1
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Deng J, Zhou Z, Liao W, Lin Q, Zhang Y. Assessing the efficacy and safety of gemcitabine-induced thrombocytopenia/neutropenia and thrombocytopenia interventions in zebrafish. J Genet Genomics 2024; 51:970-973. [PMID: 38925346 DOI: 10.1016/j.jgg.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Affiliation(s)
- Jialong Deng
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China; Department of Hematology, The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, Guangdong 528200, China
| | - Ziyuan Zhou
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Qing Lin
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China; Department of Hematology, The Sixth Affiliated Hospital, School of Medicine, South China University of Technology, Foshan, Guangdong 528200, China.
| | - Yiyue Zhang
- Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, China.
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2
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Gioacchino E, Zhang W, Koyunlar C, Zink J, de Looper H, Gussinklo KJ, Hoogenboezem R, Bosch D, Bindels E, Touw IP, de Pater E. GATA2 heterozygosity causes an epigenetic feedback mechanism resulting in myeloid and erythroid dysplasia. Br J Haematol 2024; 205:580-593. [PMID: 38887897 DOI: 10.1111/bjh.19585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
The transcription factor GATA2 has a pivotal role in haematopoiesis. Heterozygous germline GATA2 mutations result in a syndrome characterized by immunodeficiency, bone marrow failure and predispositions to myelodysplastic syndrome (MDS) and acute myeloid leukaemia. Clinical symptoms in these patients are diverse and mechanisms driving GATA2-related phenotypes are largely unknown. To explore the impact of GATA2 haploinsufficiency on haematopoiesis, we generated a zebrafish model carrying a heterozygous mutation of gata2b (gata2b+/-), an orthologue of GATA2. Morphological analysis revealed myeloid and erythroid dysplasia in gata2b+/- kidney marrow. Because Gata2b could affect both transcription and chromatin accessibility during lineage differentiation, this was assessed by single-cell (sc) RNA-seq and single-nucleus (sn) ATAC-seq. Sn-ATAC-seq showed that the co-accessibility between the transcription start site (TSS) and a -3.5-4.1 kb putative enhancer was more robust in gata2b+/- zebrafish HSPCs compared to wild type, increasing gata2b expression and resulting in higher genome-wide Gata2b motif use in HSPCs. As a result of increased accessibility of the gata2b locus, gata2b+/- chromatin was also more accessible during lineage differentiation. scRNA-seq data revealed myeloid differentiation defects, that is, impaired cell cycle progression, reduced expression of cebpa and cebpb and increased signatures of ribosome biogenesis. These data also revealed a differentiation delay in erythroid progenitors, aberrant proliferative signatures and down-regulation of Gata1a, a master regulator of erythropoiesis, which worsened with age. These findings suggest that cell-intrinsic compensatory mechanisms, needed to obtain normal levels of Gata2b in heterozygous HSPCs to maintain their integrity, result in aberrant lineage differentiation, thereby representing a critical step in the predisposition to MDS.
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Affiliation(s)
- Emanuele Gioacchino
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Wei Zhang
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Cansu Koyunlar
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Joke Zink
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Hans de Looper
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Kirsten J Gussinklo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Dennis Bosch
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ivo P Touw
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Emma de Pater
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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3
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Garg S, Ni W, Chowdhury B, Weisberg EL, Sattler M, Griffin JD. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ 2024; 31:868-880. [PMID: 38816579 PMCID: PMC11239944 DOI: 10.1038/s41418-024-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. Human HSPCs with reduced BRD9 protein levels produced lower numbers of immature mixed multipotent GEMM colonies in semi-solid media. In lineage-promoting culture conditions, cells with reduced BRD9 levels failed to differentiate into the megakaryocytic lineage and showed delayed differentiation into erythroid cells but enhanced terminal myeloid differentiation. HSPCs with BRD9 knock down (KD) had reduced long-term multilineage engraftment in a xenotransplantation assay. An increased number of downregulated genes in RNAseq analysis after BRD9 KD coupled with a gain in chromatin accessibility at the promoters of several repressive transcription factors (TF) suggest that BRD9 functions in the maintenance of active transcription during HSC differentiation. In particular, the hematopoietic master regulator GATA1 was identified as one of the core TFs regulating the gene networks modulated by BRD9 loss in HSPCs. BRD9 inhibition reduced a GATA1-luciferase reporter signal, further suggesting a role for BRD9 in regulating GATA1 activity. BRD9 is therefore an additional example of epigenetic regulation of human hematopoiesis.
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Affiliation(s)
- Swati Garg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Wei Ni
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Basudev Chowdhury
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Ellen L Weisberg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Martin Sattler
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - James D Griffin
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA.
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA.
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4
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Hegazy AN, Peine C, Niesen D, Panse I, Vainshtein Y, Kommer C, Zhang Q, Brunner TM, Peine M, Fröhlich A, Ishaque N, Marek RM, Zhu J, Höfer T, Löhning M. Plasticity and lineage commitment of individual T H1 cells are determined by stable T-bet expression quantities. SCIENCE ADVANCES 2024; 10:eadk2693. [PMID: 38838155 PMCID: PMC11152138 DOI: 10.1126/sciadv.adk2693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/01/2024] [Indexed: 06/07/2024]
Abstract
T helper 1 (TH1) cell identity is defined by the expression of the lineage-specifying transcription factor T-bet. Here, we examine the influence of T-bet expression heterogeneity on subset plasticity by leveraging cell sorting of distinct in vivo-differentiated TH1 cells based on their quantitative expression of T-bet and interferon-γ. Heterogeneous T-bet expression states were regulated by virus-induced type I interferons and were stably maintained even after secondary viral infection. Exposed to alternative differentiation signals, the sorted subpopulations exhibited graded levels of plasticity, particularly toward the TH2 lineage: T-bet quantities were inversely correlated with the ability to express the TH2 lineage-specifying transcription factor GATA-3 and TH2 cytokines. Reprogramed TH1 cells acquired graded mixed TH1 + TH2 phenotypes with a hybrid epigenetic landscape. Continuous presence of T-bet in differentiated TH1 cells was essential to ensure TH1 cell stability. Thus, innate cytokine signals regulate TH1 cell plasticity via an individual cell-intrinsic rheostat to enable T cell subset adaptation to subsequent challenges.
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Affiliation(s)
- Ahmed N. Hegazy
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Medical Department of Gastroenterology, Infectious Diseases and Rheumatology, 12203 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Inflammatory Mechanisms, 10117 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Caroline Peine
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Dominik Niesen
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Isabel Panse
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Yevhen Vainshtein
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, 69120 Heidelberg, Germany
- University of Heidelberg, Bioquant Center, 69120 Heidelberg, Germany
| | - Christoph Kommer
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, 69120 Heidelberg, Germany
- University of Heidelberg, Bioquant Center, 69120 Heidelberg, Germany
| | - Qin Zhang
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, 69120 Heidelberg, Germany
- University of Heidelberg, Bioquant Center, 69120 Heidelberg, Germany
| | - Tobias M. Brunner
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Michael Peine
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Anja Fröhlich
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Naveed Ishaque
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, 69120 Heidelberg, Germany
- University of Heidelberg, Bioquant Center, 69120 Heidelberg, Germany
| | - Roman M. Marek
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
| | - Jinfang Zhu
- National Institute of Allergy and Infectious Diseases, Laboratory of Immune System Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Höfer
- German Cancer Research Center (DKFZ), Division of Theoretical Systems Biology, 69120 Heidelberg, Germany
- University of Heidelberg, Bioquant Center, 69120 Heidelberg, Germany
| | - Max Löhning
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental Immunology and Osteoarthritis Research, Department of Rheumatology and Clinical Immunology, 10117 Berlin, Germany
- German Rheumatism Research Center (DRFZ), a Leibniz Institute, Pitzer Laboratory of Osteoarthritis Research, 10117 Berlin, Germany
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5
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Zhou J, Chng WJ. Unveiling novel insights in acute myeloid leukemia through single-cell RNA sequencing. Front Oncol 2024; 14:1365330. [PMID: 38711849 PMCID: PMC11070491 DOI: 10.3389/fonc.2024.1365330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Acute myeloid leukemia (AML) is a complex and heterogeneous group of aggressive hematopoietic stem cell disease. The presence of diverse and functionally distinct populations of leukemia cells within the same patient's bone marrow or blood poses a significant challenge in diagnosing and treating AML. A substantial proportion of AML patients demonstrate resistance to induction chemotherapy and a grim prognosis upon relapse. The rapid advance in next generation sequencing technologies, such as single-cell RNA-sequencing (scRNA-seq), has revolutionized our understanding of AML pathogenesis by enabling high-resolution interrogation of the cellular heterogeneity in the AML ecosystem, and their transcriptional signatures at a single-cell level. New studies have successfully characterized the inextricably intertwined interactions among AML cells, immune cells and bone marrow microenvironment and their contributions to the AML development, therapeutic resistance and relapse. These findings have deepened and broadened our understanding the complexity and heterogeneity of AML, which are difficult to detect with bulk RNA-seq. This review encapsulates the burgeoning body of knowledge generated through scRNA-seq, providing the novel insights and discoveries it has unveiled in AML biology. Furthermore, we discuss the potential implications of scRNA-seq in therapeutic opportunities, focusing on immunotherapy. Finally, we highlight the current limitations and future direction of scRNA-seq in the field.
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Affiliation(s)
- Jianbiao Zhou
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Center for Translational Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Center for Cancer Research, Center for Translational Medicine, Singapore, Singapore
- Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Singapore
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6
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Lynch J, Troadec E, Fung TK, Gladysz K, Virely C, Lau PNI, Cheung N, Zeisig B, Wong JWH, Lopes M, Huang S, So CWE. Hematopoietic stem cell quiescence and DNA replication dynamics maintained by the resilient β-catenin/Hoxa9/Prmt1 axis. Blood 2024; 143:1586-1598. [PMID: 38211335 PMCID: PMC11103100 DOI: 10.1182/blood.2023022082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/04/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
ABSTRACT Maintenance of quiescence and DNA replication dynamics are 2 paradoxical requirements for the distinct states of dormant and active hematopoietic stem cells (HSCs), which are required to preserve the stem cell reservoir and replenish the blood cell system in response to hematopoietic stress, respectively. Here, we show that key self-renewal factors, β-catenin or Hoxa9, largely dispensable for HSC integrity, in fact, have dual functions in maintaining quiescence and enabling efficient DNA replication fork dynamics to preserve the functionality of hematopoietic stem and progenitor cells (HSPCs). Although β-catenin or Hoxa9 single knockout (KO) exhibited mostly normal hematopoiesis, their coinactivation led to severe hematopoietic defects stemmed from aberrant cell cycle, DNA replication, and damage in HSPCs. Mechanistically, β-catenin and Hoxa9 function in a compensatory manner to sustain key transcriptional programs that converge on the pivotal downstream target and epigenetic modifying enzyme, Prmt1, which protects the quiescent state and ensures an adequate supply of DNA replication and repair factors to maintain robust replication fork dynamics. Inactivation of Prmt1 phenocopied both cellular and molecular phenotypes of β-catenin/Hoxa9 combined KO, which at the same time could also be partially rescued by Prmt1 expression. The discovery of the highly resilient β-catenin/Hoxa9/Prmt1 axis in protecting both quiescence and DNA replication dynamics essential for HSCs at different key states provides not only novel mechanistic insights into their intricate regulation but also a potential tractable target for therapeutic intervention.
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Affiliation(s)
- Jennifer Lynch
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Estelle Troadec
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Tsz Kan Fung
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
- Department of Haematological Medicine, King’s College Hospital, London, United Kingdom
| | - Kornelia Gladysz
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Clemence Virely
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Priscilla Nga Ieng Lau
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Ngai Cheung
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Bernd Zeisig
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
- Department of Haematological Medicine, King’s College Hospital, London, United Kingdom
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Suming Huang
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
- Department of Haematological Medicine, King’s College Hospital, London, United Kingdom
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7
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Qu R, Cheng X, Sefik E, Stanley Iii JS, Landa B, Strino F, Platt S, Garritano J, Odell ID, Coifman R, Flavell RA, Myung P, Kluger Y. Gene trajectory inference for single-cell data by optimal transport metrics. Nat Biotechnol 2024:10.1038/s41587-024-02186-3. [PMID: 38580861 PMCID: PMC11452571 DOI: 10.1038/s41587-024-02186-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2024] [Indexed: 04/07/2024]
Abstract
Single-cell RNA sequencing has been widely used to investigate cell state transitions and gene dynamics of biological processes. Current strategies to infer the sequential dynamics of genes in a process typically rely on constructing cell pseudotime through cell trajectory inference. However, the presence of concurrent gene processes in the same group of cells and technical noise can obscure the true progression of the processes studied. To address this challenge, we present GeneTrajectory, an approach that identifies trajectories of genes rather than trajectories of cells. Specifically, optimal transport distances are calculated between gene distributions across the cell-cell graph to extract gene programs and define their gene pseudotemporal order. Here we demonstrate that GeneTrajectory accurately extracts progressive gene dynamics in myeloid lineage maturation. Moreover, we show that GeneTrajectory deconvolves key gene programs underlying mouse skin hair follicle dermal condensate differentiation that could not be resolved by cell trajectory approaches. GeneTrajectory facilitates the discovery of gene programs that control the changes and activities of biological processes.
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Affiliation(s)
- Rihao Qu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiuyuan Cheng
- Department of Mathematics, Duke University, Durham, NC, USA
| | - Esen Sefik
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Boris Landa
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | | | - Sarah Platt
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - James Garritano
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
| | - Ian D Odell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Ronald Coifman
- Program in Applied Mathematics, Yale University, New Haven, CT, USA
- Department of Mathematics, Yale University, New Haven, CT, USA
- Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Peggy Myung
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA
| | - Yuval Kluger
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Program in Applied Mathematics, Yale University, New Haven, CT, USA.
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8
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Stosik M, Tokarz-Deptuła B, Deptuła W. Innate lymphoid cells (ILCs) in teleosts against data on ILCs in humans. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109415. [PMID: 38296004 DOI: 10.1016/j.fsi.2024.109415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
It is assumed that cells corresponding to innate lymphoid cells (ILCs) in humans, in addition to lymphoid tissue inducer cells (LTi), are also found in teleosts. In this systematic group of organisms, however, they are a poorly understood cell population. In contrast to the data on ILCs in humans, which also remain incomplete despite advanced research, in teleosts, these cells require much more attention. ILCs in teleosts have been presented as cells that may be evolutionary precursors of NK cells or ILCs identified in mammals, including humans. It is a highly heterogeneous group of cells in both humans and fish and their properties, as revealed by studies in humans, are most likely to remain strictly dependent on the location of these cells and the physiological state of the individual from which they originate. They form a bridge between innate and adaptive immunity. The premise of this paper is to review the current knowledge of ILCs in teleosts, taking into account data on similar cells in humans. A review of the knowledge concerning these particular cells, elements of innate immunity mechanisms as equivalent to, or perhaps dominant over, adaptive immunity mechanisms in teleosts, as presented, may inspire the need for further research.
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Affiliation(s)
- Michał Stosik
- Institute of Biological Sciences, University of Zielona Góra, Poland
| | | | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Poland
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9
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Calderon A, Mestvirishvili T, Boccalatte F, Ruggles KV, David G. Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells. Epigenetics Chromatin 2024; 17:2. [PMID: 38254205 PMCID: PMC10804615 DOI: 10.1186/s13072-024-00526-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Blood homeostasis requires the daily production of millions of terminally differentiated effector cells that all originate from hematopoietic stem cells (HSCs). HSCs are rare and exhibit unique self-renewal and multipotent properties, which depend on their ability to maintain quiescence through ill-defined processes. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignancy. In particular, the molecular mechanisms tying cell cycle re-entry to cell fate commitment in HSCs remain elusive. Previous studies have identified chromatin coordination as a key regulator of differentiation in embryonic stem cells. RESULTS Here, we utilized genetic inactivation of the chromatin-associated Sin3B protein to manipulate cell cycle control and found dysregulated chromatin accessibility and cell cycle progression in HSCs. Single cell transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) inactivated for Sin3B reveals aberrant progression through the G1 phase of the cell cycle, which correlates with the engagement of specific signaling pathways, including aberrant expression of cell adhesion molecules and the interferon signaling program in LT-HSCs. In addition, we uncover the Sin3B-dependent accessibility of genomic elements controlling HSC differentiation, which points to cell cycle progression possibly dictating the priming of HSCs for differentiation. CONCLUSIONS Our findings provide new insights into controlled cell cycle progression as a potential regulator of HSC lineage commitment through the modulation of chromatin features.
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Affiliation(s)
- Alexander Calderon
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Tamara Mestvirishvili
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Francesco Boccalatte
- Department of Pathology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Gregory David
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
- Department of Urology, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, 10016, USA.
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10
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Uehata T, Yamada S, Ori D, Vandenbon A, Giladi A, Jelinski A, Murakawa Y, Watanabe H, Takeuchi K, Toratani K, Mino T, Kiryu H, Standley DM, Tsujimura T, Ikawa T, Kondoh G, Landthaler M, Kawamoto H, Rodewald HR, Amit I, Yamamoto R, Miyazaki M, Takeuchi O. Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz. Blood 2024; 143:243-257. [PMID: 37922454 PMCID: PMC10808253 DOI: 10.1182/blood.2023020903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/05/2023] Open
Abstract
ABSTRACT Regulation of lineage biases in hematopoietic stem and progenitor cells (HSPCs) is pivotal for balanced hematopoietic output. However, little is known about the mechanism behind lineage choice in HSPCs. Here, we show that messenger RNA (mRNA) decay factors regnase-1 (Reg1; Zc3h12a) and regnase-3 (Reg3; Zc3h12c) are essential for determining lymphoid fate and restricting myeloid differentiation in HSPCs. Loss of Reg1 and Reg3 resulted in severe impairment of lymphopoiesis and a mild increase in myelopoiesis in the bone marrow. Single-cell RNA sequencing analysis revealed that Reg1 and Reg3 regulate lineage directions in HSPCs via the control of a set of myeloid-related genes. Reg1- and Reg3-mediated control of mRNA encoding Nfkbiz, a transcriptional and epigenetic regulator, was essential for balancing lymphoid/myeloid lineage output in HSPCs in vivo. Furthermore, single-cell assay for transposase-accessible chromatin sequencing analysis revealed that Reg1 and Reg3 control the epigenetic landscape on myeloid-related gene loci in early stage HSPCs via Nfkbiz. Consistently, an antisense oligonucleotide designed to inhibit Reg1- and Reg3-mediated Nfkbiz mRNA degradation primed hematopoietic stem cells toward myeloid lineages by enhancing Nfkbiz expression. Collectively, the collaboration between posttranscriptional control and chromatin remodeling by the Reg1/Reg3-Nfkbiz axis governs HSPC lineage biases, ultimately dictating the fate of lymphoid vs myeloid differentiation.
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Affiliation(s)
- Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinnosuke Yamada
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Ori
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Alexis Vandenbon
- Laboratory of Tissue Homeostasis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Adam Jelinski
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yasuhiro Murakawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuhiro Takeuchi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Kazunori Toratani
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tohru Tsujimura
- Department of Pathology, Hyogo College of Medicine, Hyogo, Japan
| | - Tomokatsu Ikawa
- Division of Immunology and Allergy, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Sciences, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine Berlin, Berlin Institute for Molecular Systems Biology, Berlin, Germany
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hans-Reimer Rodewald
- Division for Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Ryo Yamamoto
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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11
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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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12
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Jiang H, Liu J, Song Y, Lei J. Quantitative Modeling of Stemness in Single-Cell RNA Sequencing Data: A Nonlinear One-Class Support Vector Machine Method. J Comput Biol 2024; 31:41-57. [PMID: 38010500 DOI: 10.1089/cmb.2022.0484] [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: 11/29/2023] Open
Abstract
Intratumoral heterogeneity and the presence of cancer stem cells are challenging issues in cancer therapy. An appropriate quantification of the stemness of individual cells for assessing the potential for self-renewal and differentiation from the cell of origin can define a measurement for quantifying different cell states, which is important in understanding the dynamics of cancer evolution, and might further provide possible targeted therapies aimed at tumor stem cells. Nevertheless, it is usually difficult to quantify the stemness of a cell based on molecular information associated with the cell. In this study, we proposed a stemness definition method with one-class Hadamard kernel support vector machine (OCHSVM) based on single-cell RNA sequencing (scRNA-seq) data. Applications of the proposed OCHSVM stemness are assessed by various data sets, including preimplantation embryo cells, induced pluripotent stem cells, or tumor cells. We further compared the OCHSVM model with state-of-the-art methods CytoTRACE, one-class logistic regression, or one-class SVM methods with different kernels. The computational results demonstrate that the OCHSVM method is more suitable for stemness identification using scRNA-seq data.
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Affiliation(s)
- Hao Jiang
- School of Mathematics, Renmin University of China, Beijing, China
| | - Jingxin Liu
- School of Software, Beihang University, Beijing, China
| | - You Song
- School of Software, Beihang University, Beijing, China
| | - Jinzhi Lei
- School of Mathematical Sciences, Center for Applied Mathematics, Tiangong University, Tianjin, China
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13
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Teefy BB, Lemus AJJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. Cell Rep 2023; 42:113237. [PMID: 37837621 PMCID: PMC10842523 DOI: 10.1016/j.celrep.2023.113237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J J Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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14
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Ghersi JJ, Baldissera G, Hintzen J, Luff SA, Cheng S, Xia IF, Sturgeon CM, Nicoli S. Haematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic endothelium. Nat Cell Biol 2023; 25:1135-1145. [PMID: 37460694 PMCID: PMC10415179 DOI: 10.1038/s41556-023-01187-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/09/2023] [Indexed: 08/12/2023]
Abstract
Definitive haematopoietic stem and progenitor cells (HSPCs) generate erythroid, lymphoid and myeloid lineages. HSPCs are produced in the embryo via transdifferentiation of haemogenic endothelial cells in the aorta-gonad-mesonephros (AGM). HSPCs in the AGM are heterogeneous in differentiation and proliferative output, but how these intrinsic differences are acquired remains unanswered. Here we discovered that loss of microRNA (miR)-128 in zebrafish leads to an expansion of HSPCs in the AGM with different cell cycle states and a skew towards erythroid and lymphoid progenitors. Manipulating miR-128 in differentiating haemogenic endothelial cells, before their transition to HSPCs, recapitulated the lineage skewing in both zebrafish and human pluripotent stem cells. miR-128 promotes Wnt and Notch signalling in the AGM via post-transcriptional repression of the Wnt inhibitor csnk1a1 and the Notch ligand jag1b. De-repression of cskn1a1 resulted in replicative and erythroid-biased HSPCs, whereas de-repression of jag1b resulted in G2/M and lymphoid-biased HSPCs with long-term consequence on the respective blood lineages. We propose that HSPC heterogeneity arises in the AGM endothelium and is programmed in part by Wnt and Notch signalling.
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Affiliation(s)
- Joey J Ghersi
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Gabriel Baldissera
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Jared Hintzen
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie A Luff
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Siyuan Cheng
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Ivan Fan Xia
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA
| | - Christopher M Sturgeon
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stefania Nicoli
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
- Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT, USA.
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15
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Rattigan KM, Zarou MM, Helgason GV. Metabolism in stem cell-driven leukemia: parallels between hematopoiesis and immunity. Blood 2023; 141:2553-2565. [PMID: 36634302 PMCID: PMC10646800 DOI: 10.1182/blood.2022018258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Our understanding of cancer metabolism spans from its role in cellular energetics and supplying the building blocks necessary for proliferation, to maintaining cellular redox and regulating the cellular epigenome and transcriptome. Cancer metabolism, once thought to be solely driven by upregulated glycolysis, is now known to comprise multiple pathways with great plasticity in response to extrinsic challenges. Furthermore, cancer cells can modify their surrounding niche during disease initiation, maintenance, and metastasis, thereby contributing to therapy resistance. Leukemia is a paradigm model of stem cell-driven cancer. In this study, we review how leukemia remodels the niche and rewires its metabolism, with particular attention paid to therapy-resistant stem cells. Specifically, we aim to give a global, nonexhaustive overview of key metabolic pathways. By contrasting the metabolic rewiring required by myeloid-leukemic stem cells with that required for hematopoiesis and immune cell function, we highlight the metabolic features they share. This is a critical consideration when contemplating anticancer metabolic inhibitor options, especially in the context of anticancer immune therapies. Finally, we examine pathways that have not been studied in leukemia but are critical in solid cancers in the context of metastasis and interaction with new niches. These studies also offer detailed mechanisms that are yet to be investigated in leukemia. Given that cancer (and normal) cells can meet their energy requirements by not only upregulating metabolic pathways but also utilizing systemically available substrates, we aim to inform how interlinked these metabolic pathways are, both within leukemic cells and between cancer cells and their niche.
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Affiliation(s)
- Kevin M. Rattigan
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Martha M. Zarou
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - G. Vignir Helgason
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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16
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Teefy BB, Lemus AJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539616. [PMID: 37214847 PMCID: PMC10197525 DOI: 10.1101/2023.05.05.539616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J.J. Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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17
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Urbanus J, Cosgrove J, Beltman JB, Elhanati Y, Moral RA, Conrad C, van Heijst JW, Tubeuf E, Velds A, Kok L, Merle C, Magnusson JP, Guyonnet L, Frisén J, Fre S, Walczak AM, Mora T, Jacobs H, Schumacher TN, Perié L. DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age. Nat Commun 2023; 14:2184. [PMID: 37069150 PMCID: PMC10110593 DOI: 10.1038/s41467-023-37167-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.
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Affiliation(s)
- Jos Urbanus
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Joost B Beltman
- Division of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | | | - Rafael A Moral
- Department of Mathematics and Statistics, Maynooth University, Maynooth, Ireland
| | - Cecile Conrad
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Jeroen W van Heijst
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Emilie Tubeuf
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France
| | - Arno Velds
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lianne Kok
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Candice Merle
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Jens P Magnusson
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Léa Guyonnet
- Cytometry Platform, Institut Curie, 75005, Paris, France
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Silvia Fre
- Institut Curie, Laboratory of Genetics and Developmental Biology, PSL Research University, INSERM U934, CNRS UMR3215, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'École Normale Supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, Paris, France
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005, Paris, France.
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18
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Calderon A, Mestvirishvili T, Boccalatte F, Ruggles K, David G. The Sin3B chromatin modifier restricts cell cycle progression to dictate hematopoietic stem cell differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525185. [PMID: 36747851 PMCID: PMC9900761 DOI: 10.1101/2023.01.23.525185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To maintain blood homeostasis, millions of terminally differentiated effector cells are produced every day. At the apex of this massive and constant blood production lie hematopoietic stem cells (HSCs), a rare cell type harboring unique self-renewal and multipotent properties. A key feature of HSCs is their ability to temporarily exit the cell cycle in a state termed quiescence. Defective control of cell cycle progression can eventually lead to bone marrow failure or malignant transformation. Recent work in embryonic stem cells has suggested that cells can more robustly respond to differentiation cues in the early phases of the cell cycle, owing to a discrete chromatin state permissive to cell fate commitment. However, the molecular mechanisms tying cell cycle re-entry to cell fate commitment in adult stem cells such as HSCs remain elusive. Here, we report that the chromatin-associated Sin3B protein is necessary for HSCs' commitment to differentiation, but dispensable for their self-renewal or survival. Transcriptional profiling of hematopoietic stem and progenitor cells (HSPCs) genetically inactivated for Sin3B at the single cell level reveals aberrant cell cycle gene expression, correlating with the defective engagement of discrete signaling programs. In particular, the loss of Sin3B in the hematopoietic compartment results in aberrant expression of cell adhesion molecules and essential components of the interferon signaling cascade in LT-HSCs. Finally, chromatin accessibility profiling in LT-HSCs suggests a link between Sin3B-dependent cell cycle progression and priming of hematopoietic stem cells for differentiation. Together, these results point to controlled progression through the G1 phase of the cell cycle as a likely regulator of HSC lineage commitment through the modulation of chromatin features.
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19
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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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20
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Wu J, Li J, Chen K, Liu G, Zhou Y, Chen W, Zhu X, Ni TT, Zhang B, Jin D, Li D, Kang L, Wu Y, Zhu P, Xie P, Zhong TP. Atf7ip and Setdb1 interaction orchestrates the hematopoietic stem and progenitor cell state with diverse lineage differentiation. Proc Natl Acad Sci U S A 2023; 120:e2209062120. [PMID: 36577070 PMCID: PMC9910619 DOI: 10.1073/pnas.2209062120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/21/2022] [Indexed: 12/29/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are a heterogeneous group of cells with expansion, differentiation, and repopulation capacities. How HSPCs orchestrate the stemness state with diverse lineage differentiation at steady condition or acute stress remains largely unknown. Here, we show that zebrafish mutants that are deficient in an epigenetic regulator Atf7ip or Setdb1 methyltransferase undergo excessive myeloid differentiation with impaired HSPC expansion, manifesting a decline in T cells and erythroid lineage. We find that Atf7ip regulates hematopoiesis through Setdb1-mediated H3K9me3 modification and chromatin remodeling. During hematopoiesis, the interaction of Atf7ip and Setdb1 triggers H3K9me3 depositions in hematopoietic regulatory genes including cebpβ and cdkn1a, preventing HSPCs from loss of expansion and premature differentiation into myeloid lineage. Concomitantly, loss of Atf7ip or Setdb1 derepresses retrotransposons that instigate the viral sensor Mda5/Rig-I like receptor (RLR) signaling, leading to stress-driven myelopoiesis and inflammation. We find that ATF7IP or SETDB1 depletion represses human leukemic cell growth and induces myeloid differentiation with retrotransposon-triggered inflammation. These findings establish that Atf7ip/Setdb1-mediated H3K9me3 deposition constitutes a genome-wide checkpoint that impedes the myeloid potential and maintains HSPC stemness for diverse blood cell production, providing unique insights into potential intervention in hematological malignancy.
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Affiliation(s)
- Jiaxin Wu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Juan Li
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Kang Chen
- School of Life Sciences and Technology, Tongji University, Shanghai200092, China
| | - Guolong Liu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Yating Zhou
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Wenqi Chen
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Xiangzhan Zhu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Terri T. Ni
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Bianhong Zhang
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Daqing Jin
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Lan Kang
- School of Life Sciences and Technology, Tongji University, Shanghai200092, China
| | - Yuxuan Wu
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
| | - Ping Zhu
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong510100, China
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu210096, China
| | - Tao P. Zhong
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Institute of Molecular Medicine, East China Normal University School of Life Sciences, Shanghai200241, China
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21
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Albayrak E, Kocabaş F. Therapeutic targeting and HSC proliferation by small molecules and biologicals. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:425-496. [PMID: 37061339 DOI: 10.1016/bs.apcsb.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Hematopoietic stem cells (HSCs) have considerably therapeutic value on autologous and allogeneic transplantation for many malignant/non-malignant hematological diseases, especially with improvement of gene therapy. However, acquirement of limited cell dose from HSC sources is the main handicap for successful transplantation. Therefore, many strategies based on the utilization of various cytokines, interaction of stromal cells, modulation of several extrinsic and intrinsic factors have been developed to promote ex vivo functional HSC expansion with high reconstitution ability until today. Besides all these strategies, small molecules become prominent with their ease of use and various advantages when they are translated to the clinic. In the last two decades, several small molecule compounds have been investigated in pre-clinical studies and, some of them were evaluated in different stages of clinical trials for their safety and efficiencies. In this chapter, we will present an overview of HSC biology, function, regulation and also, pharmacological HSC modulation with small molecules from pre-clinical and clinical perspectives.
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Kranert K, Woźny M, Podlasz P, Wąsowicz K, Brzuzan P. MiR92b-3p synthetic analogue impairs zebrafish embryonic development, leading to ocular defects, decreased movement and hatching rate, and increased mortality. J Appl Genet 2023; 64:145-157. [PMID: 36274083 PMCID: PMC9837005 DOI: 10.1007/s13353-022-00732-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/04/2022] [Accepted: 10/12/2022] [Indexed: 01/17/2023]
Abstract
The aim of this study was to examine the effect of microRNA 92b-3p (MiR92b-3p) overexpression on the embryonic development of zebrafish. A synthetic MiR92b-3p analogue (mirVana™ mimic, in vivo-ready) was injected at doses up to 5 ng/embryo into the yolk sac of embryos (2-16 cell stage). At 24 h post fertilization (hpf), the locomotor activity of the embryos was measured, and after hatching (72 hpf), the rates of malformation occurrence, hatching, and mortality were determined. Next, the larvae were fixed for histological and molecular examinations. Exposure to the MiR92b-3p mimic impaired embryonic development, leading to increased occurrence of malformations (i.e., pericardial edema, spine curvature, smaller eyes), decreased locomotor activity and hatching rate, and increased mortality. Importantly, the mimic affected retinal differentiation and lens formation during zebrafish embryogenesis, which suggests that MiR92b-3p could be an important factor in the regulation of fish embryogenesis and ocular development. The expression level of MiR92b-3p was substantially higher in the exposed larvae than in the untreated larvae, indicating that the mimic was successfully delivered to the zebrafish. Although screening of potential MiR92b-3p target genes suggested some changes in their expression levels, these results were inconclusive. Together, this study indicates that MiR92b-3p mimic impairs zebrafish embryonic development, and further research is necessary to identify the MiR92b-3p-regulated cell pathways involved in the impairment of the fish's development.
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Affiliation(s)
- Kilian Kranert
- grid.412607.60000 0001 2149 6795Department of Environmental Biotechnology, Institute of Engineering and Environment Protection, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709 Olsztyn, Poland
| | - Maciej Woźny
- grid.412607.60000 0001 2149 6795Department of Environmental Biotechnology, Institute of Engineering and Environment Protection, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709 Olsztyn, Poland
| | - Piotr Podlasz
- grid.412607.60000 0001 2149 6795Department of Pathophysiology, Forensic Veterinary Medicine and Administration, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 13, 10-718 Olsztyn, Poland
| | - Krzysztof Wąsowicz
- grid.412607.60000 0001 2149 6795Department of Pathophysiology, Forensic Veterinary Medicine and Administration, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 13, 10-718 Olsztyn, Poland
| | - Paweł Brzuzan
- grid.412607.60000 0001 2149 6795Department of Environmental Biotechnology, Institute of Engineering and Environment Protection, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709 Olsztyn, Poland
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23
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Abstract
Single-cell studies are enabling our understanding of the molecular processes of normal cell development and the onset of several pathologies. For instance, single-cell RNA sequencing (scRNA-Seq) measures the transcriptome-wide gene expression at a single-cell resolution, allowing for studying the heterogeneity among the cells of the same population and revealing complex and rare cell populations. On the other hand, single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-Seq) can be used to define transcriptional and epigenetic changes by analyzing the chromatin accessibility at the single-cell level. However, the integration of multi-omics data still remains one of the most difficult tasks in bioinformatics. In this chapter, we focus on the combination of scRNA-Seq and scATACSeq data to perform an integrative analysis of the single-cell transcriptome and chromatin accessibility of human fetal progenitors.
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24
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Damkham N, Issaragrisil S, Lorthongpanich C. Role of YAP as a Mechanosensing Molecule in Stem Cells and Stem Cell-Derived Hematopoietic Cells. Int J Mol Sci 2022; 23:14634. [PMID: 36498961 PMCID: PMC9737411 DOI: 10.3390/ijms232314634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/11/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1, also known as TAZ) are transcriptional coactivators in the Hippo signaling pathway. Both are well-known regulators of cell proliferation and organ size control, and they have significant roles in promoting cell proliferation and differentiation. The roles of YAP and TAZ in stem cell pluripotency and differentiation have been extensively studied. However, the upstream mediators of YAP and TAZ are not well understood. Recently, a novel role of YAP in mechanosensing and mechanotransduction has been reported. The present review updates information on the regulation of YAP by mechanical cues such as extracellular matrix stiffness, fluid shear stress, and actin cytoskeleton tension in stem cell behaviors and differentiation. The review explores mesenchymal stem cell fate decisions, pluripotent stem cells (PSCs), self-renewal, pluripotency, and differentiation to blood products. Understanding how cells sense their microenvironment or niche and mimic those microenvironments in vitro could improve the efficiency of producing stem cell products and the efficacy of the products.
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Affiliation(s)
- Nattaya Damkham
- Siriraj Center of Excellence for Stem cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Surapol Issaragrisil
- Siriraj Center of Excellence for Stem cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Hematology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Bangkok Hematology Center, Wattanosoth Hospital, BDMS Center of Excellence for Cancer, Bangkok 10310, Thailand
| | - Chanchao Lorthongpanich
- Siriraj Center of Excellence for Stem cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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25
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Chen M, Xu C, Xu Z, He W, Zhang H, Su J, Song Q. Uncovering the dynamic effects of DEX treatment on lung cancer by integrating bioinformatic inference and multiscale modeling of scRNA-seq and proteomics data. Comput Biol Med 2022; 149:105999. [PMID: 35998480 PMCID: PMC9717711 DOI: 10.1016/j.compbiomed.2022.105999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/16/2022] [Accepted: 08/14/2022] [Indexed: 11/18/2022]
Abstract
Lung cancer is one of the leading causes of cancer-related death, with a five-year survival rate of 18%. It is a priority for us to understand the underlying mechanisms affecting lung cancer therapeutics' implementation and effectiveness. In this study, we combine the power of Bioinformatics and Systems Biology to comprehensively uncover functional and signaling pathways of drug treatment using bioinformatics inference and multiscale modeling of both scRNA-seq data and proteomics data. Based on a time series of lung adenocarcinoma derived A549 cells after DEX treatment, we first identified the differentially expressed genes (DEGs) in those lung cancer cells. Through the interrogation of regulatory network of those DEGs, we identified key hub genes including TGFβ, MYC, and SMAD3 varied underlie DEX treatment. Further gene set enrichment analysis revealed the TGFβ signaling pathway as the top enriched term. Those genes involved in the TGFβ pathway and their crosstalk with the ERBB pathway presented a strong survival prognosis in clinical lung cancer samples. With the basis of biological validation and literature-based curation, a multiscale model of tumor regulation centered on both TGFβ-induced and ERBB-amplified signaling pathways was developed to characterize the dynamic effects of DEX therapy on lung cancer cells. Our simulation results were well matched to available data of SMAD2, FOXO3, TGFβ1, and TGFβR1 over the time course. Moreover, we provided predictions of different doses to illustrate the trend and therapeutic potential of DEX treatment. The innovative and cross-disciplinary approach can be further applied to other computational studies in tumorigenesis and oncotherapy. We released the approach as a user-friendly tool named BIMM (Bioinformatic Inference and Multiscale Modeling), with all the key features available at https://github.com/chenm19/BIMM.
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Affiliation(s)
- Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA
| | - Chunrui Xu
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Ziang Xu
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, USA; Department of Chemistry, Wake Forest University, Winston-Salem, NC, USA
| | - Wei He
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA
| | - Haorui Zhang
- Department of Mathematics and Statistics, Wake Forest University, Winston-Salem, NC, USA
| | - Jing Su
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qianqian Song
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston Salem, NC, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, USA.
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26
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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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27
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Nagaharu K, Kojima Y, Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K. A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics. Cell Rep 2022; 40:111260. [PMID: 36044861 DOI: 10.1016/j.celrep.2022.111260] [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: 10/19/2021] [Revised: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
Hematopoiesis was considered a hierarchical stepwise process but was revised to a continuous process following single-cell RNA sequencing. However, the uncertainty or fluctuation of single-cell transcriptome dynamics during differentiation was not considered, and the dendritic cell (DC) pathway in the lymphoid context remains unclear. Here, we identify human B-plasmacytoid DC (pDC) bifurcation as large fluctuating transcriptome dynamics in the putative B/NK progenitor region by dry and wet methods. By converting splicing kinetics into diffusion dynamics in a deep generative model, our original computational methodology reveals strong fluctuation at B/pDC bifurcation in IL-7Rα+ regions, and LFA-1 fluctuates positively in the pDC direction at the bifurcation. These expectancies are validated by the presence of B/pDC progenitors in the IL-7Rα+ fraction and preferential expression of LFA-1 in pDC-biased progenitors with a niche-like culture system. We provide a model of fluctuation-based differentiation, which reconciles continuous and discrete models and is applicable to other developmental systems.
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Affiliation(s)
- Keiki Nagaharu
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yasuhiro Kojima
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kodai Minoura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Hirohito Minami
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuki Kageyama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuka Sugimoto
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Masahiro Masuya
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Shigeru Nii
- Shiroko Women's Hospital, Suzuka 510-0235, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Isao Tawara
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Naoyuki Katayama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan; Division of Cancer Immunology, Research Institute, National Cancer Center, Tokyo 104-0045, Japan; Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba 277-8577, Japan.
| | - Kohshi Ohishi
- Department of Transfusion Medicine and Cell Therapy, Mie University Hospital, Tsu 514-8507, Japan.
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28
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Zhou Y, Sharpee TO. Using Global t-SNE to Preserve Intercluster Data Structure. Neural Comput 2022; 34:1637-1651. [PMID: 35798323 PMCID: PMC10010455 DOI: 10.1162/neco_a_01504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/22/2022] [Indexed: 11/04/2022]
Abstract
The t-distributed stochastic neighbor embedding (t-SNE) method is one of the leading techniques for data visualization and clustering. This method finds lower-dimensional embedding of data points while minimizing distortions in distances between neighboring data points. By construction, t-SNE discards information about large-scale structure of the data. We show that adding a global cost function to the t-SNE cost function makes it possible to cluster the data while preserving global intercluster data structure. We test the new global t-SNE (g-SNE) method on one synthetic and two real data sets on flower shapes and human brain cells. We find that significant and meaningful global structure exists in both the plant and human brain data sets. In all cases, g-SNE outperforms t-SNE and UMAP in preserving the global structure. Topological analysis of the clustering result makes it possible to find an appropriate trade-off of data distribution across scales. We find differences in how data are distributed across scales between the two subjects that were part of the human brain data set. Thus, by striving to produce both accurate clustering and positioning between clusters, the g-SNE method can identify new aspects of data organization across scales.
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Affiliation(s)
- Yuansheng Zhou
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A.,Division of Biological Sciences, University of California San Diego, La Jolla, CA 92037, U.S.A.
| | - Tatyana O Sharpee
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, U.S.A.,Department of Physics, University of California San Diego, La Jolla, CA 92037, U.S.A.
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29
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Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development. Nat Genet 2022; 54:1051-1061. [PMID: 35817981 DOI: 10.1038/s41588-022-01118-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 06/01/2022] [Indexed: 12/21/2022]
Abstract
Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell differentiation. Recent advances in single-cell genomics are altering our understanding of the Waddington landscape, yet the molecular mechanisms of cell-fate decisions remain poorly understood. We constructed a cell landscape of mouse lineage differentiation during development at the single-cell level and described both lineage-common and lineage-specific regulatory programs during cell-type maturation. We also found lineage-common regulatory programs that are broadly active during the development of invertebrates and vertebrates. In particular, we identified Xbp1 as an evolutionarily conserved regulator of cell-fate determinations across different species. We demonstrated that Xbp1 transcriptional regulation is important for the stabilization of the gene-regulatory networks for a wide range of mouse cell types. Our results offer genetic and molecular insights into cellular gene-regulatory programs and will serve as a basis for further advancing the understanding of cell-fate decisions.
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30
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Stosik M, Tokarz-Deptuła B, Deptuła W. Haematopoiesis in Zebrafish (Danio Rerio). Front Immunol 2022; 13:902941. [PMID: 35720291 PMCID: PMC9201100 DOI: 10.3389/fimmu.2022.902941] [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: 03/23/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Haematopoiesis in fish and mammals is a complex process, and many aspects regarding its model and the differentiation of haematopoietic stem cells (HSCs) still remain enigmatic despite advanced studies. The effects of microenvironmental factors or HSCs niche and signalling pathways on haematopoiesis are also unclear. This review presents Danio rerio as a model organism for studies on haematopoiesis in vertebrates and discusses the development of this process during the embryonic period and in adult fish. It describes the role of the microenvironment of the haematopoietic process in regulating the formation and function of HSCs/HSPCs (hematopoietic stem/progenitor cells) and highlights facts and research areas important for haematopoiesis in fish and mammals.
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Affiliation(s)
- Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | | | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
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31
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Goldberg LR, Dooner MS, Papa E, Pereira M, Del Tatto M, Cheng Y, Wen S, Quesenberry PJ. Differentiation Epitopes Define Hematopoietic Stem Cells and Change with Cell Cycle Passage. Stem Cell Rev Rep 2022; 18:2351-2364. [PMID: 35503199 PMCID: PMC9489557 DOI: 10.1007/s12015-022-10374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2022] [Indexed: 11/25/2022]
Abstract
Hematopoietic stem cells express differentiation markers B220 and Gr1 and are proliferative. We have shown that the expression of these entities changes with cell cycle passage. Overall, we conclude that primitive hematopoietic stem cells alter their differentiation potential with cell cycle progression. Murine derived long-term hematopoietic stem cells (LT-HSC) are cycling and thus always changing phenotype. Here we show that over one half of marrow LT-HSC are in the population expressing differentiation epitopes and that B220 and Gr-1 positive populations are replete with LT-HSC after a single FACS separation but if subjected to a second separation these cells no longer contain LT-HSC. However, with second separated cells there is a population appearing that is B220 negative and replete with cycling c-Kit, Sca-1 CD150 positive LT-HSC. There is a 3-4 h interval between the first and second B220 or GR-1 FACS separation during which the stem cells continue to cycle. Thus, the LT-HSC have lost B220 or GR-1 expression as the cells progress through cell cycle, although they have maintained the c-kit, Sca-1 and CD150 stem cells markers over this time interval. These data indicate that cycling stem cells express differentiation epitopes and alter their differentiation potential with cell cycle passage.
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Affiliation(s)
- Laura R Goldberg
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Mark S Dooner
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA.
| | - Elaine Papa
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Mandy Pereira
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Michael Del Tatto
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Yan Cheng
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Sicheng Wen
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
| | - Peter J Quesenberry
- Division of Hematology/Oncology, Rhode Island Hospital/Brown University, 1 Hoppin St Coro West Building suite 5.01, Providence, RI, 02903, USA
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32
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Gilchrist AE, Harley BA. Engineered Tissue Models to Replicate Dynamic Interactions within the Hematopoietic Stem Cell Niche. Adv Healthc Mater 2022; 11:e2102130. [PMID: 34936239 PMCID: PMC8986554 DOI: 10.1002/adhm.202102130] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/19/2021] [Indexed: 12/19/2022]
Abstract
Hematopoietic stem cells are the progenitors of the blood and immune system and represent the most widely used regenerative therapy. However, their rarity and limited donor base necessitate the design of ex vivo systems that support HSC expansion without the loss of long-term stem cell activity. This review describes recent advances in biomaterials systems to replicate features of the hematopoietic niche. Inspired by the native bone marrow, these instructive biomaterials provide stimuli and cues from cocultured niche-associated cells to support HSC encapsulation and expansion. Engineered systems increasingly enable study of the dynamic nature of the matrix and biomolecular environment as well as the role of cell-cell signaling (e.g., autocrine feedback vs paracrine signaling between dissimilar cells). The inherent coupling of material properties, biotransport of cell-secreted factors, and cell-mediated remodeling motivate dynamic biomaterial systems as well as characterization and modeling tools capable of evaluating a temporally evolving tissue microenvironment. Recent advances in HSC identification and tracking, model-based experimental design, and single-cell culture platforms facilitate the study of the effect of constellations of matrix, cell, and soluble factor signals on HSC fate. While inspired by the HSC niche, these tools are amenable to the broader stem cell engineering community.
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Affiliation(s)
- Aidan E. Gilchrist
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Brendan A.C. Harley
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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33
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Parker J, Guslund NC, Jentoft S, Roth O. Characterization of Pipefish Immune Cell Populations Through Single-Cell Transcriptomics. Front Immunol 2022; 13:820152. [PMID: 35154138 PMCID: PMC8828949 DOI: 10.3389/fimmu.2022.820152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 01/16/2023] Open
Abstract
Teleost adaptive immune systems have evolved with more flexibility than previously assumed. A particularly enigmatic system to address immune system modifications in the evolutionary past is represented by the Syngnathids, the family of pipefishes, seahorses and seadragons. These small fishes with their unique male pregnancy have lost the spleen as an important immune organ as well as a functional major histocompatibility class II (MHC II) pathway. How these evolutionary changes have impacted immune cell population dynamics have up to this point remained unexplored. Here, we present the first immune cell repertoire characterization of a syngnathid fish (Syngnathus typhle) using single-cell transcriptomics. Gene expression profiles of individual cells extracted from blood and head-kidney clustered in twelve putative cell populations with eight belonging to those with immune function. Upregulated cell marker genes identified in humans and teleosts were used to define cell clusters. While the suggested loss of CD4+ T-cells accompanied the loss of the MHC II pathway was supported, the upregulation of specific subtype markers within the T-cell cluster indicates subpopulations of regulatory T-cells (il2rb) and cytotoxic T-cells (gzma). Utilizing single-cell RNA sequencing this report is the first to characterize immune cell populations in syngnathids and provides a valuable foundation for future cellular classification and experimental work within the lineage.
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Affiliation(s)
- Jamie Parker
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Marine Evolutionary Biology, Christian-Albrechts-University, Kiel, Germany
| | - Naomi Croft Guslund
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.,Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Olivia Roth
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.,Marine Evolutionary Biology, Christian-Albrechts-University, Kiel, Germany
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Erythropoietin receptor contributes to thrombopoietin receptor (Mpl)-independent thrombocytopoiesis in zebrafish. Leukemia 2022; 36:1193-1197. [PMID: 35039636 DOI: 10.1038/s41375-021-01495-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/01/2021] [Accepted: 12/08/2021] [Indexed: 11/08/2022]
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35
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Song Q, Liu L. Single-Cell RNA-Seq Technologies and Computational Analysis Tools: Application in Cancer Research. Methods Mol Biol 2022; 2413:245-255. [PMID: 35044670 DOI: 10.1007/978-1-0716-1896-7_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The recent maturation of single-cell RNA sequencing (scRNA-seq) provides unique opportunities for researchers to uncover new and potentially unexpected biological discoveries and to understand the complexity of tissues by transcriptomic profiling in individual cells. This review introduces the latest scRNA-seq techniques and platforms as well as their advantages and disadvantages. Moreover, we review computational tools and pipelines for analyzing scRNA-seq data, and their applications in cancer research, highlighting the important role of scRNA-seq techniques in this area.
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Affiliation(s)
- Qianqian Song
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Liang Liu
- Department of Cancer Biology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA.
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36
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Bresciani E, Carrington B, Yu K, Kim EM, Zhen T, Guzman VS, Broadbridge E, Bishop K, Kirby M, Harper U, Wincovitch S, Dell’Orso S, Sartorelli V, Sood R, Liu P. Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development. Blood Adv 2021; 5:4949-4962. [PMID: 34492681 PMCID: PMC9153008 DOI: 10.1182/bloodadvances.2020003969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
RUNX1 is essential for the generation of hematopoietic stem cells (HSCs). Runx1-null mouse embryos lack definitive hematopoiesis and die in mid-gestation. However, although zebrafish embryos with a runx1 W84X mutation have defects in early definitive hematopoiesis, some runx1W84X/W84X embryos can develop to fertile adults with blood cells of multilineages, raising the possibility that HSCs can emerge without RUNX1. Here, using 3 new zebrafish runx1-/- lines, we uncovered the compensatory mechanism for runx1-independent hematopoiesis. We show that, in the absence of a functional runx1, a cd41-green fluorescent protein (GFP)+ population of hematopoietic precursors still emerge from the hemogenic endothelium and can colonize the hematopoietic tissues of the mutant embryos. Single-cell RNA sequencing of the cd41-GFP+ cells identified a set of runx1-/--specific signature genes during hematopoiesis. Significantly, gata2b, which normally acts upstream of runx1 for the generation of HSCs, was increased in the cd41-GFP+ cells in runx1-/- embryos. Interestingly, genetic inactivation of both gata2b and its paralog gata2a did not affect hematopoiesis. However, knocking out runx1 and any 3 of the 4 alleles of gata2a and gata2b abolished definitive hematopoiesis. Gata2 expression was also upregulated in hematopoietic cells in Runx1-/- mice, suggesting the compensatory mechanism is conserved. Our findings indicate that RUNX1 and GATA2 serve redundant roles for HSC production, acting as each other's safeguard.
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Affiliation(s)
| | | | - Kai Yu
- Oncogenesis and Development Section
| | | | - Tao Zhen
- Oncogenesis and Development Section
| | | | | | | | | | | | - Stephen Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Raman Sood
- Oncogenesis and Development Section
- Zebrafish Core
| | - Paul Liu
- Oncogenesis and Development Section
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Georgolopoulos G, Psatha N, Iwata M, Nishida A, Som T, Yiangou M, Stamatoyannopoulos JA, Vierstra J. Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation. Nat Commun 2021; 12:6790. [PMID: 34815405 PMCID: PMC8611072 DOI: 10.1038/s41467-021-27159-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. Here we perform dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit the stem and progenitor stage. Collectively, these data provide insights into the temporally regulated synergy of the cis- and the trans-regulatory components underlying hematopoietic lineage commitment and differentiation.
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Affiliation(s)
- Grigorios Georgolopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | - Mineo Iwata
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Tannishtha Som
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Minas Yiangou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jeff Vierstra
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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39
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Peña OA, Lubin A, Rowell J, Hoade Y, Khokhar N, Lemmik H, Mahony C, Dace P, Umamahesan C, Payne EM. Differential Requirement of Gata2a and Gata2b for Primitive and Definitive Myeloid Development in Zebrafish. Front Cell Dev Biol 2021; 9:708113. [PMID: 34589480 PMCID: PMC8475954 DOI: 10.3389/fcell.2021.708113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/10/2021] [Indexed: 11/14/2022] Open
Abstract
Germline loss or mutation of one copy of the transcription factor GATA2 in humans leads to a range of clinical phenotypes affecting hematopoietic, lymphatic and vascular systems. GATA2 heterozygous mice show only a limited repertoire of the features observed in humans. Zebrafish have two copies of the Gata2 gene as a result of an additional round of ancestral whole genome duplication. These genes, Gata2a and Gata2b, show distinct but overlapping expression patterns, and between them, highlight a significantly broader range of the phenotypes observed in GATA2 deficient syndromes, than each one alone. In this manuscript, we use mutants for Gata2a and Gata2b to interrogate the effects on hematopoiesis of these two ohnologs, alone and in combination, during development in order to further define the role of GATA2 in developmental hematopoiesis. We define unique roles for each ohnolog at different stages of developmental myelopoiesis and for the emergence of hematopoietic stem and progenitor cells. These effects are not additive in the haploinsufficient state suggesting a redundancy between these two genes in hematopoietic stem and progenitor cells. Rescue studies additionally support that Gata2b can compensate for the effects of Gata2a loss. Finally we show that adults with loss of combined heterozygosity show defects in the myeloid compartment consistent with GATA2 loss in humans. These results build on existing knowledge from other models of GATA2 deficiency and refine our understanding of the early developmental effects of GATA2. In addition, these studies shed light on the complexity and potential structure-function relationships as well as sub-functionalization of Gata2 genes in the zebrafish model.
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Affiliation(s)
- Oscar A. Peña
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Alexandra Lubin
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Jasmine Rowell
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Yvette Hoade
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Noreen Khokhar
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Hanna Lemmik
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Christopher Mahony
- Department of Pathology and Immunology, School of Medicine, University of Geneva, Geneva, Switzerland
| | - Phoebe Dace
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Chianna Umamahesan
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
| | - Elspeth M. Payne
- Research Department of Haematology, Cancer Institute, University College London, London, United Kingdom
- National Institute for Health Research (NIHR)/UCLH Clinical Research Facility, University College London Hospitals NHS Foundation Trust, London, United Kingdom
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Abstract
PURPOSE OF REVIEW In the last few decades, revolutionary advances in next-generation sequencing have led to single-cell lineage tracing technologies that now enable researchers to identify and quantify hematopoietic cell behavior with unprecedented detail. Combined readouts of cell lineage and cell state from the same cell mitigate the need to prospectively isolate populations of interest, and allow a system-level understanding of dynamic developmental processes. We will discuss the advantages and shortcomings of these technologies, the intriguing discoveries that stemmed from lineage tracing hematopoiesis at the single-cell level and the directions toward which the field is moving. RECENT FINDINGS Single-cell lineage tracing studies unveiled extensive functional heterogeneity within discrete immunophenotypic populations. Recently, several groups merged lineage tracing with single-cell RNA sequencing to visualize clonal relationships directly on transcriptional landscapes without the requirement for prospective isolation of cell types by FACS. To study the cell dynamics of hematopoiesis, without perturbation in their native niche, researchers have developed mouse models with endogenous single-cell lineage tracing systems, which can simultaneously trace thousands of hematopoietic progenitor cells in a single mouse, without transplantation. The emerging picture is that multiple hematopoietic hierarchies coexist within a single individual, each with distinct regulatory features. These hierarchies are imprinted during development much earlier than previously predicted, persisting well into adulthood and even after injury and transplantation. SUMMARY Clone-tracking experiments allow stem-cell researchers to characterize lineage hierarchies during blood development and regeneration. Combined with single-cell genomics analyses, these studies are allowing system-level description of hematopoiesis in mice and humans. Early exploratory studies have unveiled features with important implications for human biology and disease. VIDEO ABSTRACT.
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Gioacchino E, Koyunlar C, Zink J, de Looper H, de Jong M, Dobrzycki T, Mahony CB, Hoogenboezem R, Bosch D, van Strien PMH, van Royen ME, French PJ, Bindels E, Gussinklo KJ, Monteiro R, Touw IP, de Pater E. Essential role for Gata2 in modulating lineage output from hematopoietic stem cells in zebrafish. Blood Adv 2021; 5:2687-2700. [PMID: 34170285 PMCID: PMC8288679 DOI: 10.1182/bloodadvances.2020002993] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 01/22/2023] Open
Abstract
The differentiation of hematopoietic stem cells (HSCs) is tightly controlled to ensure a proper balance between myeloid and lymphoid cell output. GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of HSCs. GATA2 is expressed throughout development, but because of early embryonic lethality in mice, its role during adult hematopoiesis is incompletely understood. Zebrafish contains 2 orthologs of GATA2: Gata2a and Gata2b, which are expressed in different cell types. We show that the mammalian functions of GATA2 are split between these orthologs. Gata2b-deficient zebrafish have a reduction in embryonic definitive hematopoietic stem and progenitor cell (HSPC) numbers, but are viable. This allows us to uniquely study the role of GATA2 in adult hematopoiesis. gata2b mutants have impaired myeloid lineage differentiation. Interestingly, this defect arises not in granulocyte-monocyte progenitors, but in HSPCs. Gata2b-deficient HSPCs showed impaired progression of the myeloid transcriptional program, concomitant with increased coexpression of lymphoid genes. This resulted in a decrease in myeloid-programmed progenitors and a relative increase in lymphoid-programmed progenitors. This shift in the lineage output could function as an escape mechanism to avoid a block in lineage differentiation. Our study helps to deconstruct the functions of GATA2 during hematopoiesis and shows that lineage differentiation flows toward a lymphoid lineage in the absence of Gata2b.
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Affiliation(s)
| | - Cansu Koyunlar
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Joke Zink
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Hans de Looper
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC, Rotterdam, The Netherlands
| | - Madelon de Jong
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Tomasz Dobrzycki
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Christopher B. Mahony
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | | | - Dennis Bosch
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Martin E. van Royen
- Department of Pathology, Cancer Treatment Screening Facility, Erasmus MC Optical Imaging Centre, and
| | - Pim J. French
- Department of Neurology, Cancer Treatment Screening Facility, Erasmus MC, Rotterdam, The Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom; and
| | - Ivo P. Touw
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Emma de Pater
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
- Cancer Genome Editing Center, Erasmus MC, Rotterdam, The Netherlands
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42
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Mondal PK, Saha US, Mukhopadhyay I. PseudoGA: cell pseudotime reconstruction based on genetic algorithm. Nucleic Acids Res 2021; 49:7909-7924. [PMID: 34244782 PMCID: PMC8661435 DOI: 10.1093/nar/gkab457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/03/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Dynamic regulation of gene expression is often governed by progression through transient cell states. Bulk RNA-seq analysis can only detect average change in expression levels and is unable to identify this dynamics. Single cell RNA-seq presents an unprecedented opportunity that helps in placing the cells on a hypothetical time trajectory that reflects gradual transition of their transcriptomes. This continuum trajectory or ‘pseudotime’, may reveal the developmental pathway and provide us with information on dynamic transcriptomic changes and other biological processes. Existing approaches to build pseudotime heavily depend on reducing huge dimension to extremely low dimensional subspaces and may lead to loss of information. We propose PseudoGA, a genetic algorithm based approach to order cells assuming that gene expressions vary according to a smooth curve along the pseudotime trajectory. We observe superior accuracy of our method in simulated as well as benchmarking real datasets. Generality of the assumption behind PseudoGA and no dependence on dimensionality reduction technique make it a robust choice for pseudotime estimation from single cell transcriptome data. PseudoGA is also time efficient when applied to a large single cell RNA-seq data and adaptable to parallel computing. R code for PseudoGA is freely available at https://github.com/indranillab/pseudoga.
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Affiliation(s)
- Pronoy Kanti Mondal
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, West Bengal, India
| | - Udit Surya Saha
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, West Bengal, India
| | - Indranil Mukhopadhyay
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata 700108, West Bengal, India
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43
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Abstract
Single-cell omics is transforming our understanding of cell biology and disease, yet the systems-level analysis and interpretation of single-cell data faces many challenges. In this Perspective, we describe the impact that fundamental concepts from statistical mechanics, notably entropy, stochastic processes and critical phenomena, are having on single-cell data analysis. We further advocate the need for more bottom-up modelling of single-cell data and to embrace a statistical mechanics analysis paradigm to help attain a deeper understanding of single-cell systems biology.
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Affiliation(s)
- Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- UCL Cancer Institute, University College London, London, UK.
| | - Andrew P Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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44
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The twilight zone: plasticity and mixed ontogeny of neutrophil and eosinophil granulocyte subsets. Semin Immunopathol 2021; 43:337-346. [PMID: 34009400 PMCID: PMC8132041 DOI: 10.1007/s00281-021-00862-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022]
Abstract
It is now becoming clear that neutrophils and eosinophils are heterogeneous cells with potentially multiple subsets in health and disease. With greater marker coverage by multi-color flow cytometry and single-cell level sequencing of granulocyte populations, novel phenotypes of these cells began to emerge. Intriguingly, many newly described subsets blend distinctions between classical myeloid lineage phenotypes, which are especially true for tissue resident or recruited cells in contexts of inflammation and disease. This includes reports of neutrophils with features of eosinophils, monocytes and dendritic cells, and eosinophil subsets expressing neutrophil markers. Moreover, novel studies show the ability of immature neutrophils to transdifferentiate into mature cells belonging to other myeloid lineages (eosinophils, monocytes/macrophages). In this review, we summarize novel findings in this exciting research frontier and shed light on potential processes driving the plasticity and heterogeneity of granulocyte subsets. Specifically, we discuss the hematopoietic flexibility of granulocyte precursors in bone marrow and the adaptation of myeloid cells to local tissue microenvironments. The understanding of such intermediate and developmental phenotypes is very important, as it can teach us about origins of functionally distinct myeloid cells during inflammation, and explain reasons for successes and failures of biologics targeting terminally differentiated granulocytes.
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45
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Transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates. Dev Biol 2021; 475:156-164. [PMID: 33689804 DOI: 10.1016/j.ydbio.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/20/2022]
Abstract
Hematopoietic stem cells (HSCs) are the foundation of adult hematopoiesis that produce all types of mature blood lineages. In vertebrates, HSC development is a stepwise process, coordinately regulated by chromatin architectures and a group of transcriptional and epigenetic regulators. A deeper understanding of the molecular mechanisms governing the generation, expansion, and function of HSCs holds great promise in the generation and expansion of engraftable HSCs in vitro for clinical applications. This study reviewed recent advances in transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates.
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46
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Ranzoni AM, Tangherloni A, Berest I, Riva SG, Myers B, Strzelecka PM, Xu J, Panada E, Mohorianu I, Zaugg JB, Cvejic A. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis. Cell Stem Cell 2021; 28:472-487.e7. [PMID: 33352111 PMCID: PMC7939551 DOI: 10.1016/j.stem.2020.11.015] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/18/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023]
Abstract
Regulation of hematopoiesis during human development remains poorly defined. Here we applied single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) to over 8,000 human immunophenotypic blood cells from fetal liver and bone marrow. We inferred their differentiation trajectory and identified three highly proliferative oligopotent progenitor populations downstream of hematopoietic stem cells (HSCs)/multipotent progenitors (MPPs). Along this trajectory, we observed opposing patterns of chromatin accessibility and differentiation that coincided with dynamic changes in the activity of distinct lineage-specific transcription factors. Integrative analysis of chromatin accessibility and gene expression revealed extensive epigenetic but not transcriptional priming of HSCs/MPPs prior to their lineage commitment. Finally, we refined and functionally validated the sorting strategy for the HSCs/MPPs and achieved around 90% enrichment. Our study provides a useful framework for future investigation of human developmental hematopoiesis in the context of blood pathologies and regenerative medicine.
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Affiliation(s)
- Anna Maria Ranzoni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Andrea Tangherloni
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Ivan Berest
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Simone Giovanni Riva
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Brynelle Myers
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Paulina M Strzelecka
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Jiarui Xu
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Elisa Panada
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Irina Mohorianu
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69115 Heidelberg, Germany
| | - Ana Cvejic
- University of Cambridge, Department of Haematology, Cambridge CB2 0AW, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 0AW, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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47
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Nayak R, Hasija Y. A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines. Genomics 2021; 113:606-619. [PMID: 33485955 DOI: 10.1016/j.ygeno.2021.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 12/30/2020] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to the accumulation of massive cellular transcription data at an astounding resolution of single cells. It provides valuable insights into cells previously unachieved by bulk cell analysis and is proving crucial in uncovering cellular heterogeneity, identifying rare cell populations, distinct cell-lineage trajectories, and mechanisms involved in complex cellular processes. SCT data is highly complex and necessitates advanced statistical and computational methods for analysis. This review provides a comprehensive overview of the steps in a typical SCT workflow, starting from experimental protocol to data analysis, deliberating various pipelines used. We discuss recent trends, challenges, machine learning methods for data analysis, and future prospects. We conclude by listing the multitude of scRNA-seq data applications and how it shall revolutionize our understanding of cellular biology and diseases.
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Affiliation(s)
- Richa Nayak
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India
| | - Yasha Hasija
- Department of Biotechnology, Delhi Technological University, Delhi 110042, India.
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48
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Pretschner A, Pabel S, Haas M, Heiner M, Marwan W. Regulatory Dynamics of Cell Differentiation Revealed by True Time Series From Multinucleate Single Cells. Front Genet 2021; 11:612256. [PMID: 33488676 PMCID: PMC7820898 DOI: 10.3389/fgene.2020.612256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/07/2020] [Indexed: 12/31/2022] Open
Abstract
Dynamics of cell fate decisions are commonly investigated by inferring temporal sequences of gene expression states by assembling snapshots of individual cells where each cell is measured once. Ordering cells according to minimal differences in expression patterns and assuming that differentiation occurs by a sequence of irreversible steps, yields unidirectional, eventually branching Markov chains with a single source node. In an alternative approach, we used multi-nucleate cells to follow gene expression taking true time series. Assembling state machines, each made from single-cell trajectories, gives a network of highly structured Markov chains of states with different source and sink nodes including cycles, revealing essential information on the dynamics of regulatory events. We argue that the obtained networks depict aspects of the Waddington landscape of cell differentiation and characterize them as reachability graphs that provide the basis for the reconstruction of the underlying gene regulatory network.
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Affiliation(s)
- Anna Pretschner
- Magdeburg Centre for Systems Biology and Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Sophie Pabel
- Magdeburg Centre for Systems Biology and Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Markus Haas
- Magdeburg Centre for Systems Biology and Institute of Biology, Otto von Guericke University, Magdeburg, Germany
| | - Monika Heiner
- Computer Science Institute, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Wolfgang Marwan
- Magdeburg Centre for Systems Biology and Institute of Biology, Otto von Guericke University, Magdeburg, Germany
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49
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Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. Nat Immunol 2021; 22:1577-1589. [PMID: 34811546 PMCID: PMC8642243 DOI: 10.1038/s41590-021-01059-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023]
Abstract
Single-cell genomics technology has transformed our understanding of complex cellular systems. However, excessive cost and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high-content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all main hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables the functional capacities of precisely mapped cell states to be measured at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.
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50
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Olson OC, Kang YA, Passegué E. Normal Hematopoiesis Is a Balancing Act of Self-Renewal and Regeneration. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a035519. [PMID: 31988205 DOI: 10.1101/cshperspect.a035519] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The hematopoietic system is highly organized to maintain its functional integrity and to meet lifelong organismal demands. Hematopoietic stem cells (HSCs) must balance self-renewal with differentiation and the regeneration of the blood system. It is a complex balancing act between these competing HSC functions. Although highly quiescent at steady state, HSCs become activated in response to inflammatory cytokines and regenerative challenges. This activation phase leads to many intrinsic stresses such as replicative, metabolic, and oxidative stress, which can cause functional decline, impaired self-renewal, and exhaustion of HSCs. To cope with these insults, HSCs use both built-in and emergency-triggered stress-response mechanisms to maintain homeostasis and to defend against disease development. In this review, we discuss how the hematopoietic system operates in steady state and stress conditions, what strategies are used to maintain functional integrity, and how deregulation in the balance between self-renewal and regeneration can drive malignant transformation.
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Affiliation(s)
- Oakley C Olson
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Yoon-A Kang
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York 10032, USA
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University Irving Medical Center, New York, New York 10032, USA
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