMRS).Conclusion: Cell communication-related genes can be used as important markers for predicting patient prognosis and immunotherapy responses. The TMRS panel is a reliable tool for prognostic prediction and chemotherapeutic decision-making in CCA.
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20
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Luo H, Xia X, Huang LB, An H, Cao M, Kim GD, Chen HN, Zhang WH, Shu Y, Kong X, Ren Z, Li PH, Liu Y, Tang H, Sun R, Li C, Bai B, Jia W, Liu Y, Zhang W, Yang L, Peng Y, Dai L, Hu H, Jiang Y, Hu Y, Zhu J, Jiang H, Li Z, Caulin C, Park J, Xu H. Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment. Nat Commun 2022; 13:6619. [PMID: 36333338 PMCID: PMC9636408 DOI: 10.1038/s41467-022-34395-2] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) are the predominant components of the tumor microenvironment (TME) and influence cancer hallmarks, but without systematic investigation on their ubiquitous characteristics across different cancer types. Here, we perform pan-cancer analysis on 226 samples across 10 solid cancer types to profile the TME at single-cell resolution, illustrating the commonalities/plasticity of heterogenous CAFs. Activation trajectory of the major CAF types is divided into three states, exhibiting distinct interactions with other cell components, and relating to prognosis of immunotherapy. Moreover, minor CAF components represent the alternative origin from other TME components (e.g., endothelia and macrophages). Particularly, the ubiquitous presentation of endothelial-to-mesenchymal transition CAF, which may interact with proximal SPP1+ tumor-associated macrophages, is implicated in endothelial-to-mesenchymal transition and survival stratifications. Our study comprehensively profiles the shared characteristics and dynamics of CAFs, and highlight their heterogeneity and plasticity across different cancer types. Browser of integrated pan-cancer single-cell information is available at https://gist-fgl.github.io/sc-caf-atlas/ .
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Affiliation(s)
- Han Luo
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Division of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Xuyang Xia
- grid.412901.f0000 0004 1770 1022Division of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Li-Bin Huang
- grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Division of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hyunsu An
- grid.61221.360000 0001 1033 9831School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Minyuan Cao
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Gyeong Dae Kim
- grid.61221.360000 0001 1033 9831School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hai-Ning Chen
- grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Colorectal Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Wei-Han Zhang
- grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Shu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Xiangyu Kong
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Zhixiang Ren
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Pei-Heng Li
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yang Liu
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Department of General Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Huairong Tang
- grid.412901.f0000 0004 1770 1022Health Promotion Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Ronghao Sun
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.54549.390000 0004 0369 4060Department of Head and Neck Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Chao Li
- grid.54549.390000 0004 0369 4060Department of Head and Neck Surgery, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan China
| | - Bing Bai
- grid.218292.20000 0000 8571 108XState Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan China
| | - Weiguo Jia
- grid.412901.f0000 0004 1770 1022Center for Geriatrics medicine, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yi Liu
- grid.13291.380000 0001 0807 1581Division of Rheumatism & Immunology, Rare Diseases Center, West Chia Hospital, Sichuan University, Chengdu, Sichuan China
| | - Wei Zhang
- grid.452223.00000 0004 1757 7615Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Li Yang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yong Peng
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Lunzhi Dai
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hongbo Hu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yong Jiang
- grid.412901.f0000 0004 1770 1022Division of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yiguo Hu
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Jingqiang Zhu
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hong Jiang
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Zhihui Li
- grid.412901.f0000 0004 1770 1022Division of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of thyroid and parathyroid disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Carlos Caulin
- grid.134563.60000 0001 2168 186XDepartment of Otolaryngology - Head & Neck Surgery and University of Arizona Cancer Center, University of Arizona, Tucson, AZ USA
| | - Jihwan Park
- grid.61221.360000 0001 1033 9831School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Heng Xu
- grid.412901.f0000 0004 1770 1022Division of Laboratory Medicine/Research Centre of Clinical Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
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21
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Zebrafish Model of Severe Combined Immunodeficiency (SCID) Due to JAK3 Mutation. Biomolecules 2022; 12:biom12101521. [PMID: 36291730 PMCID: PMC9599616 DOI: 10.3390/biom12101521] [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: 09/15/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
JAK3 is principally activated by members of the interleukin-2 receptor family and plays an essential role in lymphoid development, with inactivating JAK3 mutations causing autosomal-recessive severe combined immunodeficiency (SCID). This study aimed to generate an equivalent zebrafish model of SCID and to characterize the model across the life-course. Genome editing of zebrafish jak3 created mutants similar to those observed in human SCID. Homozygous jak3 mutants showed reduced embryonic T lymphopoiesis that continued through the larval stage and into adulthood, with B cell maturation and adult NK cells also reduced and neutrophils impacted. Mutant fish were susceptible to lymphoid leukemia. This model has many of the hallmarks of human SCID resulting from inactivating JAK3 mutations and will be useful for a variety of pre-clinical applications.
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22
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Ascoli C, Schott CA, Huang Y, Turturice BA, Wang W, Ecanow N, Sweiss NJ, Perkins DL, Finn PW. Altered transcription factor targeting is associated with differential peripheral blood mononuclear cell proportions in sarcoidosis. Front Immunol 2022; 13:848759. [PMID: 36311769 PMCID: PMC9608777 DOI: 10.3389/fimmu.2022.848759] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
IntroductionIn sarcoidosis, peripheral lymphopenia and anergy have been associated with increased inflammation and maladaptive immune activity, likely promoting development of chronic and progressive disease. However, the molecular mechanisms that lead to reduced lymphocyte proportions, particularly CD4+ T-cells, have not been fully elucidated. We posit that paradoxical peripheral lymphopenia is characterized by a dysregulated transcriptomic network associated with cell function and fate that results from altered transcription factor targeting activity.MethodsMessenger RNA-sequencing (mRNA-seq) was performed on peripheral blood mononuclear cells (PBMCs) from ACCESS study subjects with sarcoidosis and matched controls and findings validated on a sarcoidosis case-control cohort and a sarcoidosis case series. Preserved PBMC transcriptomic networks between case-control cohorts were assessed to establish cellular associations with gene modules and define regulatory targeting involved in sarcoidosis immune dysregulation utilizing weighted gene co-expression network analysis and differential transcription factor involvement analysis. Network centrality measures identified master transcriptional regulators of subnetworks related to cell proliferation and death. Predictive models of differential PBMC proportions constructed from ACCESS target gene expression corroborated the relationship between aberrant transcription factor regulatory activity and imputed and clinical PBMC populations in the validation cohorts.ResultsWe identified two unique and preserved gene modules significantly associated with sarcoidosis immune dysregulation. Strikingly, increased expression of a monocyte-driven, and not a lymphocyte-driven, gene module related to innate immunity and cell death was the best predictor of peripheral CD4+ T-cell proportions. Within the gene network of this monocyte-driven module, TLE3 and CBX8 were determined to be master regulators of the cell death subnetwork. A core gene signature of differentially over-expressed target genes of TLE3 and CBX8 involved in cellular communication and immune response regulation accurately predicted imputed and clinical monocyte expansion and CD4+ T-cell depletion.ConclusionsAltered transcriptional regulation associated with aberrant gene expression of a monocyte-driven transcriptional network likely influences lymphocyte function and survival. Although further investigation is warranted, this indicates that crosstalk between hyperactive monocytes and lymphocytes may instigate peripheral lymphopenia and underlie sarcoidosis immune dysregulation and pathogenesis. Future therapies selectively targeting master regulators, or their targets, may mitigate dysregulated immune processes in sarcoidosis and disease progression.
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Affiliation(s)
- Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Cody A. Schott
- University of Illinois at Chicago College of Medicine, Chicago, IL, United States
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | | | - Wangfei Wang
- Department of Bioengineering, University of Illinois at Chicago College of Engineering and Medicine, Chicago, IL, United States
| | - Naomi Ecanow
- University of Illinois at Chicago College of Medicine, Chicago, IL, United States
| | - Nadera J. Sweiss
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
- Division of Rheumatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - David L. Perkins
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Patricia W. Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States
- *Correspondence: Patricia W. Finn,
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23
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Zhao S, Zhang A, Zhu H, Wen Z. The ETS transcription factor Spi2 regulates hematopoietic cell development in zebrafish. Development 2022; 149:276980. [DOI: 10.1242/dev.200881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The E26 transformation-specific or E-twenty-six (ETS) genes encode a superfamily of transcription factors involved in diverse biological processes. Here, we report the identification and characterization of a previously unidentified member of the ETS transcription factors, Spi2, that is found exclusively in the ray-finned fish kingdom. We show that the expression of spi2 is restricted to hemogenic endothelial cells (HECs) and to hematopoietic stem and progenitor cells (HSPCs) in zebrafish. Using bacteria artificial chromosome transgenesis, we generate a spi2 reporter line, TgBAC(spi2:P2a-GFP), which manifests the GFP pattern recapitulating the endogenous spi2 expression. Genetic ablation of spi2 has little effect on HEC formation and the endothelial-to-hematopoietic transition, but results in compromised proliferation of HSPCs in the caudal hematopoietic tissue (CHT) during early development and in severe myeloid lineage defect in adulthood. Epistatic analysis shows that spi2 acts downstream of runx1 in regulating HSPC development in the CHT. Our study identifies Spi2 as an essential regulator for definitive hematopoietic cell development and creates a TgBAC(spi2:P2a-GFP) reporter line for tracking HECs, HSPCs, myeloid cells and thrombocytes from early development to adulthood.
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Affiliation(s)
- Shizheng Zhao
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Ao Zhang
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Hao Zhu
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology 1 Division of Life Science , , Clear Water Bay, Hong Kong , China
- Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen Peking University−Hong Kong University of Science and Technology Medical Center 2 , Shenzhen 518055 , China
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24
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Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. J Exp Med 2022; 219:e20220038. [PMID: 35938989 PMCID: PMC9365674 DOI: 10.1084/jem.20220038] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.
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Affiliation(s)
- Sara A. Rubin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Chloé S. Baron
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Cecilia Pessoa Rodrigues
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexandra F. Corbin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Song P. Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA
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25
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Zheng H, Wang S, Li X, Hu H. INSISTC: Incorporating network structure information for single-cell type classification. Genomics 2022; 114:110480. [PMID: 36075505 DOI: 10.1016/j.ygeno.2022.110480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/27/2022]
Abstract
Uncovering gene regulatory mechanisms in individual cells can provide insight into cell heterogeneity and function. Recent accumulated Single-Cell RNA-Seq data have made it possible to analyze gene regulation at single-cell resolution. Understanding cell-type-specific gene regulation can assist in more accurate cell type and state identification. Computational approaches utilizing such relationships are under development. Methods pioneering in integrating gene regulatory mechanism discovery with cell-type classification encounter challenges such as determine gene regulatory relationships and incorporate gene regulatory network structure. To fill this gap, we developed INSISTC, a computational method to incorporate gene regulatory network structure information for single-cell type classification. INSISTC is capable of identifying cell-type-specific gene regulatory mechanisms while performing single-cell type classification. INSISTC demonstrated its accuracy in cell type classification and its potential for providing insight into molecular mechanisms specific to individual cells. In comparison with the alternative methods, INSISTC demonstrated its complementary performance for gene regulation interpretation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA.
| | - Haiyan Hu
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA.
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26
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Single-cell multiomics analysis reveals regulatory programs in clear cell renal cell carcinoma. Cell Discov 2022; 8:68. [PMID: 35853872 PMCID: PMC9296597 DOI: 10.1038/s41421-022-00415-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
The clear cell renal cell carcinoma (ccRCC) microenvironment consists of many different cell types and structural components that play critical roles in cancer progression and drug resistance, but the cellular architecture and underlying gene regulatory features of ccRCC have not been fully characterized. Here, we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to generate transcriptional and epigenomic landscapes of ccRCC. We identified tumor cell-specific regulatory programs mediated by four key transcription factors (TFs) (HOXC5, VENTX, ISL1, and OTP), and these TFs have prognostic significance in The Cancer Genome Atlas (TCGA) database. Targeting these TFs via short hairpin RNAs (shRNAs) or small molecule inhibitors decreased tumor cell proliferation. We next performed an integrative analysis of chromatin accessibility and gene expression for CD8+ T cells and macrophages to reveal the different regulatory elements in their subgroups. Furthermore, we delineated the intercellular communications mediated by ligand–receptor interactions within the tumor microenvironment. Taken together, our multiomics approach further clarifies the cellular heterogeneity of ccRCC and identifies potential therapeutic targets.
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27
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Mohammadi A, Sorensen GL, Pilecki B. MFAP4-Mediated Effects in Elastic Fiber Homeostasis, Integrin Signaling and Cancer, and Its Role in Teleost Fish. Cells 2022; 11:cells11132115. [PMID: 35805199 PMCID: PMC9265350 DOI: 10.3390/cells11132115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Microfibrillar-associated protein 4 (MFAP4) is an extracellular matrix (ECM) protein belonging to the fibrinogen-related domain superfamily. MFAP4 is highly expressed in elastin-rich tissues such as lung, blood vessels and skin. MFAP4 is involved in organization of the ECM, regulating proper elastic fiber assembly. On the other hand, during pathology MFAP4 actively contributes to disease development and progression due to its interactions with RGD-dependent integrin receptors. Both tissue expression and circulating MFAP4 levels are associated with various disorders, including liver fibrosis and cancer. In other experimental models, such as teleost fish, MFAP4 appears to participate in host defense as a macrophage-specific innate immune molecule. The aim of this review is to summarize the accumulating evidence that indicates the importance of MFAP4 in homeostasis as well as pathological conditions, discuss its known biological functions with special focus on elastic fiber assembly, integrin signaling and cancer, as well as describe the reported functions of non-mammalian MFAP4 in fish. Overall, our work provides a comprehensive overview on the role of MFAP4 in health and disease.
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28
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Satarkar D, Patra C. Evolution, Expression and Functional Analysis of CXCR3 in Neuronal and Cardiovascular Diseases: A Narrative Review. Front Cell Dev Biol 2022; 10:882017. [PMID: 35794867 PMCID: PMC9252580 DOI: 10.3389/fcell.2022.882017] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Chemokines form a sophisticated communication network wherein they maneuver the spatiotemporal migration of immune cells across a system. These chemical messengers are recognized by chemokine receptors, which can trigger a cascade of reactions upon binding to its respective ligand. CXC chemokine receptor 3 (CXCR3) is a transmembrane G protein-coupled receptor, which can selectively bind to CXCL9, CXCL10, and CXCL11. CXCR3 is predominantly expressed on immune cells, including activated T lymphocytes and natural killer cells. It thus plays a crucial role in immunological processes like homing of effector cells to infection sites and for pathogen clearance. Additionally, it is expressed on several cell types of the central nervous system and cardiovascular system, due to which it has been implicated in several central nervous system disorders, including Alzheimer's disease, multiple sclerosis, dengue viral disease, and glioblastoma, as well as cardiovascular diseases like atherosclerosis, Chronic Chagas cardiomyopathy, and hypertension. This review provides a narrative description of the evolution, structure, function, and expression of CXCR3 and its corresponding ligands in mammals and zebrafish and the association of CXCR3 receptors with cardiovascular and neuronal disorders. Unraveling the mechanisms underlying the connection of CXCR3 and disease could help researchers investigate the potential of CXCR3 as a biomarker for early diagnosis and as a therapeutic target for pharmacological intervention, along with developing robust zebrafish disease models.
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Affiliation(s)
- Devi Satarkar
- Department of Developmental Biology, Agharkar Research Institute, Pune, India
| | - Chinmoy Patra
- Department of Developmental Biology, Agharkar Research Institute, Pune, India
- SP Phule University, Pune, India
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29
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Liu Y, Kassack ME, McFaul ME, Christensen LN, Siebert S, Wyatt SR, Kamei CN, Horst S, Arroyo N, Drummond IA, Juliano CE, Draper BW. Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary. eLife 2022; 11:76014. [PMID: 35588359 PMCID: PMC9191896 DOI: 10.7554/elife.76014] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function and the transcriptome profiles will provide a valuable resource for future studies.
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Affiliation(s)
- Yulong Liu
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Michelle E Kassack
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Matthew E McFaul
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Lana N Christensen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Sydney R Wyatt
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Caramai N Kamei
- Mount Desert Island Biological Laboratory, Bar Harbor, United States
| | - Samuel Horst
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Nayeli Arroyo
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Iain A Drummond
- Mount Desert Island Biological Laboratory, Bar Harbor, United States
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Bruce W Draper
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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30
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Chen L, Su B, Yu J, Wang J, Hu H, Ren HQ, Wu B. Combined effects of arsenic and 2,2-dichloroacetamide on different cell populations of zebrafish liver. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:152961. [PMID: 35031379 DOI: 10.1016/j.scitotenv.2022.152961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Arsenic (As) and disinfection by-products are important health risk factors in the water environment. However, their combined effects on different cell populations in the liver are not well known. Here, zebrafish were exposed to 100 μg/L As, 300 μg/L 2,2-dichloroacetamide (DCAcAm), and their combination for 23 days. Then transcriptome profiles of cell populations in zebrafish liver were analyzed by single-cell RNA sequencing (scRNA-seq). A total of 13,563 cells were obtained, which were identified as hepatocytes, hepatic duct cells, endothelial cells and macrophages. Hepatocytes were the main target cell subtype of As and DCAcAm exposures. DCAcAm exposure induced higher toxicity in male hepatocytes, which specifically changed amino acid metabolism, response to hormone and cofactor metabolism. However, As exposure caused higher toxicity in female hepatocytes, which altered lipid metabolism, carbon metabolism, and peroxisome. Combined exposure to As and DCAcAm decreased toxicities in hepatocytes compared to each one alone. Female hepatocytes had higher tolerance to co-exposure of As and DCAcAm than male hepatocytes. Further, combined exposure to As and DCAcAm induced functional changes in macrophages similar to As alone groups, which mainly altered the transfer of sterol and cholesterol. Hepatic duct cells and endothelial cells were not influenced by exposures to As and DCAcAm. This study for the first time highlights the cell-specific combined responses of As and DCAcAm in zebrafish liver, which provide useful information for their health risk assessment in a co-exposure environment.
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Affiliation(s)
- Ling Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bei Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jing Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Jinfeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Hong-Qiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China
| | - Bing Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, PR China.
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An Integrative Bioinformatics Analysis of the Potential Mechanisms Involved in Propofol Affecting Hippocampal Neuronal Cells. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:4911773. [PMID: 35515499 PMCID: PMC9064519 DOI: 10.1155/2022/4911773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 12/18/2022]
Abstract
The aim of this study is to probe the possible molecular mechanisms underlying the effects of propofol on HT22 cells. HT22 cells treated with different concentrations were sequenced, and then the results of the sequencing were analyzed for dynamic trends. Expression pattern clustering analysis was performed to demonstrate the expression of genes in the significant trend modules in each group of samples. We first chose the genes related to the trend module for WGCNA analysis, then constructed the PPI network of module genes related to propofol treatment group, and screened the key genes. Finally, GSEA analysis was performed on the key genes. Overall, 2,506 genes showed a decreasing trend with increasing propofol concentration, and 1,871 genes showed an increasing trend with increasing propofol concentration. WGCNA analysis showed that among them, turquoise panel genes were negatively correlated with propofol treatment, and genes with Cor R >0.9 in the turquoise panel were selected for PPI network construction. The MCC algorithm screened a total of five key genes (CD86, IL10RA, PTPRC, SPI1, and ITGAM). GSEA analysis showed that CD86, IL10RA, PTPRC, SPI1, and ITGAM are involved in the PRION_DISEASES pathway. Our study showed that propofol sedation can affect mRNA expression in the hippocampus, providing new ideas to identify treatment of nerve injury induced by propofol anesthesia.
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32
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Tang WJ, Watson CJ, Olmstead T, Allan CH, Kwon RY. Single-cell resolution of MET- and EMT-like programs in osteoblasts during zebrafish fin regeneration. iScience 2022; 25:103784. [PMID: 35169687 PMCID: PMC8829776 DOI: 10.1016/j.isci.2022.103784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/15/2021] [Accepted: 01/14/2022] [Indexed: 12/04/2022] Open
Abstract
Zebrafish regenerate fin rays following amputation through epimorphic regeneration, a process that has been proposed to involve the epithelial-to-mesenchymal transition (EMT). We performed single-cell RNA sequencing (scRNA-seq) to elucidate osteoblastic transcriptional programs during zebrafish caudal fin regeneration. We show that osteoprogenitors are enriched with components associated with EMT and its reverse, mesenchymal-to-epithelial transition (MET), and provide evidence that the EMT markers cdh11 and twist2 are co-expressed in dedifferentiating cells at the amputation stump at 1 dpa, and in differentiating osteoblastic cells in the regenerate, the latter of which are enriched in EMT signatures. We also show that esrp1, a regulator of alternative splicing in epithelial cells that is associated with MET, is expressed in a subset of osteoprogenitors during outgrowth. This study provides a single cell resource for the study of osteoblastic cells during zebrafish fin regeneration, and supports the contribution of MET- and EMT-associated components to this process. Osteoblasts express EMT/MET signatures during zebrafish fin regeneration De/re-differentiating osteoblasts express cdh11, an EMT marker A subset of osteoprogenitors express the MET marker esrp1 Our scRNA-seq data can be explored online
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Affiliation(s)
- W Joyce Tang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Claire J Watson
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Theresa Olmstead
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Christopher H Allan
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Ronald Y Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
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33
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Ulloa BA, Habbsa SS, Potts KS, Lewis A, McKinstry M, Payne SG, Flores JC, Nizhnik A, Feliz Norberto M, Mosimann C, Bowman TV. Definitive hematopoietic stem cells minimally contribute to embryonic hematopoiesis. Cell Rep 2021; 36:109703. [PMID: 34525360 PMCID: PMC8928453 DOI: 10.1016/j.celrep.2021.109703] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 01/23/2023] Open
Abstract
Hematopoietic stem cells (HSCs) are rare cells that arise in the embryo
and sustain adult hematopoiesis. Although the functional potential of nascent
HSCs is detectable by transplantation, their native contribution during
development is unknown, in part due to the overlapping genesis and marker gene
expression with other embryonic blood progenitors. Using single-cell
transcriptomics, we define gene signatures that distinguish nascent HSCs from
embryonic blood progenitors. Applying a lineage-tracing approach to selectively
track HSC output in situ, we find significantly delayed
lymphomyeloid contribution. An inducible HSC injury model demonstrates a
negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are
not merely dormant at this developmental stage, as they showed robust
regeneration after injury. Combined, our findings illuminate that nascent HSCs
self-renew but display differentiation latency, while HSC-independent embryonic
progenitors sustain developmental hematopoiesis. Understanding these differences
could improve de novo generation and expansion of functional
HSCs. Ulloa et al. demonstrate that nascent HSCs robustly regenerate but
display differentiation latency, while HSC-independent embryonic progenitors
sustain developmental hematopoiesis. Their findings have implications for
dissecting the programs underlying the genesis of bona fide HSCs.
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Affiliation(s)
- Bianca A Ulloa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Samima S Habbsa
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Kathryn S Potts
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Alana Lewis
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Mia McKinstry
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Sara G Payne
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Julio C Flores
- Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Anastasia Nizhnik
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Maria Feliz Norberto
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA
| | - Christian Mosimann
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine and Children's Hospital Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Teresa V Bowman
- Albert Einstein College of Medicine, Department of Developmental and Molecular Biology, Bronx, NY, USA; Albert Einstein College of Medicine, Gottesman Institute of Stem Cell Biology and Regenerative Medicine, Bronx, NY, USA; Albert Einstein College of Medicine and Montefiore Medical Center, Department of Medicine (Oncology), Bronx, NY, USA.
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34
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Liu S, Yang Q, Chen Y, Liu Q, Wang W, Song J, Zheng Y, Liu W. Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone. Front Genet 2021; 12:695699. [PMID: 34421998 PMCID: PMC8375321 DOI: 10.3389/fgene.2021.695699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
17α-Methyltestosterone (MT) is a synthetic androgen. The objective of this study was to explore the effects of exogenous MT on the growth and gonadal development of female rare minnow Gobiocypris rarus. Female G. rarus groups were exposed to 25–100 ng/L of MT for 7 days. After exposure for 7 days, the total weight and body length were significantly decreased in the 50-ng/L MT groups. The major oocytes in the ovaries of the control group were vitellogenic oocytes (Voc) and cortical alveolus stage oocytes (Coc). In the MT exposure groups, some fish had mature ovaries with a relatively lower proportion of mature oocytes, and the diameter of the perinucleolar oocytes (Poc) was decreased compared with those of the control group. Ovarian VTG, FSH, LH, 11-KT, E2, and T were significantly increased after exposure to 50 ng/L of MT for 7 days. Unigenes (73,449), 24 known mature microRNAs (miRNAs), and 897 novel miRNAs in the gonads of G. rarus were found using high-throughput sequencing. Six mature miRNAs (miR-19, miR-183, miR-203, miR-204, miR-205, and miR-96) as well as six differentially expressed genes (fabp3, mfap4, abca1, foxo3, tgfb1, and zfp36l1) that may be associated with ovarian development and innate immune response were assayed using qPCR. Furthermore, the miR-183 cluster and miR-203 were differentially expressed in MT-exposed ovaries of the different G. rarus groups. This study provides some information about the role of miRNA–mRNA pairs in the regulation of ovarian development and innate immune system, which will facilitate future studies of the miRNA–RNA-associated regulation of teleost reproduction.
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Affiliation(s)
- Shaozhen Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qiong Yang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yue Chen
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qing Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Weiwei Wang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Jing Song
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
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35
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Metikala S, Casie Chetty S, Sumanas S. Single-cell transcriptome analysis of the zebrafish embryonic trunk. PLoS One 2021; 16:e0254024. [PMID: 34234366 PMCID: PMC8263256 DOI: 10.1371/journal.pone.0254024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/17/2021] [Indexed: 11/27/2022] Open
Abstract
During embryonic development, cells differentiate into a variety of distinct cell types and subtypes with diverse transcriptional profiles. To date, transcriptomic signatures of different cell lineages that arise during development have been only partially characterized. Here we used single-cell RNA-seq to perform transcriptomic analysis of over 20,000 cells disaggregated from the trunk region of zebrafish embryos at the 30 hpf stage. Transcriptional signatures of 27 different cell types and subtypes were identified and annotated during this analysis. This dataset will be a useful resource for many researchers in the fields of developmental and cellular biology and facilitate the understanding of molecular mechanisms that regulate cell lineage choices during development.
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Affiliation(s)
- Sanjeeva Metikala
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL, United States of America
| | - Satish Casie Chetty
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Molecular and Developmental Biology Graduate Program, University of Cincinnati, Cincinnati, OH, United States of America
| | - Saulius Sumanas
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, Tampa, FL, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States of America
- * E-mail:
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36
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Xie Y, Xie J, Meijer AH, Schaaf MJM. Glucocorticoid-Induced Exacerbation of Mycobacterial Infection Is Associated With a Reduced Phagocytic Capacity of Macrophages. Front Immunol 2021; 12:618569. [PMID: 34046029 PMCID: PMC8148013 DOI: 10.3389/fimmu.2021.618569] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 04/13/2021] [Indexed: 01/20/2023] Open
Abstract
Glucocorticoids are effective drugs for treating immune-related diseases, but prolonged therapy is associated with an increased risk of various infectious diseases, including tuberculosis. In this study, we have used a larval zebrafish model for tuberculosis, based on Mycobacterium marinum (Mm) infection, to study the effect of glucocorticoids. Our results show that the synthetic glucocorticoid beclomethasone increases the bacterial burden and the dissemination of a systemic Mm infection. The exacerbated Mm infection was associated with a decreased phagocytic activity of macrophages, higher percentages of extracellular bacteria, and a reduced rate of infected cell death, whereas the bactericidal capacity of the macrophages was not affected. The inhibited phagocytic capacity of macrophages was associated with suppression of the transcription of genes involved in phagocytosis in these cells. The decreased bacterial phagocytosis by macrophages was not specific for Mm, since it was also observed upon infection with Salmonella Typhimurium. In conclusion, our results show that glucocorticoids inhibit the phagocytic activity of macrophages, which may increase the severity of bacterial infections like tuberculosis.
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Affiliation(s)
- Yufei Xie
- Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jiajun Xie
- Institute of Biology, Leiden University, Leiden, Netherlands
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37
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Sullivan C, Soos BL, Millard PJ, Kim CH, King BL. Modeling Virus-Induced Inflammation in Zebrafish: A Balance Between Infection Control and Excessive Inflammation. Front Immunol 2021; 12:636623. [PMID: 34025644 PMCID: PMC8138431 DOI: 10.3389/fimmu.2021.636623] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
The inflammatory response to viral infection in humans is a dynamic process with complex cell interactions that are governed by the immune system and influenced by both host and viral factors. Due to this complexity, the relative contributions of the virus and host factors are best studied in vivo using animal models. In this review, we describe how the zebrafish (Danio rerio) has been used as a powerful model to study host-virus interactions and inflammation by combining robust forward and reverse genetic tools with in vivo imaging of transparent embryos and larvae. The innate immune system has an essential role in the initial inflammatory response to viral infection. Focused studies of the innate immune response to viral infection are possible using the zebrafish model as there is a 4-6 week timeframe during development where they have a functional innate immune system dominated by neutrophils and macrophages. During this timeframe, zebrafish lack a functional adaptive immune system, so it is possible to study the innate immune response in isolation. Sequencing of the zebrafish genome has revealed significant genetic conservation with the human genome, and multiple studies have revealed both functional conservation of genes, including those critical to host cell infection and host cell inflammatory response. In addition to studying several fish viruses, zebrafish infection models have been developed for several human viruses, including influenza A, noroviruses, chikungunya, Zika, dengue, herpes simplex virus type 1, Sindbis, and hepatitis C virus. The development of these diverse viral infection models, coupled with the inherent strengths of the zebrafish model, particularly as it relates to our understanding of macrophage and neutrophil biology, offers opportunities for far more intensive studies aimed at understanding conserved host responses to viral infection. In this context, we review aspects relating to the evolution of innate immunity, including the evolution of viral pattern recognition receptors, interferons and interferon receptors, and non-coding RNAs.
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Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States
| | - Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
| | - Paul J Millard
- Department of Environmental and Sustainable Engineering, University at Albany, Albany, NY, United States
| | - Carol H Kim
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States.,Department of Biological Sciences, University at Albany, Albany, NY, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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38
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Voisin M, Shrestha E, Rollet C, Nikain CA, Josefs T, Mahé M, Barrett TJ, Chang HR, Ruoff R, Schneider JA, Garabedian ML, Zoumadakis C, Yun C, Badwan B, Brown EJ, Mar AC, Schneider RJ, Goldberg IJ, Pineda-Torra I, Fisher EA, Garabedian MJ. Inhibiting LXRα phosphorylation in hematopoietic cells reduces inflammation and attenuates atherosclerosis and obesity in mice. Commun Biol 2021; 4:420. [PMID: 33772096 PMCID: PMC7997930 DOI: 10.1038/s42003-021-01925-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/26/2021] [Indexed: 12/25/2022] Open
Abstract
Atherosclerosis and obesity share pathological features including inflammation mediated by innate and adaptive immune cells. LXRα plays a central role in the transcription of inflammatory and metabolic genes. LXRα is modulated by phosphorylation at serine 196 (LXRα pS196), however, the consequences of LXRα pS196 in hematopoietic cell precursors in atherosclerosis and obesity have not been investigated. To assess the importance of LXRα phosphorylation, bone marrow from LXRα WT and S196A mice was transplanted into Ldlr-/- mice, which were fed a western diet prior to evaluation of atherosclerosis and obesity. Plaques from S196A mice showed reduced inflammatory monocyte recruitment, lipid accumulation, and macrophage proliferation. Expression profiling of CD68+ and T cells from S196A mouse plaques revealed downregulation of pro-inflammatory genes and in the case of CD68+ upregulation of mitochondrial genes characteristic of anti-inflammatory macrophages. Furthermore, S196A mice had lower body weight and less visceral adipose tissue; this was associated with transcriptional reprograming of the adipose tissue macrophages and T cells, and resolution of inflammation resulting in less fat accumulation within adipocytes. Thus, reducing LXRα pS196 in hematopoietic cells attenuates atherosclerosis and obesity by reprogramming the transcriptional activity of LXRα in macrophages and T cells to promote an anti-inflammatory phenotype.
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Affiliation(s)
- Maud Voisin
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Elina Shrestha
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Claire Rollet
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Cyrus A Nikain
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Tatjana Josefs
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Mélanie Mahé
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Tessa J Barrett
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Hye Rim Chang
- Division of Endocrinology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Rachel Ruoff
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | | | - Michela L Garabedian
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | | | - Chi Yun
- Ordaos, Inc, New York, NY, USA
| | | | - Emily J Brown
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Adam C Mar
- Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University Medical Center, New York, NY, USA
| | | | - Ira J Goldberg
- Division of Endocrinology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Inés Pineda-Torra
- Centre for Cardiometabolic and Vascular Science, University College of London, London, UK
| | - Edward A Fisher
- Division of Cardiology, Marc and Ruti Bell Program in Vascular Biology, Department of Medicine, NYU School of Medicine, New York, NY, USA.
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Merselis LC, Rivas ZP, Munson GP. Breaching the Bacterial Envelope: The Pivotal Role of Perforin-2 (MPEG1) Within Phagocytes. Front Immunol 2021; 12:597951. [PMID: 33692780 PMCID: PMC7937864 DOI: 10.3389/fimmu.2021.597951] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
The membrane attack complex (MAC) of the complement system and Perforin-1 are well characterized innate immune effectors. MAC is composed of C9 and other complement proteins that target the envelope of gram-negative bacteria. Perforin-1 is deployed when killer lymphocytes degranulate to destroy virally infected or cancerous cells. These molecules polymerize with MAC-perforin/cholesterol-dependent cytolysin (MACPF/CDC) domains of each monomer deploying amphipathic β-strands to form pores through target lipid bilayers. In this review we discuss one of the most recently discovered members of this family; Perforin-2, the product of the Mpeg1 gene. Since their initial description more than 100 years ago, innumerable studies have made macrophages and other phagocytes some of the best understood cells of the immune system. Yet remarkably it was only recently revealed that Perforin-2 underpins a pivotal function of phagocytes; the destruction of phagocytosed microbes. Several studies have established that phagocytosed bacteria persist and in some cases flourish within phagocytes that lack Perforin-2. When challenged with either gram-negative or gram-positive pathogens Mpeg1 knockout mice succumb to infectious doses that the majority of wild-type mice survive. As expected by their immunocompromised phenotype, bacterial pathogens replicate and disseminate to deeper tissues of Mpeg1 knockout mice. Thus, this evolutionarily ancient gene endows phagocytes with potent bactericidal capability across taxa spanning sponges to humans. The recently elucidated structures of mammalian Perforin-2 reveal it to be a homopolymer that depends upon low pH, such as within phagosomes, to transition to its membrane-spanning pore conformation. Clinical manifestations of Mpeg1 missense mutations further highlight the pivotal role of Perforin-2 within phagocytes. Controversies and gaps within the field of Perforin-2 research are also discussed as well as animal models that may be used to resolve the outstanding issues. Our review concludes with a discussion of bacterial counter measures against Perforin-2.
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Affiliation(s)
- Leidy C Merselis
- Department of Microbiology and Immunology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Zachary P Rivas
- Department of Microbiology and Immunology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
| | - George P Munson
- Department of Microbiology and Immunology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
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40
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Krämer A. Master regulators as order parameters of gene expression states. Phys Rev E 2021; 103:012409. [PMID: 33601603 DOI: 10.1103/physreve.103.012409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/22/2020] [Indexed: 11/07/2022]
Abstract
Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that form concurrent positive feedback loops with a large number of downstream regulated genes. The order parameter free energy then defines an epigenetic landscape in which local minima correspond to stable cell states. The model is applied to gene expression data in the context of hematopoiesis.
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41
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Li J, Meng P, Zhou R, Zhang Y, Lin Q. Famciclovir leads to failure of hematopoiesis, but may have the benefit of relieving myeloid expansion in MDS-like zebrafish. Toxicol Appl Pharmacol 2020; 410:115334. [PMID: 33207248 DOI: 10.1016/j.taap.2020.115334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 10/23/2022]
Abstract
Famciclovir (FCV) is an antiviral drug that is often utilized after bone marrow transplantation to prevent viral infection. Yet, its role in hematopoiesis is poorly understood. Here, by utilizing a zebrafish model, we found that FCV exposure led to hematopoietic failure by impairing the proliferation of hematopoietic stem and progenitor cell (HSPC) and inducing HSPC apoptosis. On the other hand, FCV treatment could effectively relieve myeloid malignancies in the c-mybhyper MDS-like fish model, and played a role not only in the embryonic stage but also in adult zebrafish. This study reveals that FCV functions as a double-edged sword, with hematotoxicity at a high level, but that appropriate FCV treatment may be beneficial for the treatment of MDS.
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Affiliation(s)
- Jing Li
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China; Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, PR China
| | - Panpan Meng
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China; Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, PR China
| | - Riyang Zhou
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Yiyue Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, PR China; Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, PR China.
| | - Qing Lin
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, PR China.
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42
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Hou Y, Lee HJ, Chen Y, Ge J, Osman FOI, McAdow AR, Mokalled MH, Johnson SL, Zhao G, Wang T. Cellular diversity of the regenerating caudal fin. SCIENCE ADVANCES 2020; 6:eaba2084. [PMID: 32851162 PMCID: PMC7423392 DOI: 10.1126/sciadv.aba2084] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/26/2020] [Indexed: 05/03/2023]
Abstract
Zebrafish faithfully regenerate their caudal fin after amputation. During this process, both differentiated cells and resident progenitors migrate to the wound site and undergo lineage-restricted, programmed cellular state transitions to populate the new regenerate. Until now, systematic characterizations of cells comprising the new regenerate and molecular definitions of their state transitions have been lacking. We hereby characterize the dynamics of gene regulatory programs during fin regeneration by creating single-cell transcriptome maps of both preinjury and regenerating fin tissues at 1/2/4 days post-amputation. We consistently identified epithelial, mesenchymal, and hematopoietic populations across all stages. We found common and cell type-specific cell cycle programs associated with proliferation. In addition to defining the processes of epithelial replenishment and mesenchymal differentiation, we also identified molecular signatures that could better distinguish epithelial and mesenchymal subpopulations in fish. The insights for natural cell state transitions during regeneration point to new directions for studying this regeneration model.
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Affiliation(s)
- Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jiaxin Ge
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Fujr Osman Ibrahim Osman
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Maryville University of St Louis, St. Louis, MO 63141, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Mayssa H. Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Stephen L. Johnson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63108, USA
- Corresponding author. (G.Z.); (T.W.)
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Corresponding author. (G.Z.); (T.W.)
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43
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Ong SLM, de Vos IJHM, Meroshini M, Poobalan Y, Dunn NR. Microfibril-associated glycoprotein 4 (Mfap4) regulates haematopoiesis in zebrafish. Sci Rep 2020; 10:11801. [PMID: 32678226 PMCID: PMC7366704 DOI: 10.1038/s41598-020-68792-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/19/2020] [Indexed: 12/13/2022] Open
Abstract
Microfibril-associated glycoprotein 4 (MFAP4) is an extracellular matrix protein belonging to the fibrinogen-related protein superfamily. MFAP4 is produced by vascular smooth muscle cells and is highly enriched in the blood vessels of the heart and lung, where it is thought to contribute to the structure and function of elastic fibers. Genetic studies in humans have implicated MFAP4 in the pathogenesis of Smith-Magenis syndrome, in which patients present with multiple congenital abnormalities and mental retardation, as well as in the severe cardiac malformation left-sided congenital heart disease. Comprehensive genetic analysis of the role of MFAP4 orthologues in model organisms during development and tissue homeostasis is however lacking. Here, we demonstrate that zebrafish mfap4 transcripts are detected embryonically, resolving to the macrophage lineage by 24 h post fertilization. mfap4 null mutant zebrafish are unexpectedly viable and fertile, without ostensible phenotypes. However, tail fin amputation assays reveal that mfap4 mutants have reduced numbers of macrophages, with a concomitant increase in neutrophilic granulocytes, although recruitment of both cell types to the site of injury was unaffected. Molecular analyses suggest that loss of Mfap4 alters the balance between myeloid and lymphoid lineages during both primitive and definitive haematopoiesis, which could significantly impact the downstream function of the immune system.
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Affiliation(s)
- Sheena L M Ong
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore.,Department of Pathology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Ivo J H M de Vos
- Skin Research Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 11 Mandalay Road, Clinical Sciences Building, #17-01, Singapore, 308232, Singapore.,Department of Genetics, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
| | - M Meroshini
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore
| | - Yogavalli Poobalan
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore.,Engine Biosciences, 160 Robinson Road, 23-20 SBF Center, Singapore, 068914, Singapore
| | - N Ray Dunn
- Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore. .,Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Clinical Sciences Building, Singapore, 308232, Singapore.
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44
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Ölander M, Wiśniewski JR, Artursson P. Cell-type-resolved proteomic analysis of the human liver. Liver Int 2020; 40:1770-1780. [PMID: 32243721 DOI: 10.1111/liv.14452] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/31/2020] [Accepted: 03/21/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND & AIMS The human liver functions through a complex interplay between parenchymal and non-parenchymal cells. Mass spectrometry-based proteomic analysis of intact tissue has provided an in-depth view of the human liver proteome. However, the predominance of parenchymal cells (hepatocytes) means that the total tissue proteome mainly reflects hepatocyte expression. Here we therefore set out to analyse the proteomes of the major parenchymal and non-parenchymal cell types in the human liver. METHODS We applied quantitative label-free proteomic analysis on the major cell types of the human liver: hepatocytes, liver endothelial cells, Kupffer cells and hepatic stellate cells. RESULTS We identified 9791 proteins, revealing distinct protein expression profiles across cell types, whose in vivo relevance was shown by the presence of cell-type-specific proteins. Analysis of proteins related to the immune system indicated that mechanisms of immune-mediated liver injury include the involvement of several cell types. Furthermore, in-depth investigation of proteins related to the absorption, distribution, metabolism, excretion and toxicity (ADMET) of xenobiotics showed that ADMET-related tasks are not exclusively confined to hepatocytes, and that non-parenchymal cells may contribute to drug transport and metabolism. CONCLUSIONS Overall, the data we provide constitute a unique resource for exploring the proteomes of the major types of human liver cells, which will facilitate an improved understanding of the human liver in health and disease.
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Affiliation(s)
- Magnus Ölander
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Per Artursson
- Department of Pharmacy and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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45
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Chen J, Zhang S, Tong J, Teng X, Zhang Z, Li S, Teng X. Whole transcriptome-based miRNA-mRNA network analysis revealed the mechanism of inflammation-immunosuppressive damage caused by cadmium in common carp spleens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137081. [PMID: 32070891 DOI: 10.1016/j.scitotenv.2020.137081] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/20/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Cadmium (Cd) is a well-known environmental pollutant and can damage fish. MicroRNAs (miRNAs) can involve in inflammation and immunosuppression. However, the mechanisms of miRNAs are still unclear in common carp (Cyprinus carpio L.) treated by Cd. In current study, 54 juvenile common carp were randomly divided into the control group and the Cd group (0.26 mg L-1 Cd) and were cultured for 30 days. The results revealed inflammatory damage in the spleens of common carp after Cd exposure using morphological construction. There were 23 differentially expressed miRNAs including 17 up-regulated differentially expressed miRNAs (miR-1-4-3p, miR-7-1-5p, miR-7-2-5p, miR-10-43-5p, miR-34-3-5p, miR-128-4-3p, miR-128-5-3p, miR-132-2-5p, miR-132-6-5p, miR-216-3-5p, miR-216-4-5p, miR-375-2-3p, miR-375-4-3p, miR-375-5-3p, miR-375-7-3p, miR-375-8-3p, and miR-724-5p) and 6 down-regulated differentially expressed miRNAs (miR-9-6-5p, miR-25-9-3p, miR-31-3-5p, miR-31-12-5p, miR-103-5-5p, and miR-122-1-3p). The 23 miRNAs regulated 2022 target mRNAs. There were 10 pathways and 9 annotation clusters on 2022 target mRNAs using KEGG and GO analysis, respectively. Among them, 5 pathways (NF-κB signaling pathway, Jak-STAT signaling pathway, MAPK signaling pathway, Th1 and Th2 cell differentiation, and Toll-like receptor signaling pathway) and 7 GO terms (negative regulation of immune system process, T cell mediated immunity, regulation of immune response, inflammatory response, positive regulation of inflammatory response, regulation of inflammatory response, and inflammasome complex) were associated with inflammatory response and immunosuppression. miR-375-4-3p, NF-κB, COX-2, PTGES, and IL-4/13A increased and miR-31-12-5p, miR-9-6-5p, MMP9, IL-11, SPI1, and T-Bet decreased using transcriptome sequencing and RT-qPCR in Cd-treated common carp spleens, which revealed that our results were reliable. Our data indicated that miRNAs mediated inflammation-immunosuppressive injury caused by Cd in common carp spleens using whole transcriptome-based miRNA-mRNA network analysis. Our study provided new insights into the toxicology of Cd exposure.
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Affiliation(s)
- Jianqing Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Shuai Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Jianyu Tong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xiaojie Teng
- Grassland Workstation in Heilongjiang Province, Harbin 150067, China
| | - Zhongyuan Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Shu Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China.
| | - Xiaohua Teng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China; Harbin Hualong Feed Development Co., Ltd., Harbin 150078, China.
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Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Genome Biol 2020; 21:36. [PMID: 32051003 PMCID: PMC7017576 DOI: 10.1186/s13059-020-1949-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way. RESULTS To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community. CONCLUSIONS Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.
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Affiliation(s)
- Christian H Holland
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
- Department of Knowledge Technologies, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Javier Perales-Patón
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Gleixner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Manu P Kumar
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Elisabetta Mereu
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Brian A Joughin
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Biology, MIT, Cambridge, MA, USA
| | - Oliver Stegle
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bence Szalai
- Faculty of Medicine, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.
- Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Faculty of Medicine, Aachen, Germany.
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47
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Wang L, Gao S, Wang H, Xue C, Liu X, Yuan H, Wang Z, Chen S, Chen Z, de Thé H, Zhang Y, Zhang W, Zhu J, Zhou J. Interferon regulatory factor 2 binding protein 2b regulates neutrophil versus macrophage fate during zebrafish definitive myelopoiesis. Haematologica 2020; 105:325-337. [PMID: 31123027 PMCID: PMC7012491 DOI: 10.3324/haematol.2019.217596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Aproper choice of neutrophil-macrophage progenitor cell fate is essential for the generation of adequate myeloid subpopulations during embryonic development and in adulthood. The network governing neutrophil-macrophage progenitor cell fate has several key determinants, such as myeloid master regulators CCAAT enhancer binding protein alpha (C/EBPα) and spleen focus forming virus proviral integration oncogene (PU.1). Nevertheless, more regulators remain to be identified and characterized. To ensure balanced commitment of neutrophil-macrophage progenitors toward each lineage, the interplay among these determinants is not only synergistic, but also antagonistic. Depletion of interferon regulatory factor 2 binding protein 2b (Irf2bp2b), a well-known negative transcription regulator, results in a bias in neutrophil-macrophage progenitor cell fate in favor of macrophages at the expense of neutrophils during the stage of definitive myelopoiesis in zebrafish embryos. Mechanistic studies indicate that Irf2bp2b acts as a downstream target of C/EBPα, repressing PU.1 expression, and that SUMOylation confers the repressive function of Irf2bp2b. Thus, Irf2bp2b is a novel determinant in the choice of fate of neutrophil-macrophage progenitor cells.
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Affiliation(s)
- Luxiang Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuo Gao
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihong Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Xue
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yuan
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zixuan Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saijuan Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hugues de Thé
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Yiyue Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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48
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Shwartz A, Goessling W, Yin C. Macrophages in Zebrafish Models of Liver Diseases. Front Immunol 2019; 10:2840. [PMID: 31867007 PMCID: PMC6904306 DOI: 10.3389/fimmu.2019.02840] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatic macrophages are key components of the liver immunity and consist of two main populations. Liver resident macrophages, known as Kupffer cells in mammals, are crucial for maintaining normal liver homeostasis. Upon injury, they become activated to release proinflammatory cytokines and chemokines and recruit a large population of inflammatory monocyte-derived macrophages to the liver. During the progression of liver diseases, macrophages are highly plastic and have opposing functions depending on the signaling cues that they receive from the microenvironment. A comprehensive understanding of liver macrophages is essential for developing therapeutic interventions that target these cells in acute and chronic liver diseases. Mouse studies have provided the bulk of our current knowledge of liver macrophages. The emergence of various liver disease models and availability of transgenic tools to visualize and manipulate macrophages have made the teleost zebrafish (Danio rerio) an attractive new vertebrate model to study liver macrophages. In this review, we summarize the origin and behaviors of macrophages in healthy and injured livers in zebrafish. We highlight the roles of macrophages in zebrafish models of alcoholic and non-alcoholic liver diseases, hepatocellular carcinoma, and liver regeneration, and how they compare with the roles that have been described in mammals. We also discuss the advantages and challenges of using zebrafish to study liver macrophages.
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Affiliation(s)
- Arkadi Shwartz
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Wolfram Goessling
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States.,Harvard Stem Cell Institute, Cambridge, MA, United States.,Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States.,Broad Institute, Massachusetts Institute of Technology and Harvard, Cambridge, MA, United States.,Division of Health Sciences and Technology, Harvard and Massachusetts Institute of Technology, Boston, MA, United States.,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Chunyue Yin
- Division of Gastroenterology, Hepatology and Nutrition and Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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49
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Wegner S, Uhlemann R, Boujon V, Ersoy B, Endres M, Kronenberg G, Gertz K. Endothelial Cell-Specific Transcriptome Reveals Signature of Chronic Stress Related to Worse Outcome After Mild Transient Brain Ischemia in Mice. Mol Neurobiol 2019; 57:1446-1458. [PMID: 31758402 PMCID: PMC7060977 DOI: 10.1007/s12035-019-01822-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022]
Abstract
Vascular mechanisms underlying the adverse effects that depression and stress-related mental disorders have on stroke outcome are only partially understood. Identifying the transcriptomic signature of chronic stress in endothelium harvested from the ischemic brain is an important step towards elucidating the biological processes involved. Here, we subjected male 129S6/SvEv mice to a 28-day model of chronic stress. The ischemic lesion was quantified after 30 min filamentous middle cerebral artery occlusion (MCAo) and 48 h reperfusion by T2-weighted MRI. RNA sequencing was used to profile transcriptomic changes in cerebrovascular endothelial cells (ECs) from the infarct. Mice subjected to the stress procedure displayed reduced weight gain, increased adrenal gland weight, and increased hypothalamic FKBP5 mRNA and protein expression. Chronic stress conferred increased lesion volume upon MCAo. Stress-exposed mice showed a higher number of differentially expressed genes between ECs isolated from the ipsilateral and contralateral hemisphere than control mice. The genes in question are enriched for roles in biological processes closely linked to endothelial proliferation and neoangiogenesis. MicroRNA-34a was associated with nine of the top 10 biological process Gene Ontology terms selectively enriched in ECs from stressed mice. Moreover, expression of mature miR-34a-5p and miR-34a-3p in ischemic brain tissue was positively related to infarct size and negatively related to sirtuin 1 (Sirt1) mRNA transcription. In conclusion, this study represents the first EC-specific transcriptomic analysis of chronic stress in brain ischemia. The stress signature uncovered relates to worse stroke outcome and is directly relevant to endothelial mechanisms in the pathogenesis of stroke.
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Affiliation(s)
- Stephanie Wegner
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ria Uhlemann
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Valérie Boujon
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Burcu Ersoy
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Matthias Endres
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.,DZHK (German Center for Cardiovascular Research), Partner site Berlin, 10115, Berlin, Germany.,Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 10117, Berlin, Germany
| | - Golo Kronenberg
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.,University of Leicester and Leicestershire Partnership NHS Trust, Leicester, UK
| | - Karen Gertz
- Klinik für Neurologie, Charité Campus Mitte, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. .,DZHK (German Center for Cardiovascular Research), Partner site Berlin, 10115, Berlin, Germany.
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50
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Luo H, Li QQ, Wu N, Shen YG, Liao WT, Yang Y, Dong E, Zhang GM, Liu BR, Yue XZ, Tang XQ, Yang HS. Chronological in vivo imaging reveals endothelial inflammation prior to neutrophils accumulation and lipid deposition in HCD-fed zebrafish. Atherosclerosis 2019; 290:125-135. [DOI: 10.1016/j.atherosclerosis.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/20/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022]
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