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Sobah ML, Liongue C, Ward AC. Stat3 Regulates Developmental Hematopoiesis and Impacts Myeloid Cell Function via Canonical and Non-Canonical Modalities. J Innate Immun 2024; 16:262-282. [PMID: 38643762 PMCID: PMC11249464 DOI: 10.1159/000538364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 03/12/2024] [Indexed: 04/23/2024] Open
Abstract
INTRODUCTION Signal transducer and activator of transcription (STAT) 3 is extensively involved in the development, homeostasis, and function of immune cells, with STAT3 disruption associated with human immune-related disorders. The roles ascribed to STAT3 have been assumed to be due to its canonical mode of action as an inducible transcription factor downstream of multiple cytokines, although alternative noncanonical functional modalities have also been identified. The relative involvement of each mode was further explored in relevant zebrafish models. METHODS Genome editing with CRISPR/Cas9 was used to generate mutants of the conserved zebrafish Stat3 protein: a loss of function knockout (KO) mutant and a mutant lacking C-terminal sequences including the transactivation domain (ΔTAD). Lines harboring these mutations were analyzed with respect to blood and immune cell development and function in comparison to wild-type zebrafish. RESULTS The Stat3 KO mutant showed perturbation of hematopoietic lineages throughout primitive and early definitive hematopoiesis. Neutrophil numbers did not increase in response to lipopolysaccharide (LPS) or granulocyte colony-stimulating factor (G-CSF) and their migration was significantly diminished, the latter correlating with abrogation of the Cxcl8b/Cxcr2 pathway, with macrophage responses perturbed. Intriguingly, many of these phenotypes were not shared by the Stat3 ΔTAD mutant. Indeed, only neutrophil and macrophage development were disrupted in these mutants with responsiveness to LPS and G-CSF maintained, and neutrophil migration actually increased. CONCLUSION This study has identified roles for zebrafish Stat3 within hematopoietic stem cells impacting multiple lineages throughout primitive and early definitive hematopoiesis, myeloid cell responses to G-CSF and LPS and neutrophil migration. Many of these roles showed conservation, but notably several involved noncanonical modalities, providing additional insights for relevant diseases.
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Affiliation(s)
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
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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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Liongue C, Ratnayake T, Basheer F, Ward AC. Janus Kinase 3 (JAK3): A Critical Conserved Node in Immunity Disrupted in Immune Cell Cancer and Immunodeficiency. Int J Mol Sci 2024; 25:2977. [PMID: 38474223 DOI: 10.3390/ijms25052977] [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: 01/17/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
The Janus kinase (JAK) family is a small group of protein tyrosine kinases that represent a central component of intracellular signaling downstream from a myriad of cytokine receptors. The JAK3 family member performs a particularly important role in facilitating signal transduction for a key set of cytokine receptors that are essential for immune cell development and function. Mutations that impact JAK3 activity have been identified in a number of human diseases, including somatic gain-of-function (GOF) mutations associated with immune cell malignancies and germline loss-of-function (LOF) mutations associated with immunodeficiency. The structure, function and impacts of both GOF and LOF mutations of JAK3 are highly conserved, making animal models highly informative. This review details the biology of JAK3 and the impact of its perturbation in immune cell-related diseases, including relevant animal studies.
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Affiliation(s)
- Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
| | | | - Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
| | - Alister C Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
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Fallatah W, Mary J, Jagadeeswaran P. Zebrafish Thrombocyte Transcriptome Analysis and Functional Genomics. Methods Mol Biol 2024; 2812:193-201. [PMID: 39068363 DOI: 10.1007/978-1-0716-3886-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Our laboratory is interested in investigating the maturation process of zebrafish thrombocytes, which are functional equivalents to human platelets. We have adopted the zebrafish model to gain insights into mammalian platelet production, or thrombopoiesis. Notably, zebrafish exhibit two distinct populations of thrombocytes in their circulating blood: young and mature thrombocytes. This observation is intriguing because maturation appears to occur in circulation, yet the precise mechanisms governing this maturation remain elusive. Our goal is to understand the mechanisms underlying thrombocyte maturation by conducting single-cell RNA sequencing (scRNA-Seq) on young and mature thrombocytes, analyzing these transcriptomes to identify genes specific to each thrombocyte population, and elucidating the role of these genes in the maturation process, by quantifying thrombocyte numbers after the piggyback knockdown of each of these genes. In this chapter, we present a comprehensive, step-by-step protocol detailing the multifaceted methodology involved in understanding thrombocyte maturation, which encompasses the collection of zebrafish blood, the separation of young and mature thrombocytes using flow cytometry, scRNA-Seq analysis of these distinct thrombocyte populations, identification of genes specific to young and mature thrombocytes, and subsequent validation through gene knockdown techniques.
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Affiliation(s)
- Weam Fallatah
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Jabila Mary
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Pudur Jagadeeswaran
- Department of Biological Sciences, University of North Texas, Denton, TX, USA.
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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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Mahony CB, Copper L, Vrljicak P, Noyvert B, Constantinidou C, Browne S, Pan Y, Palles C, Ott S, Higgs MR, Monteiro R. Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency. Cell Rep 2023; 42:112571. [PMID: 37256751 DOI: 10.1016/j.celrep.2023.112571] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 03/14/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Inherited bone marrow failure associated with heterozygous mutations in GATA2 predisposes toward hematological malignancies, but the mechanisms remain poorly understood. Here, we investigate the mechanistic basis of marrow failure in a zebrafish model of GATA2 deficiency. Single-cell transcriptomics and chromatin accessibility assays reveal that loss of gata2a leads to skewing toward the erythroid lineage at the expense of myeloid cells, associated with loss of cebpa expression and decreased PU.1 and CEBPA transcription factor accessibility in hematopoietic stem and progenitor cells (HSPCs). Furthermore, gata2a mutants show impaired expression of npm1a, the zebrafish NPM1 ortholog. Progressive loss of npm1a in HSPCs is associated with elevated levels of DNA damage in gata2a mutants. Thus, Gata2a maintains myeloid lineage priming through cebpa and protects against genome instability and marrow failure by maintaining expression of npm1a. Our results establish a potential mechanism underlying bone marrow failure in GATA2 deficiency.
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Affiliation(s)
- Christopher B Mahony
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Lucy Copper
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; Cancer Research UK Birmingham Centre, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Pavle Vrljicak
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Boris Noyvert
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chrystala Constantinidou
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK; Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Sofia Browne
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Yi Pan
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sascha Ott
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK; Bioinformatics Research Technology Platform, University of Warwick, Coventry, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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Liu G, Zhu C, Gao X, Zheng Y, Zhu X, Jiang H, Wei W, Jiang Q, Zhang X. Single-cell transcriptome analysis reveals a cellular immune response in freshwater dark sleeper ( Odontobutis potamophila) after infection with Aeromonas veronii. Front Physiol 2023; 14:1201914. [PMID: 37275236 PMCID: PMC10233152 DOI: 10.3389/fphys.2023.1201914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
The bacterium Aeromonas veronii is a co-pathogenic species that can negatively impact the health of both humans and aquatic animals. In this study, we used single-cell transcriptome analysis (scRNA-seq) to investigate the effects of infection with A. veronii on head kidney cells and the regulation of gene expression in the dark sleeper (Odontobutis potamophila). scRNA-seq was used to assess the effects of infection with A. veronii in O. potamophila B cells, endothelial cells, macrophages, and granulocytes, and differential enrichment analysis of gene expression in B cells and granulocytes was performed. The analyses revealed a significant increase in neutrophils and decrease in eosinophils in granulocytes infected with A. veronii. Activation of neutrophils enhanced ribosome biogenesis by up-regulating the expression of RPS12 and RPL12 to fight against invading pathogens. Crucial pro-inflammatory mediators IL1B, IGHV1-4, and the major histocompatibility class II genes MHC2A and MHC2DAB, which are involved in virulence processes, were upregulated, suggesting that A. veronii activates an immune response that presents antigens and activates immunoglobulin receptors in B cells. These cellular immune responses triggered by infection with A. veronii enriched the available scRNA-seq data for teleosts, and these results are important for understanding the evolution of cellular immune defense and functional differentiation of head kidney cells.
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Affiliation(s)
- Guoxing Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial Science and Technology Resources (Agricultural Germplasm Resources) Coordination Service Platform, Nanjing, China
| | - Chenxi Zhu
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Xiaojian Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - You Zheng
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial Science and Technology Resources (Agricultural Germplasm Resources) Coordination Service Platform, Nanjing, China
| | - Xinhai Zhu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hucheng Jiang
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial Science and Technology Resources (Agricultural Germplasm Resources) Coordination Service Platform, Nanjing, China
| | - Wanhong Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qichen Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
- Low-temperature Germplasm Bank of Important Economic Fish (Freshwater Fisheries Research Institute of Jiangsu Province) of Jiangsu Provincial Science and Technology Resources (Agricultural Germplasm Resources) Coordination Service Platform, Nanjing, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Heidary S, Awasthi N, Page N, Allnutt T, Lewis RS, Liongue C, Ward AC. A zebrafish model of growth hormone insensitivity syndrome with immune dysregulation 1 (GHISID1). Cell Mol Life Sci 2023; 80:109. [PMID: 36995466 PMCID: PMC10063521 DOI: 10.1007/s00018-023-04759-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/03/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
Signal transducer and activator of transcription (STAT) proteins act downstream of cytokine receptors to facilitate changes in gene expression that impact a range of developmental and homeostatic processes. Patients harbouring loss-of-function (LOF) STAT5B mutations exhibit postnatal growth failure due to lack of responsiveness to growth hormone as well as immune perturbation, a disorder called growth hormone insensitivity syndrome with immune dysregulation 1 (GHISID1). This study aimed to generate a zebrafish model of this disease by targeting the stat5.1 gene using CRISPR/Cas9 and characterising the effects on growth and immunity. The zebrafish Stat5.1 mutants were smaller, but exhibited increased adiposity, with concomitant dysregulation of growth and lipid metabolism genes. The mutants also displayed impaired lymphopoiesis with reduced T cells throughout the lifespan, along with broader disruption of the lymphoid compartment in adulthood, including evidence of T cell activation. Collectively, these findings confirm that zebrafish Stat5.1 mutants mimic the clinical impacts of human STAT5B LOF mutations, establishing them as a model of GHISID1.
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Affiliation(s)
- Somayyeh Heidary
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia
| | - Nagendra Awasthi
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia
| | - Nicole Page
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia
| | - Theo Allnutt
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia
| | - Rowena S Lewis
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia
- IMPACT, Deakin University, Geelong, VIC, 3216, Australia
| | - Alister C Ward
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia.
- IMPACT, Deakin University, Geelong, VIC, 3216, Australia.
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Basheer F, Sertori R, Liongue C, Ward AC. Zebrafish: A Relevant Genetic Model for Human Primary Immunodeficiency (PID) Disorders? Int J Mol Sci 2023; 24:ijms24076468. [PMID: 37047441 PMCID: PMC10095346 DOI: 10.3390/ijms24076468] [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: 03/06/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Primary immunodeficiency (PID) disorders, also commonly referred to as inborn errors of immunity, are a heterogenous group of human genetic diseases characterized by defects in immune cell development and/or function. Since these disorders are generally uncommon and occur on a variable background profile of potential genetic and environmental modifiers, animal models are critical to provide mechanistic insights as well as to create platforms to underpin therapeutic development. This review aims to review the relevance of zebrafish as an alternative genetic model for PIDs. It provides an overview of the conservation of the zebrafish immune system and details specific examples of zebrafish models for a multitude of specific human PIDs across a range of distinct categories, including severe combined immunodeficiency (SCID), combined immunodeficiency (CID), multi-system immunodeficiency, autoinflammatory disorders, neutropenia and defects in leucocyte mobility and respiratory burst. It also describes some of the diverse applications of these models, particularly in the fields of microbiology, immunology, regenerative biology and oncology.
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Affiliation(s)
- Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
| | - Robert Sertori
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
| | - Alister C Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
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Transgenic IDH2 R172K and IDH2 R140Q zebrafish models recapitulated features of human acute myeloid leukemia. Oncogene 2023; 42:1272-1281. [PMID: 36739363 PMCID: PMC10101851 DOI: 10.1038/s41388-023-02611-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/06/2023]
Abstract
Isocitrate dehydrogenase 2 (IDH2) mutations occur in more than 15% of cytogenetically normal acute myeloid leukemia (CN-AML) but comparative studies of their roles in leukemogenesis have been scarce. We generated zebrafish models of IDH2R172K and IDH2R140Q AML and reported their pathologic, functional and transcriptomic features and therapeutic responses to target therapies. Transgenic embryos co-expressing FLT3ITD and IDH2 mutations showed accentuation of myelopoiesis. As these embryos were raised to adulthood, full-blown leukemia ensued with multi-lineage dysplasia, increase in myeloblasts and marrow cellularity and splenomegaly. The leukemia cells were transplantable into primary and secondary recipients and resulted in more aggressive disease. Tg(Runx1:FLT3ITDIDH2R172K) but not Tg(Runx1:FLT3ITDIDH2R140Q) zebrafish showed an increase in T-cell development at embryonic and adult stages. Single-cell transcriptomic analysis revealed increased myeloid skewing, differentiation blockade and enrichment of leukemia-associated gene signatures in both zebrafish models. Tg(Runx1:FLT3ITDIDH2R172K) but not Tg(Runx1:FLT3ITDIDH2R140Q) zebrafish showed an increase in interferon signals at the adult stage. Leukemic phenotypes in both zebrafish could be ameliorated by quizartinib and enasidenib. In conclusion, the zebrafish models of IDH2 mutated AML recapitulated the morphologic, clinical, functional and transcriptomic characteristics of human diseases, and provided the prototype for developing zebrafish leukemia models of other genotypes that would become a platform for high throughput drug screening.
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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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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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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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14
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Taznin T, Perera K, Gibert Y, Ward AC, Liongue C. Cytokine Receptor-Like Factor 3 (CRLF3) Contributes to Early Zebrafish Hematopoiesis. Front Immunol 2022; 13:910428. [PMID: 35795682 PMCID: PMC9251315 DOI: 10.3389/fimmu.2022.910428] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022] Open
Abstract
Cytokine receptor-like factor 3 (CRLF3) is an ancient protein conserved across metazoans that contains an archetypal cytokine receptor homology domain (CHD). This domain is found in cytokine receptors present in bilateria, including higher vertebrates, that play key roles in a variety of developmental and homeostatic processes, particularly relating to blood and immune cells. However, understanding of CRLF3 itself remains very limited. This study aimed to investigate this evolutionarily significant protein by studying its embryonic expression and function in early development, particularly of blood and immune cells, using zebrafish as a model. Expression of crlf3 was identified in mesoderm-derived tissues in early zebrafish embryos, including the somitic mesoderm and both anterior and posterior lateral plate mesoderm. Later expression was observed in the thymus, brain, retina and exocrine pancreas. Zebrafish crlf3 mutants generated by genome editing technology exhibited a significant reduction in primitive hematopoiesis and early definitive hematopoiesis, with decreased early progenitors impacting on multiple lineages. No other obvious phenotypes were observed in the crlf3 mutants.
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Affiliation(s)
- Tarannum Taznin
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | | | - Yann Gibert
- School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
- *Correspondence: Clifford Liongue,
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15
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In vivo impact of JAK3 A573V mutation revealed using zebrafish. Cell Mol Life Sci 2022; 79:322. [PMID: 35622134 PMCID: PMC9142468 DOI: 10.1007/s00018-022-04361-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022]
Abstract
Background Janus kinase 3 (JAK3) acts downstream of the interleukin-2 (IL-2) receptor family to play a pivotal role in the regulation of lymphoid cell development. Activating JAK3 mutations are associated with a number of lymphoid and other malignancies, with mutations within the regulatory pseudokinase domain common. Methods The pseudokinase domain mutations A572V and A573V were separately introduced into the highly conserved zebrafish Jak3 and transiently expressed in cell lines and zebrafish embryos to examine their activity and impact on early T cells. Genome editing was subsequently used to introduce the A573V mutation into the zebrafish genome to study the effects of JAK3 activation on lymphoid cells in a physiologically relevant context throughout the life-course. Results Zebrafish Jak3 A573V produced the strongest activation of downstream STAT5 in vitro and elicited a significant increase in T cells in zebrafish embryos. Zebrafish carrying just a single copy of the Jak3 A573V allele displayed elevated embryonic T cells, which continued into adulthood. Hematopoietic precursors and NK cells were also increased, but not B cells. The lymphoproliferative effects of Jak3 A573V in embryos was shown to be dependent on zebrafish IL-2Rγc, JAK1 and STAT5B equivalents, and could be suppressed with the JAK3 inhibitor Tofacitinib. Conclusions This study demonstrates that a single JAK3 A573V allele expressed from the endogenous locus was able to enhance lymphopoiesis throughout the life-course, which was mediated via an IL-2Rγc/JAK1/JAK3/STAT5 signaling pathway and was sensitive to Tofacitinib. This extends our understanding of oncogenic JAK3 mutations and creates a novel model to underpin further translational investigations. Supplementary Information The online version contains supplementary material available at 10.1007/s00018-022-04361-8.
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16
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Li M, Zhao X, Xie J, Tong X, Shan J, Shi M, Wang G, Ye W, Liu Y, Unger BH, Cheng Y, Zhang W, Wu N, Xia XQ. Dietary Inclusion of Seabuckthorn ( Hippophae rhamnoides) Mitigates Foodborne Enteritis in Zebrafish Through the Gut-Liver Immune Axis. Front Physiol 2022; 13:831226. [PMID: 35464096 PMCID: PMC9019508 DOI: 10.3389/fphys.2022.831226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
To help prevent foodborne enteritis in aquaculture, several feed additives, such as herbal medicine, have been added to fish diets. Predictions of effective herb medicines for treating fish foodborne enteritis from key regulated DEGs (differentially expressed genes) in transcriptomic data can aid in the development of feed additives using the Traditional Chinese Medicine Integrated Database. Seabuckthorn has been assessed as a promising candidate for treating grass carp soybean-induced enteritis (SBMIE). In the present study, the SBMIE zebrafish model was used to assess seabuckthorn's therapeutic or preventative effects. The results showed that intestinal and hepatic inflammation was reduced when seabuckthorn was added, either pathologically (improved intestinal villi morphology, less oil-drops) or growth-related (body fat deposition). Moreover, seabuckthorn may block the intestinal p53 signaling pathway, while activating the PPAR signaling pathway and fatty acid metabolism in the liver. 16S rRNA gene sequencing results also indicated a significant increase in OTU numbers and skewed overlapping with the fish meal group following the addition of seabuckthorn. Additionally, there were signs of altered gut microbiota taxa composition, particularly for reduced TM7, Sphingomonas, and Shigella, following the addition of seabuckthorn. Hindgut imaging of fluorescent immune cells in SBMIE larvae revealed the immune regulatory mechanisms at the cellular level. Seabuckthorn may significantly inhibit the inflammatory gathering of neutrophils, macrophages, and mature T cells, as well as cellular protrusions' formation. On the other hand, in larvae, seabuckthorn inhibited the inflammatory aggregation of lck+ T cells but not immature lymphocytes, indicating that it affected intestinal adaptive immunity. Although seabuckthorn did not affect the distribution of intestinal CD4+ cells, the number of hepatic CD4+ cells were reduced in fish from the seabuckthorn supplementation group. Thus, the current data indicate that seabuckthorn may alleviate foodborne gut-liver symptoms by enhancing intestinal mucosal immunity and microbiota while simultaneously inhibiting hepatic adipose disposition, making it a potential additive for preventing fish foodborne gut-liver symptoms.
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Affiliation(s)
- Ming Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Xuyang Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Jiayuan Xie
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Junwei Shan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guangxin Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Weidong Ye
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | | | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Nan Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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17
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Research Techniques Made Simple: Zebrafish Models for Human Dermatologic Disease. J Invest Dermatol 2022; 142:499-506.e1. [DOI: 10.1016/j.jid.2021.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022]
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18
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Peterson EA, Sun J, Wang J. Leukocyte-Mediated Cardiac Repair after Myocardial Infarction in Non-Regenerative vs. Regenerative Systems. J Cardiovasc Dev Dis 2022; 9:63. [PMID: 35200716 PMCID: PMC8877434 DOI: 10.3390/jcdd9020063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Innate and adaptive leukocytes rapidly mobilize to ischemic tissues after myocardial infarction in response to damage signals released from necrotic cells. Leukocytes play important roles in cardiac repair and regeneration such as inflammation initiation and resolution; the removal of dead cells and debris; the deposition of the extracellular matrix and granulation tissue; supporting angiogenesis and cardiomyocyte proliferation; and fibrotic scar generation and resolution. By organizing and comparing the present knowledge of leukocyte recruitment and function after cardiac injury in non-regenerative to regenerative systems, we propose that the leukocyte response to cardiac injury differs in non-regenerative adult mammals such as humans and mice in comparison to cardiac regenerative models such as neonatal mice and adult zebrafish. Specifically, extensive neutrophil, macrophage, and T-cell persistence contributes to a lengthy inflammatory period in non-regenerative systems for adverse cardiac remodeling and heart failure development, whereas their quick removal supports inflammation resolution in regenerative systems for new contractile tissue formation and coronary revascularization. Surprisingly, other leukocytes have not been examined in regenerative model systems. With this review, we aim to encourage the development of improved immune cell markers and tools in cardiac regenerative models for the identification of new immune targets in non-regenerative systems to develop new therapies.
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Affiliation(s)
| | | | - Jinhu Wang
- Division of Cardiology, School of Medicine, Emory University, Atlanta, GA 30322, USA; (E.A.P.); (J.S.)
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19
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Sertori R, Jones R, Basheer F, Rivera L, Dawson S, Loke S, Heidary S, Dhillon A, Liongue C, Ward AC. Generation and Characterization of a Zebrafish IL-2Rγc SCID Model. Int J Mol Sci 2022; 23:ijms23042385. [PMID: 35216498 PMCID: PMC8875600 DOI: 10.3390/ijms23042385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 12/14/2022] Open
Abstract
The IL-2 family of cytokines act via receptor complexes that share the interleukin-2 receptor gamma common (IL-2Rγc) chain to play key roles in lymphopoiesis. Inactivating IL-2Rγc mutations results in severe combined immunodeficiency (SCID) in humans and other species. This study sought to generate an equivalent zebrafish SCID model. The zebrafish il2rga gene was targeted for genome editing using TALENs and presumed loss-of-function alleles analyzed with respect to immune cell development and impacts on intestinal microbiota and tumor immunity. Knockout of zebrafish Il-2rγc.a resulted in a SCID phenotype, including a significant reduction in T cells, with NK cells also impacted. This resulted in dysregulated intestinal microbiota and defective immunity to tumor xenotransplants. Collectively, this establishes a useful zebrafish SCID model.
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Affiliation(s)
- Robert Sertori
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
| | - Realla Jones
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
| | - Faiza Basheer
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Leni Rivera
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Samantha Dawson
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Stella Loke
- School of Life and Environmental Science, Deakin University, Burwood, VIC 3125, Australia;
| | - Somayyeh Heidary
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Amardeep Dhillon
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
| | - Alister C. Ward
- School of Medicine, Deakin University, Geelong, VIC 3216, Australia; (R.S.); (R.J.); (F.B.); (L.R.); (S.D.); (S.H.); (A.D.); (C.L.)
- Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC 3216, Australia
- Correspondence:
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20
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Chan JTH, Kadri S, Köllner B, Rebl A, Korytář T. RNA-Seq of Single Fish Cells - Seeking Out the Leukocytes Mediating Immunity in Teleost Fishes. Front Immunol 2022; 13:798712. [PMID: 35140719 PMCID: PMC8818700 DOI: 10.3389/fimmu.2022.798712] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 01/01/2023] Open
Abstract
The immune system is a complex and sophisticated biological system, spanning multiple levels of complexity, from the molecular level to that of tissue. Our current understanding of its function and complexity, of the heterogeneity of leukocytes, is a result of decades of concentrated efforts to delineate cellular markers using conventional methods of antibody screening and antigen identification. In mammalian models, this led to in-depth understanding of individual leukocyte subsets, their phenotypes, and their roles in health and disease. The field was further propelled forward by the development of single-cell (sc) RNA-seq technologies, offering an even broader and more integrated view of how cells work together to generate a particular response. Consequently, the adoption of scRNA-seq revealed the unexpected plasticity and heterogeneity of leukocyte populations and shifted several long-standing paradigms of immunology. This review article highlights the unprecedented opportunities offered by scRNA-seq technology to unveil the individual contributions of leukocyte subsets and their crosstalk in generating the overall immune responses in bony fishes. Single-cell transcriptomics allow identifying unseen relationships, and formulating novel hypotheses tailored for teleost species, without the need to rely on the limited number of fish-specific antibodies and pre-selected markers. Several recent studies on single-cell transcriptomes of fish have already identified previously unnoticed expression signatures and provided astonishing insights into the diversity of teleost leukocytes and the evolution of vertebrate immunity. Without a doubt, scRNA-seq in tandem with bioinformatics tools and state-of-the-art methods, will facilitate studying the teleost immune system by not only defining key markers, but also teaching us about lymphoid tissue organization, development/differentiation, cell-cell interactions, antigen receptor repertoires, states of health and disease, all across time and space in fishes. These advances will invite more researchers to develop the tools necessary to explore the immunology of fishes, which remain non-conventional animal models from which we have much to learn.
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Affiliation(s)
- Justin T. H. Chan
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Safwen Kadri
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Regenerative Biology and Medicine, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bernd Köllner
- Institute of Immunology, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Tomáš Korytář
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, České Budějovice, Czechia
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21
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Weiss JM, Lumaquin-Yin D, Montal E, Suresh S, Leonhardt CS, White RM. Shifting the focus of zebrafish toward a model of the tumor microenvironment. eLife 2022; 11:69703. [PMID: 36538362 PMCID: PMC9767465 DOI: 10.7554/elife.69703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 11/21/2022] [Indexed: 12/29/2022] Open
Abstract
Cancer cells exist in a complex ecosystem with numerous other cell types in the tumor microenvironment (TME). The composition of this tumor/TME ecosystem will vary at each anatomic site and affects phenotypes such as initiation, metastasis, and drug resistance. A mechanistic understanding of the large number of cell-cell interactions between tumor and TME requires models that allow us to both characterize as well as genetically perturb this complexity. Zebrafish are a model system optimized for this problem, because of the large number of existing cell-type-specific drivers that can label nearly any cell in the TME. These include stromal cells, immune cells, and tissue resident normal cells. These cell-type-specific promoters/enhancers can be used to drive fluorophores to facilitate imaging and also CRISPR cassettes to facilitate perturbations. A major advantage of the zebrafish is the ease by which large numbers of TME cell types can be studied at once, within the same animal. While these features make the zebrafish well suited to investigate the TME, the model has important limitations, which we also discuss. In this review, we describe the existing toolset for studying the TME using zebrafish models of cancer and highlight unique biological insights that can be gained by leveraging this powerful resource.
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Affiliation(s)
- Joshua M Weiss
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Dianne Lumaquin-Yin
- Weill-Cornel Medical College, Tri-Institutional M.D./Ph.D. ProgramNew YorkUnited States
| | - Emily Montal
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Shruthy Suresh
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Carl S Leonhardt
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States
| | - Richard M White
- Memorial Sloan Kettering Cancer Center, Department of Cancer Biology & GeneticsNew YorkUnited States,Department of Medicine, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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22
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Avagyan S, Henninger JE, Mannherz WP, Mistry M, Yoon J, Yang S, Weber MC, Moore JL, Zon LI. Resistance to inflammation underlies enhanced fitness in clonal hematopoiesis. Science 2021; 374:768-772. [PMID: 34735227 DOI: 10.1126/science.aba9304] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- S Avagyan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - J E Henninger
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | - M Mistry
- Harvard Chan Bioinformatics Core, Boston, MA, USA
| | - J Yoon
- Harvard Chan Bioinformatics Core, Boston, MA, USA
| | - S Yang
- Boston Children's Hospital, Boston, MA, USA
| | - M C Weber
- Boston Children's Hospital, Boston, MA, USA
| | - J L Moore
- Boston Children's Hospital, Boston, MA, USA
| | - L I Zon
- Boston Children's Hospital, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
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23
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Stosik M, Tokarz-Deptuła B, Deptuła W. Immunological memory in teleost fish. FISH & SHELLFISH IMMUNOLOGY 2021; 115:95-103. [PMID: 34058353 DOI: 10.1016/j.fsi.2021.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
Immunological memory can be regarded as the key aspect of adaptive immunity, i.e. a specific response to first contact with an antigen, which in mammals is determined by the properties of T, B and NK cells. Re-exposure to the same antigen results in a more rapid response of the activated specific cells, which have a unique property that is the immunological memory acquired upon first contact with the antigen. Such a state of immune activity is also to be understood as related to "altered behavior of the immune system" due to genetic alterations, presumably maintained independently of the antigen. It also indicates a possible alternative mechanism of maintaining the immune state at a low level of the immune response, "directed" by an antigen or dependent on an antigen, associated with repeated exposure to the same antigen from time to time, as well as the concept of innate immune memory, associated with epigenetic reprogramming of myeloid cells, i.e. macrophages and NK cells. Studies on Teleostei have provided evidence for the presence of immunological memory determined by T and B cells and a secondary response stronger than the primary response. Research has also demonstrated that in these animals macrophages and NK-like cells (similar to mammalian NK cells) are able to respond when re-exposed to the same antigen. Regardless of previous reports on immunological memory in teleost fish, many reactions and mechanisms related to this ability require further investigation. The very nature of immunological memory and the activity of cells involved in this process, in particular macrophages and NK-like cells, need to be explained. This paper presents problems associated with adaptive and innate immune memory in teleost fish and characteristics of cells associated with this ability.
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Affiliation(s)
- Michał Stosik
- Faculty of Biological Sciences, Institute of Biological Sciences, University of Zielona Gora, Poland
| | | | - Wiesław Deptuła
- Faculty of Biological and Veterinary Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Poland
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24
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Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages. Blood Adv 2021; 5:2673-2686. [PMID: 34170284 DOI: 10.1182/bloodadvances.2020002992] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias, atypical infections, and increased risk of hematologic malignancies. Here, we generated a zebrafish mutant of gata2b that recapitulated the myelomonocytopenia and B-cell lymphopenia of GATA2 deficiency syndrome. Using single-cell assay for transposase accessible chromatin with sequencing of marrow cells, we showed that loss of gata2b led to contrasting alterations in chromosome accessibility in early myeloid and lymphoid progenitors, associated with defects in gene expression. Within the myeloid lineage in gata2b mutant zebrafish, we identified an attenuated myeloid differentiation with reduced transcriptional priming and skewing away from the monocytic program. In contrast, in early lymphoid progenitors, gata2b loss led to accumulation of B-lymphoid transcription factor accessibility coupled with increased expression of the B-cell lineage-specification program. However, gata2b mutant zebrafish had incomplete B-cell lymphopoiesis with loss of lineage-specific transcription factor accessibility in differentiating B cells, in the context of aberrantly reduced oxidative metabolic pathways. Our results establish that transcriptional events in early progenitors driven by Gata2 are required to complete normal differentiation.
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25
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Miao KZ, Kim GY, Meara GK, Qin X, Feng H. Tipping the Scales With Zebrafish to Understand Adaptive Tumor Immunity. Front Cell Dev Biol 2021; 9:660969. [PMID: 34095125 PMCID: PMC8173129 DOI: 10.3389/fcell.2021.660969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022] Open
Abstract
The future of improved immunotherapy against cancer depends on an in-depth understanding of the dynamic interactions between the immune system and tumors. Over the past two decades, the zebrafish has served as a valuable model system to provide fresh insights into both the development of the immune system and the etiologies of many different cancers. This well-established foundation of knowledge combined with the imaging and genetic capacities of the zebrafish provides a new frontier in cancer immunology research. In this review, we provide an overview of the development of the zebrafish immune system along with a side-by-side comparison of its human counterpart. We then introduce components of the adaptive immune system with a focus on their roles in the tumor microenvironment (TME) of teleosts. In addition, we summarize zebrafish models developed for the study of cancer and adaptive immunity along with other available tools and technology afforded by this experimental system. Finally, we discuss some recent research conducted using the zebrafish to investigate adaptive immune cell-tumor interactions. Without a doubt, the zebrafish will arise as one of the driving forces to help expand the knowledge of tumor immunity and facilitate the development of improved anti-cancer immunotherapy in the foreseeable future.
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Affiliation(s)
- Kelly Z Miao
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Grace Y Kim
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Grace K Meara
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Xiaodan Qin
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States
| | - Hui Feng
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, United States.,Department of Medicine, Section of Hematology and Medical Oncology, Boston University School of Medicine, Boston, MA, United States
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26
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [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: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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27
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Niu J, Huang Y, Liu X, Zhang Z, Tang J, Wang B, Lu Y, Cai J, Jian J. Single-cell RNA-seq reveals different subsets of non-specific cytotoxic cells in teleost. Genomics 2020; 112:5170-5179. [DOI: 10.1016/j.ygeno.2020.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
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28
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Tu J, Liu X, Jia H, Reilly J, Yu S, Cai C, Liu F, Lv Y, Huang Y, Lu Z, Han S, Jiang T, Shu X, Wu X, Tang Z, Lu Q, Liu M. The chromatin remodeler Brg1 is required for formation and maintenance of hematopoietic stem cells. FASEB J 2020; 34:11997-12008. [PMID: 32738093 DOI: 10.1096/fj.201903168rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/21/2020] [Accepted: 06/24/2020] [Indexed: 11/11/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) have the ability to self-renew and differentiate into various blood cells, thus playing an important role in maintenance of lifelong hematopoiesis. Brahma-related gene 1 (BRG1), which acts as the ATP subunit of mammalian SWI-SNF-related chromatin remodeling complexes, is involved in human acute myeloid leukemia and highly expresses in short-term HSPCs. But its role and regulatory mechanism for HSPC development have not yet been well established. Here, we generated a brg1 knockout zebrafish model using TALEN technology. We found that in brg1-/- embryo, the primitive hematopoiesis remained well, while definitive hematopoiesis formation was significantly impaired. The number of hemogenic endothelial cells was decreased, further affecting definitive hematopoiesis with reduced myeloid and lymphoid cells. During embryogenesis, the nitric oxide (NO) microenvironment in brg1-/- embryo was seriously damaged and the reduction of HSPCs could be partially rescued by a NO donor. Chromatin immunoprecipitation (ChIP) assays showed that BRG1 could bind to the promoter of KLF2 and trigger its transcriptional activity of NO synthase. Our findings show that Brg1 promotes klf2a expression in hemogenic endothelium and highlight a novel mechanism for HSPC formation and maintenance.
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Affiliation(s)
- Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Xiliang Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - James Reilly
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Shanshan Yu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Chen Cai
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Fei Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yuexia Lv
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yuwen Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Zhaojing Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Shanshan Han
- Medical College, China Three Gorges University, Yichang, China
| | - Tao Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Xinhua Shu
- Department of Biological and Biomedical Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Xiaoyan Wu
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaohui Tang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
| | - Mugen Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, PR China
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29
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Yi G, Zhao Y, Xie F, Zhu F, Wan Z, Wang J, Wang X, Gao K, Cao L, Li X, Chen C, Kuang Y, Qiu X, Yang H, Wang J, Su B, Chen L, Zhang W, Hou Y, Xu X, He Y, Tsun A, Liu X, Li B. Single-cell RNA-seq unveils critical regulators of human FOXP3 + regulatory T cell stability. Sci Bull (Beijing) 2020; 65:1114-1124. [PMID: 36659163 DOI: 10.1016/j.scib.2020.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/09/2019] [Accepted: 10/10/2019] [Indexed: 01/21/2023]
Abstract
The heterogeneity and plasticity of T lymphocytes is critical for determining immune response outcomes. Functional regulatory T (Treg) cells are commonly characterized by stable FOXP3 expression and have reported to exhibit heterogeneous phenotypes under inflammatory conditions. However, the interplay between inflammation and Treg cell suppressive activity still remains elusive. Here, we utilized single-cell RNA sequencing to investigate how human Treg cells respond to the pro-inflammatory cytokine interleukin-6 (IL-6). We observed that Treg cells divided into two subpopulations after IL-6 stimulation. TIGIT- unstable Treg cells lost FOXP3 expression and gained an effector-like T cell phenotype, whereas TIGIT+ Treg cells retained robust suppressive function. Single cell transcriptome analysis revealed a spectrum of cellular states of IL-6-stimulated Treg cells and how cytochrome P450 family 1 subfamily A member 1 (CYP1A1) is a crucial regulator of Treg cell suppressive capability and stability. CYP1A1-deficient human Treg cells developed a Th17-like phenotype after IL-6 stimulation. Our findings implicate CYP1A1 as a previously unidentified regulator of Treg cells that may have target potential for clinical application for biotherapies.
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Affiliation(s)
- Gang Yi
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Biotheus Inc., Zhuhai 519080, China
| | - Yi Zhao
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; BGI-Shenzhen, Shenzhen 518083, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Feng Xie
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fuxiang Zhu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ziyun Wan
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Xie Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Kai Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Lixia Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Chen Chen
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yashu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510006, China
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510006, China
| | | | - Jian Wang
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Bing Su
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lei Chen
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yinyan He
- Department of Obstetrics and Gynaecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | | | - Xiao Liu
- BGI-Shenzhen, Shenzhen 518083, China.
| | - Bin Li
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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30
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Baron CS, Barve A, Muraro MJ, van der Linden R, Dharmadhikari G, Lyubimova A, de Koning EJP, van Oudenaarden A. Cell Type Purification by Single-Cell Transcriptome-Trained Sorting. Cell 2020; 179:527-542.e19. [PMID: 31585086 PMCID: PMC6863042 DOI: 10.1016/j.cell.2019.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 01/23/2023]
Abstract
Much of current molecular and cell biology research relies on the ability to purify cell types by fluorescence-activated cell sorting (FACS). FACS typically relies on the ability to label cell types of interest with antibodies or fluorescent transgenic constructs. However, antibody availability is often limited, and genetic manipulation is labor intensive or impossible in the case of primary human tissue. To date, no systematic method exists to enrich for cell types without a priori knowledge of cell-type markers. Here, we propose GateID, a computational method that combines single-cell transcriptomics with FACS index sorting to purify cell types of choice using only native cellular properties such as cell size, granularity, and mitochondrial content. We validate GateID by purifying various cell types from zebrafish kidney marrow and the human pancreas to high purity without resorting to specific antibodies or transgenes.
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Affiliation(s)
- Chloé S Baron
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Aditya Barve
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Mauro J Muraro
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands; Single Cell Discoveries, Utrecht, the Netherlands
| | - Reinier van der Linden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands
| | - Anna Lyubimova
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands
| | - Eelco J P de Koning
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Section of Nephrology and Section of Endocrinology, Department of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexander van Oudenaarden
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands.
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31
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Park G, Burroughs-Garcia J, Foster CA, Hasan A, Borga C, Frazer JK. Zebrafish B cell acute lymphoblastic leukemia: new findings in an old model. Oncotarget 2020; 11:1292-1305. [PMID: 32341750 PMCID: PMC7170496 DOI: 10.18632/oncotarget.27555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric, and ninth most common adult, cancer. ALL can develop in either B or T lymphocytes, but B-lineage ALL (B-ALL) exceeds T-ALL clinically. As for other cancers, animal models allow study of the molecular mechanisms driving ALL. Several zebrafish (Danio rerio) T-ALL models have been reported, but until recently, robust D. rerio B-ALL models were not described. Then, D. rerio B-ALL was discovered in two related zebrafish transgenic lines; both were already known to develop T-ALL. Here, we report new B-ALL findings in one of these models, fish expressing transgenic human MYC (hMYC). We describe B-ALL incidence in a large cohort of hMYC fish, and show B-ALL in two new lines where T-ALL does not interfere with B-ALL detection. We also demonstrate B-ALL responses to steroid and radiation treatments, which effect ALL remissions, but are usually followed by prompt relapses. Finally, we report gene expression in zebrafish B lymphocytes and B-ALL, in both bulk samples and single B- and T-ALL cells. Using these gene expression profiles, we compare differences between the two new D. rerio B-ALL models, which are both driven by transgenic mammalian MYC oncoproteins. Collectively, these new data expand the utility of this new vertebrate B-ALL model.
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Affiliation(s)
- Gilseung Park
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,These authors contributed equally to this work
| | - Jessica Burroughs-Garcia
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,These authors contributed equally to this work
| | - Clay A Foster
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA.,These authors contributed equally to this work
| | - Ameera Hasan
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Chiara Borga
- Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - J Kimble Frazer
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Pediatrics, Section of Pediatric Hematology-Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.,Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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32
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Multiscale Imaging of Metastasis in Zebrafish. Trends Cancer 2019; 5:766-778. [DOI: 10.1016/j.trecan.2019.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022]
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33
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Li Q, Huang Q. Single-cell qPCR demonstrates that Repsox treatment changes cell fate from endoderm to neuroectoderm and disrupts epithelial-mesenchymal transition. PLoS One 2019; 14:e0223724. [PMID: 31600351 PMCID: PMC6786562 DOI: 10.1371/journal.pone.0223724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/26/2019] [Indexed: 01/22/2023] Open
Abstract
A definitive endodermal cell lineage is a prerequisite for the efficient generation of mature endoderm derivatives that give rise to organs, such as the pancreas and liver. We previously reported that the induction of mesenchymal definitive endoderm cells depends on autocrine TGF-β signaling and that pharmacological blockage of TGF-β signaling by Repsox disrupts endoderm specification. The definitive endoderm arises from a primitive streak, which depends largely on TGF-β signaling. If the TGF-β pathway is blocked by Repsox, cell fate after the primitive streak induction is so-far unknown. We report here, that an induced primitive streak cell-population contained many T/SOX2 co-expressing cells, and subsequent inhibition of TGF-β signaling by Repsox promoted neuroectodermal cell fate, which was characterized using single-cell qPCR analysis and immunostaining. The process of epithelial-to-mesenchymal transition, which is inherent to the process of definitive endoderm differentiation, was also disrupted upon Repsox treatment. Our findings may provide a new approach to produce neural progenitors.
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Affiliation(s)
- Qiuhong Li
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
- South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- * E-mail:
| | - Qingsong Huang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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34
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Yan C, Brunson DC, Tang Q, Do D, Iftimia NA, Moore JC, Hayes MN, Welker AM, Garcia EG, Dubash TD, Hong X, Drapkin BJ, Myers DT, Phat S, Volorio A, Marvin DL, Ligorio M, Dershowitz L, McCarthy KM, Karabacak MN, Fletcher JA, Sgroi DC, Iafrate JA, Maheswaran S, Dyson NJ, Haber DA, Rawls JF, Langenau DM. Visualizing Engrafted Human Cancer and Therapy Responses in Immunodeficient Zebrafish. Cell 2019; 177:1903-1914.e14. [PMID: 31031007 PMCID: PMC6570580 DOI: 10.1016/j.cell.2019.04.004] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 02/19/2019] [Accepted: 03/31/2019] [Indexed: 01/06/2023]
Abstract
Xenograft cell transplantation into immunodeficient mice has become the gold standard for assessing pre-clinical efficacy of cancer drugs, yet direct visualization of single-cell phenotypes is difficult. Here, we report an optically-clear prkdc-/-, il2rga-/- zebrafish that lacks adaptive and natural killer immune cells, can engraft a wide array of human cancers at 37°C, and permits the dynamic visualization of single engrafted cells. For example, photoconversion cell-lineage tracing identified migratory and proliferative cell states in human rhabdomyosarcoma, a pediatric cancer of muscle. Additional experiments identified the preclinical efficacy of combination olaparib PARP inhibitor and temozolomide DNA-damaging agent as an effective therapy for rhabdomyosarcoma and visualized therapeutic responses using a four-color FUCCI cell-cycle fluorescent reporter. These experiments identified that combination treatment arrested rhabdomyosarcoma cells in the G2 cell cycle prior to induction of apoptosis. Finally, patient-derived xenografts could be engrafted into our model, opening new avenues for developing personalized therapeutic approaches in the future.
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Affiliation(s)
- Chuan Yan
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Dalton C Brunson
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Qin Tang
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Daniel Do
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - Nicolae A Iftimia
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - John C Moore
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Madeline N Hayes
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Alessandra M Welker
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Elaine G Garcia
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Taronish D Dubash
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Xin Hong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - David T Myers
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sarah Phat
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Angela Volorio
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Dieuwke L Marvin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Matteo Ligorio
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lyle Dershowitz
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Karin M McCarthy
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA
| | - Murat N Karabacak
- Shriners Hospitals for Children-Boston, MA 02114, USA; Center for Engineering in Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02114, USA
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dennis C Sgroi
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - John A Iafrate
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Nick J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Howard Hughes Medical Institute, Bethesda, MD 20815, USA
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital Research Institute, Charlestown, MA 02129, USA; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02139, USA.
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35
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Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L. Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. Nat Commun 2019; 10:1903. [PMID: 31015418 PMCID: PMC6478907 DOI: 10.1038/s41467-019-09670-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data. We have tested STREAM on several synthetic and real datasets generated with different single-cell technologies. We further demonstrate its utility for understanding myoblast differentiation and disentangling known heterogeneity in hematopoiesis for different organisms. STREAM is an open-source software package.
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Affiliation(s)
- Huidong Chen
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Luca Albergante
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
| | - Jonathan Y Hsu
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb A Lareau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Giosuè Lo Bosco
- Department of Mathematics and Computer Science, University of Palermo, 90123, Palermo, Italy
- Department of Sciences for technological innovation, Euro-Mediterranean Institute of Science and Technology, 90139, Palermo, Italy
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, 201804, Shanghai, China
| | - Shuigeng Zhou
- Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, 200433, Shanghai, China
| | - Alexander N Gorban
- Department of Mathematics, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Daniel E Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA
| | - Martin J Aryee
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David M Langenau
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, F-75005, Paris, France
- INSERM, U900, F-75005, Paris, France
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, F-75006, Paris, France
- Lobachevsky University, Nizhni Novgorod, 603022, Russia
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Society of Fellows, Harvard University, Cambridge, MA, 02138, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| | - Luca Pinello
- Molecular Pathology Unit & Cancer Center, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, 02114, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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36
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Loontiens S, Depestel L, Vanhauwaert S, Dewyn G, Gistelinck C, Verboom K, Van Loocke W, Matthijssens F, Willaert A, Vandesompele J, Speleman F, Durinck K. Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes. BMC Genomics 2019; 20:228. [PMID: 30894119 PMCID: PMC6425699 DOI: 10.1186/s12864-019-5608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
Background Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis. Results We evaluated two suitable RNA isolation kits (the RNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5× dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results. Conclusions The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells. Electronic supplementary material The online version of this article (10.1186/s12864-019-5608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siebe Loontiens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Lisa Depestel
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Givani Dewyn
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Charlotte Gistelinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Karen Verboom
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium.
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37
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Huang XT, Li X, Qin PZ, Zhu Y, Xu SN, Chen JP. Technical Advances in Single-Cell RNA Sequencing and Applications in Normal and Malignant Hematopoiesis. Front Oncol 2018; 8:582. [PMID: 30581771 PMCID: PMC6292934 DOI: 10.3389/fonc.2018.00582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been tremendously developed in the past decade owing to overcoming challenges associated with isolation of massive quantities of single cells. Previously, cell heterogeneity and low quantities of available biological material posed significant difficulties to scRNA-seq. Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of normal and malignant hematopoietic cells; this heterogeneity has often been ignored in omics studies. The application of scRNA-seq has profoundly changed our comprehension of many biological phenomena, including organ development and carcinogenesis. Hematopoiesis, is actually a maturation process for more than ten distinct blood and immune cells, and is thought to be critically involved in hematological homeostasis and in sustaining the physiological functions. However, aberrant hematopoiesis directly leads to hematological malignancy, and a deeper understanding of malignant hematopoiesis will provide deeper insights into diagnosis and prognosis for patients with hematological malignancies. Here, we aim to review the recent technical progress and future prospects for scRNA-seq, as applied in physiological and malignant hematopoiesis, in efforts to further understand the hematopoietic hierarchy and to illuminate personalized therapy and precision medicine approaches used in the clinical treatment of hematological malignancies.
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Affiliation(s)
- Xiang-Tao Huang
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xi Li
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Pei-Zhong Qin
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yao Zhu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuang-Nian Xu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jie-Ping Chen
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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38
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Baeten JT, de Jong JLO. Genetic Models of Leukemia in Zebrafish. Front Cell Dev Biol 2018; 6:115. [PMID: 30294597 PMCID: PMC6158309 DOI: 10.3389/fcell.2018.00115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/23/2018] [Indexed: 12/21/2022] Open
Abstract
The zebrafish animal model is gaining increasing popularity as a tool for studying human disease. Over the past 15 years, many models of leukemia and other hematological malignancies have been developed in the zebrafish. These confer some significant advantages over similar models in other animals and systems, representing a powerful resource for investigation of the molecular basis of human leukemia. This review discusses the various zebrafish models of lymphoid and myeloid leukemia available, the major discoveries that have been made possible by them, and opportunities for future exploration.
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Affiliation(s)
| | - Jill L. O. de Jong
- Department of Pediatrics, University of Chicago, Chicago, IL, United States
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39
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Borga C, Park G, Foster C, Burroughs-Garcia J, Marchesin M, Shah R, Hasan A, Ahmed ST, Bresolin S, Batchelor L, Scordino T, Miles RR, Te Kronnie G, Regens JL, Frazer JK. Simultaneous B and T cell acute lymphoblastic leukemias in zebrafish driven by transgenic MYC: implications for oncogenesis and lymphopoiesis. Leukemia 2018; 33:333-347. [PMID: 30111845 PMCID: PMC6365377 DOI: 10.1038/s41375-018-0226-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/30/2018] [Accepted: 07/04/2018] [Indexed: 01/17/2023]
Abstract
Precursor-B cell acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer, but there are no useful zebrafish pre-B ALL models. We describe the first highly- penetrant zebrafish pre-B ALL, driven by human MYC. Leukemias express B lymphoblast-specific genes and are distinct from T cell ALL (T-ALL)—which these fish also develop. Zebrafish pre-B ALL shares in vivo features and expression profiles with human pre-B ALL, and these profiles differ from zebrafish T-ALL or normal B and T cells. These animals also exhibit aberrant lymphocyte development. As the only robust zebrafish pre-B ALL model and only example where T-ALL also develops, this model can reveal differences between MYC-driven pre-B vs. T-ALL and be exploited to discover novel pre-B ALL therapies.
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Affiliation(s)
- Chiara Borga
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Gilseung Park
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Clay Foster
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Jessica Burroughs-Garcia
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Matteo Marchesin
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Rikin Shah
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Ameera Hasan
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Syed T Ahmed
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Silvia Bresolin
- Department of Women's and Children's Health, University of Padua, Padua, 35128, Italy
| | - Lance Batchelor
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Teresa Scordino
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Rodney R Miles
- Department of Pathology, University of Utah and ARUP Institute for Clinical & Experimental Pathology, Salt Lake City, UT, 84108, USA
| | - Geertruy Te Kronnie
- Department of Women's and Children's Health, University of Padua, Padua, 35128, Italy
| | - James L Regens
- Center for Intelligence and National Security, University of Oklahoma, Norman, OK, 73019, USA
| | - J Kimble Frazer
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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40
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Cell of origin dictates aggression and stem cell number in acute lymphoblastic leukemia. Leukemia 2018; 32:1860-1865. [PMID: 29749398 DOI: 10.1038/s41375-018-0130-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/05/2018] [Accepted: 03/29/2018] [Indexed: 12/29/2022]
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41
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Mizgirev IV, Safina DR, Demidyuk IV, Kostrov SV. Organism-Level Tumor Models in Zebrafish Danio rerio. Acta Naturae 2018; 10:24-29. [PMID: 30116612 PMCID: PMC6087818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 11/18/2022] Open
Abstract
Development and implementation of adequate organism-level models is one of the key elements in biomedical research that focuses on experimental oncology. Over the last decade, studies using Zebrafish (Danio rerio) have gained in popularity in this area of research. This review describes the various approaches that have been used in developing highly effective models for oncological (clinical term, better cancer or tumor) studies based on D. rerio. Priority is given to transplantation models of cancer and their application to optically transparent D. rerio lines, including clonal ones, and utilization tumors of various origins bearing fluorescent labels. The combination of tumor transplantation at organism-level models in transparent clonal D. rerio lines with fluorescent microscopy, FACS-fractionation of tumor cell subsets, and transcription analysis can result in one of the most promising research approaches in providing new information on tumor formation and growth.
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Affiliation(s)
- I. V. Mizgirev
- N.N. Petrov National Medical Research Center of Oncology, Ministry of Health of Russia, Leningradskaya Str., 68, Pesochnyy Settlement, St. Petersburg, 197758, Russia
| | - D. R. Safina
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, Moscow, 123182 , Russia
| | - I. V. Demidyuk
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, Moscow, 123182 , Russia
| | - S. V. Kostrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq., 2, Moscow, 123182 , Russia
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42
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Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A. Whole-organism clone tracing using single-cell sequencing. Nature 2018; 556:108-112. [PMID: 29590089 DOI: 10.1038/nature25969] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 02/02/2018] [Indexed: 12/31/2022]
Abstract
Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.
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Affiliation(s)
- Anna Alemany
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Maria Florescu
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Chloé S Baron
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josi Peterson-Maduro
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Alexander van Oudenaarden
- Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
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43
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Chen H, Jiang M, Xiao L, Huang H. Single-cell qPCR facilitates the optimization of hematopoietic differentiation in hPSCs/OP9 coculture system. ACTA ACUST UNITED AC 2018; 51:e7183. [PMID: 29561959 PMCID: PMC5875903 DOI: 10.1590/1414-431x20187183] [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: 09/29/2017] [Accepted: 01/09/2018] [Indexed: 11/22/2022]
Abstract
Human pluripotent stem cells (hPSCs)/OP9 coculture system is a widely used hematopoietic differentiation approach. The limited understanding of this process leads to its low efficiency. Thus, we used single-cell qPCR to reveal the gene expression profiles of individual CD34+ cells from different stages of differentiation. According to the dynamic gene expression of hematopoietic transcription factors, we overexpressed specific hematopoietic transcription factors (Gata2, Lmo2, Etv2, ERG, and SCL) at an early stage of hematopoietic differentiation. After overexpression, we generated more CD34+ cells with normal expression level of CD43 and CD31, which are used to define various hematopoietic progenitors. Furthermore, these CD34+ cells possessed normal differentiation potency in colony-forming unit assays and normal gene expression profiles. In this study, we demonstrated that single-cell qPCR can provide guidance for optimization of hematopoietic differentiation and transient overexpression of selected hematopoietic transcription factors can enhance hematopoietic differentiation.
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Affiliation(s)
- Haide Chen
- College of Animal Science, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - Mengmeng Jiang
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Xiao
- College of Animal Science, Zhejiang University, Hangzhou, China.,School of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- School of Medicine, Zhejiang University, Hangzhou, China.,The 1st Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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44
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Potts KS, Bowman TV. Modeling Myeloid Malignancies Using Zebrafish. Front Oncol 2017; 7:297. [PMID: 29255698 PMCID: PMC5722844 DOI: 10.3389/fonc.2017.00297] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/20/2017] [Indexed: 02/04/2023] Open
Abstract
Human myeloid malignancies represent a substantial disease burden to individuals, with significant morbidity and death. The genetic underpinnings of disease formation and progression remain incompletely understood. Large-scale human population studies have identified a high frequency of potential driver mutations in spliceosomal and epigenetic regulators that contribute to malignancies, such as myelodysplastic syndromes (MDS) and leukemias. The high conservation of cell types and genes between humans and model organisms permits the investigation of the underlying mechanisms of leukemic development and potential therapeutic testing in genetically pliable pre-clinical systems. Due to the many technical advantages, such as large-scale screening, lineage-tracing studies, tumor transplantation, and high-throughput drug screening approaches, zebrafish is emerging as a model system for myeloid malignancies. In this review, we discuss recent advances in MDS and leukemia using the zebrafish model.
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Affiliation(s)
- Kathryn S Potts
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, United States
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45
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Kasheta M, Painter CA, Moore FE, Lobbardi R, Bryll A, Freiman E, Stachura D, Rogers AB, Houvras Y, Langenau DM, Ceol CJ. Identification and characterization of T reg-like cells in zebrafish. J Exp Med 2017; 214:3519-3530. [PMID: 29066577 PMCID: PMC5716030 DOI: 10.1084/jem.20162084] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 08/04/2017] [Accepted: 09/13/2017] [Indexed: 01/07/2023] Open
Abstract
Kasheta et al. report the identification of T reg–like cells in zebrafish, a means to track and live-image these cells, and foxp3a-deficient mutants that display lymphoproliferation, severe inflammation, and other hallmarks of T reg deficiency syndromes. Regulatory T (T reg) cells are a specialized sublineage of T lymphocytes that suppress autoreactive T cells. Functional studies of T reg cells in vitro have defined multiple suppression mechanisms, and studies of T reg–deficient humans and mice have made clear the important role that these cells play in preventing autoimmunity. However, many questions remain about how T reg cells act in vivo. Specifically, it is not clear which suppression mechanisms are most important, where T reg cells act, and how they get there. To begin to address these issues, we sought to identify T reg cells in zebrafish, a model system that provides unparalleled advantages in live-cell imaging and high-throughput genetic analyses. Using a FOXP3 orthologue as a marker, we identified CD4-enriched, mature T lymphocytes with properties of T reg cells. Zebrafish mutant for foxp3a displayed excess T lymphocytes, splenomegaly, and a profound inflammatory phenotype that was suppressed by genetic ablation of lymphocytes. This study identifies T reg–like cells in zebrafish, providing both a model to study the normal functions of these cells in vivo and mutants to explore the consequences of their loss.
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Affiliation(s)
- Melissa Kasheta
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Corrie A Painter
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Finola E Moore
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Cambridge, MA
| | - Riadh Lobbardi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Cambridge, MA
| | - Alysia Bryll
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Eli Freiman
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - David Stachura
- Department of Biological Sciences, California State University, Chico, CA
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA
| | - Yariv Houvras
- Departments of Surgery and Medicine, Weill Cornell Medical College, New York, NY
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Cambridge, MA
| | - Craig J Ceol
- Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
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46
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Tošić - Golubović S, Slavković V, Sibinović V, Guglet D, Nikolić G. D EPRESSION AMONG MEDCALLY ILL PATIENTS. ACTA MEDICA MEDIANAE 2017. [DOI: 10.5633/amm.2017.0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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Tang Q, Iyer S, Lobbardi R, Moore JC, Chen H, Lareau C, Hebert C, Shaw ML, Neftel C, Suva ML, Ceol CJ, Bernards A, Aryee M, Pinello L, Drummond IA, Langenau DM. Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing. J Exp Med 2017; 214:2875-2887. [PMID: 28878000 PMCID: PMC5626406 DOI: 10.1084/jem.20170976] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
The work by Tang et al. provides a comprehensive, single-cell, transcriptomic analysis of kidney and blood cells from the adult zebrafish, identifying novel cell types, including two classes of NK immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. Recent advances in single-cell, transcriptomic profiling have provided unprecedented access to investigate cell heterogeneity during tissue and organ development. In this study, we used massively parallel, single-cell RNA sequencing to define cell heterogeneity within the zebrafish kidney marrow, constructing a comprehensive molecular atlas of definitive hematopoiesis and functionally distinct renal cells found in adult zebrafish. Because our method analyzed blood and kidney cells in an unbiased manner, our approach was useful in characterizing immune-cell deficiencies within DNA–protein kinase catalytic subunit (prkdc), interleukin-2 receptor γ a (il2rga), and double-homozygous–mutant fish, identifying blood cell losses in T, B, and natural killer cells within specific genetic mutants. Our analysis also uncovered novel cell types, including two classes of natural killer immune cells, classically defined and erythroid-primed hematopoietic stem and progenitor cells, mucin-secreting kidney cells, and kidney stem/progenitor cells. In total, our work provides the first, comprehensive, single-cell, transcriptomic analysis of kidney and marrow cells in the adult zebrafish.
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Affiliation(s)
- Qin Tang
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Sowmya Iyer
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA
| | - Riadh Lobbardi
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - John C Moore
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
| | - Huidong Chen
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA.,Department of Computer Science and Technology, Tongji University, Shanghai, China
| | - Caleb Lareau
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Christine Hebert
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - McKenzie L Shaw
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Cyril Neftel
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Mario L Suva
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Broad Institute, Cambridge, MA
| | - Craig J Ceol
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Andre Bernards
- Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Martin Aryee
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA.,Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Luca Pinello
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA.,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
| | - Iain A Drummond
- Division of Nephrology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - David M Langenau
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA .,Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA.,Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA
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48
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Liu X, Li YS, Shinton SA, Rhodes J, Tang L, Feng H, Jette CA, Look AT, Hayakawa K, Hardy RR. Zebrafish B Cell Development without a Pre-B Cell Stage, Revealed by CD79 Fluorescence Reporter Transgenes. THE JOURNAL OF IMMUNOLOGY 2017; 199:1706-1715. [PMID: 28739882 DOI: 10.4049/jimmunol.1700552] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/27/2017] [Indexed: 11/19/2022]
Abstract
CD79a and CD79b proteins associate with Ig receptors as integral signaling components of the B cell Ag receptor complex. To study B cell development in zebrafish, we isolated orthologs of these genes and performed in situ hybridization, finding that their expression colocalized with IgH-μ in the kidney, which is the site of B cell development. CD79 transgenic lines were made by linking the promoter and upstream regulatory segments of CD79a and CD79b to enhanced GFP to identify B cells, as demonstrated by PCR analysis of IgH-μ expression in sorted cells. We crossed these CD79-GFP lines to a recombination activating gene (Rag)2:mCherry transgenic line to identify B cell development stages in kidney marrow. Initiation of CD79:GFP expression in Rag2:mCherry+ cells and the timing of Ig H and L chain expression revealed simultaneous expression of both IgH-μ- and IgL-κ-chains, without progressing through the stage of IgH-μ-chain alone. Rag2:mCherry+ cells without CD79:GFP showed the highest Rag1 and Rag2 mRNAs compared with CD79a and CD79b:GFP+ B cells, which showed strongly reduced Rag mRNAs. Thus, B cell development in zebrafish does not go through a Raghi CD79+IgH-μ+ pre-B cell stage, different from mammals. After the generation of CD79:GFP+ B cells, decreased CD79 expression occurred upon differentiation to Ig secretion, as detected by alteration from membrane to secreted IgH-μ exon usage, similar to in mammals. This confirmed a conserved role for CD79 in B cell development and differentiation, without the requirement of a pre-B cell stage in zebrafish.
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Affiliation(s)
- Xingjun Liu
- Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Yue-Sheng Li
- Fox Chase Cancer Center, Philadelphia, PA 19111.,DNA Sequencing and Genomic Core, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | - Hui Feng
- The Center for Cancer Research, Boston University School of Medicine, Boston, MA 02118
| | - Cicely A Jette
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84103; and
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
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49
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Suffiotti M, Carmona SJ, Jandus C, Gfeller D. Identification of innate lymphoid cells in single-cell RNA-Seq data. Immunogenetics 2017; 69:439-450. [PMID: 28534222 DOI: 10.1007/s00251-017-1002-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/11/2017] [Indexed: 12/20/2022]
Abstract
Innate lymphoid cells (ILCs) consist of natural killer (NK) cells and non-cytotoxic ILCs that are broadly classified into ILC1, ILC2, and ILC3 subtypes. These cells recently emerged as important early effectors of innate immunity for their roles in tissue homeostasis and inflammation. Over the last few years, ILCs have been extensively studied in mouse and human at the functional and molecular level, including gene expression profiling. However, sorting ILCs with flow cytometry for gene expression analysis is a delicate and time-consuming process. Here we propose and validate a novel framework for studying ILCs at the transcriptomic level using single-cell RNA-Seq data. Our approach combines unsupervised clustering and a new cell type classifier trained on mouse ILC gene expression data. We show that this approach can accurately identify different ILCs, especially ILC2 cells, in human lymphocyte single-cell RNA-Seq data. Our new model relies only on genes conserved across vertebrates, thereby making it in principle applicable in any vertebrate species. Considering the rapid increase in throughput of single-cell RNA-Seq technology, our work provides a computational framework for studying ILC2 cells in single-cell transcriptomic data and may help exploring their conservation in distant vertebrate species.
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Affiliation(s)
- Madeleine Suffiotti
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Santiago J Carmona
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
| | - Camilla Jandus
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland
| | - David Gfeller
- Ludwig Centre for Cancer Research, University of Lausanne, 1066, Epalinges, Switzerland.
- Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland.
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50
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Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJT, Cvejic A, Gfeller D. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 2017; 27:451-461. [PMID: 28087841 PMCID: PMC5340972 DOI: 10.1101/gr.207704.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022]
Abstract
The immune system of vertebrate species consists of many different cell types that have distinct functional roles and are subject to different evolutionary pressures. Here, we first analyzed conservation of genes specific for all major immune cell types in human and mouse. Our results revealed higher gene turnover and faster evolution of trans-membrane proteins in NK cells compared with other immune cell types, and especially T cells, but similar conservation of nuclear and cytoplasmic protein coding genes. To validate these findings in a distant vertebrate species, we used single-cell RNA sequencing of lck:GFP cells in zebrafish and obtained the first transcriptome of specific immune cell types in a nonmammalian species. Unsupervised clustering and single-cell TCR locus reconstruction identified three cell populations, T cells, a novel type of NK-like cells, and a smaller population of myeloid-like cells. Differential expression analysis uncovered new immune-cell-specific genes, including novel immunoglobulin-like receptors, and neofunctionalization of recently duplicated paralogs. Evolutionary analyses confirmed the higher gene turnover of trans-membrane proteins in NK cells compared with T cells in fish species, suggesting that this is a general property of immune cell types across all vertebrates.
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Affiliation(s)
- Santiago J Carmona
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Lauren Ferreira
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - Iain C Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, United Kingdom
- Wellcome Trust-Medical Research Council, Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
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