1
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Shiomi A, Kaneko T, Nishikawa K, Tsuchida A, Isoshima T, Sato M, Toyooka K, Doi K, Nishikii H, Shintaku H. High-throughput mechanical phenotyping and transcriptomics of single cells. Nat Commun 2024; 15:3812. [PMID: 38760380 PMCID: PMC11101642 DOI: 10.1038/s41467-024-48088-5] [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: 07/11/2023] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
The molecular system regulating cellular mechanical properties remains unexplored at single-cell resolution mainly due to a limited ability to combine mechanophenotyping with unbiased transcriptional screening. Here, we describe an electroporation-based lipid-bilayer assay for cell surface tension and transcriptomics (ELASTomics), a method in which oligonucleotide-labelled macromolecules are imported into cells via nanopore electroporation to assess the mechanical state of the cell surface and are enumerated by sequencing. ELASTomics can be readily integrated with existing single-cell sequencing approaches and enables the joint study of cell surface mechanics and underlying transcriptional regulation at an unprecedented resolution. We validate ELASTomics via analysis of cancer cell lines from various malignancies and show that the method can accurately identify cell types and assess cell surface tension. ELASTomics enables exploration of the relationships between cell surface tension, surface proteins, and transcripts along cell lineages differentiating from the haematopoietic progenitor cells of mice. We study the surface mechanics of cellular senescence and demonstrate that RRAD regulates cell surface tension in senescent TIG-1 cells. ELASTomics provides a unique opportunity to profile the mechanical and molecular phenotypes of single cells and can dissect the interplay among these in a range of biological contexts.
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Affiliation(s)
- Akifumi Shiomi
- Cluster for Pioneering Research, RIKEN, Saitama, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | | | | | | | | | - Mayuko Sato
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | | | - Kentaro Doi
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi, Japan
| | | | - Hirofumi Shintaku
- Cluster for Pioneering Research, RIKEN, Saitama, Japan.
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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2
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Zhang Q, Olofzon R, Konturek-Ciesla A, Yuan O, Bryder D. Ex vivo expansion potential of murine hematopoietic stem cells is a rare property only partially predicted by phenotype. eLife 2024; 12:RP91826. [PMID: 38446538 PMCID: PMC10942641 DOI: 10.7554/elife.91826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After 3 weeks of culture, only 0.1% of cells exhibited the input HSC phenotype, but these accounted for almost all functional long-term HSC activity. Input HSCs displayed varying potential for ex vivo self-renewal, with alternative outcomes revealed by single-cell multimodal RNA and ATAC sequencing profiling. While most HSC progeny offered only transient in vivo reconstitution, these cells efficiently rescued mice from lethal myeloablation. The amplification of functional HSC activity allowed for long-term multilineage engraftment in unconditioned hosts that associated with a return of HSCs to quiescence. Thereby, our findings identify several key considerations for ex vivo HSC expansion, with major implications also for assessment of normal HSC activity.
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Affiliation(s)
- Qinyu Zhang
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund UniversityLundSweden
| | - Rasmus Olofzon
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund UniversityLundSweden
| | - Anna Konturek-Ciesla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund UniversityLundSweden
| | - Ouyang Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund UniversityLundSweden
| | - David Bryder
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund UniversityLundSweden
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3
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Meaker GA, Wilkinson AC. Ex vivo hematopoietic stem cell expansion technologies: recent progress, applications, and open questions. Exp Hematol 2024; 130:104136. [PMID: 38072133 DOI: 10.1016/j.exphem.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 12/27/2023]
Abstract
Hematopoietic stem cells (HSCs) are a rare but potent cell type that support life-long hematopoiesis and stably regenerate the entire blood and immune system following transplantation. HSC transplantation represents a mainstay treatment for various diseases of the blood and immune systems. The ex vivo expansion and manipulation of HSCs therefore represents an important approach to ask biological questions in experimental hematology and to help improve clinical HSC transplantation therapies. However, it has remained challenging to expand transplantable HSCs ex vivo. This review summarizes recent progress in ex vivo HSC expansion technologies and their applications to biological and clinical problems and discusses current questions in the field.
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Affiliation(s)
- Grace A Meaker
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adam C Wilkinson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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4
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Becker HJ, Yamazaki S. Understanding genetic heterogeneity in gene-edited hematopoietic stem cell products. Exp Hematol 2024; 129:104133. [PMID: 38036097 DOI: 10.1016/j.exphem.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
Abstract
CRISPR/Cas gene editing has transformed genetic research and is poised to drive the next generation of gene therapies targeting hematopoietic stem cells (HSCs). However, the installation of the "desired" edit is most often only achieved in a minor subset of alleles. The array of cellular pathways triggered by gene editing tools produces a broad spectrum of "undesired" editing outcomes, including short insertions and deletions (indels) and chromosome rearrangements, leading to considerable genetic heterogeneity in gene-edited HSC populations. This heterogeneity may undermine the effect of the genetic intervention since only a subset of cells will carry the intended modification. Also, undesired mutations represent a potential safety concern as gene editing advances toward broader clinical use. Here, we will review the different sources of "undesired" edits and will discuss strategies for their mitigation and control.
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Affiliation(s)
- Hans Jiro Becker
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Satoshi Yamazaki
- Laboratory for Stem Cell Therapy, Faculty of Medicine, Tsukuba University, Tsukuba, Japan; Division of Cell Regulation, Center of Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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5
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Li Z, Su M, Xie X, Wang P, Bi H, Li E, Ren K, Dong L, Lv Z, Ma X, Liu Y, Zhao B, Peng Y, Liu J, Liu L, Yang J, Ji P, Mei Y. mDia formins form hetero-oligomers and cooperatively maintain murine hematopoiesis. PLoS Genet 2023; 19:e1011084. [PMID: 38157491 PMCID: PMC10756686 DOI: 10.1371/journal.pgen.1011084] [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: 05/12/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
mDia formin proteins regulate the dynamics and organization of the cytoskeleton through their linear actin nucleation and polymerization activities. We previously showed that mDia1 deficiency leads to aberrant innate immune activation and induces myelodysplasia in a mouse model, and mDia2 regulates enucleation and cytokinesis of erythroblasts and the engraftment of hematopoietic stem and progenitor cells (HSPCs). However, whether and how mDia formins interplay and regulate hematopoiesis under physiological and stress conditions remains unknown. Here, we found that both mDia1 and mDia2 are required for HSPC regeneration under stress, such as serial plating, aging, and reconstitution after myeloid ablation. We showed that mDia1 and mDia2 form hetero-oligomers through the interactions between mDia1 GBD-DID and mDia2 DAD domains. Double knockout of mDia1 and mDia2 in hematopoietic cells synergistically impaired the filamentous actin network and serum response factor-involved transcriptional signaling, which led to declined HSPCs, severe anemia, and significant mortality in neonates and newborn mice. Our data demonstrate the potential roles of mDia hetero-oligomerization and their non-rodent functions in the regulation of HSPCs activity and orchestration of hematopoiesis.
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Affiliation(s)
- Zhaofeng Li
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Meng Su
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Xinshu Xie
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Pan Wang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Honghao Bi
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Ermin Li
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Kehan Ren
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Lili Dong
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Zhiyi Lv
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Xuezhen Ma
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Yijie Liu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Baobing Zhao
- Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yuanliang Peng
- Department of Hematology, the Second Xiangya Hospital; Molecular Biology Research Center, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University; Changsha, China
| | - Jing Liu
- Department of Hematology, the Second Xiangya Hospital; Molecular Biology Research Center, School of Life Sciences; Hunan Province Key Laboratory of Basic and Applied Hematology, Central South University; Changsha, China
| | - Lu Liu
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
| | - Jing Yang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Peng Ji
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Yang Mei
- Hunan Provincial Key Laboratory of Animal Model and Molecular Medicine, Hunan University, Changsha, China
- School of Biomedical Sciences, Hunan University, Changsha, China
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6
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Rubio-Lara JA, Igarashi KJ, Sood S, Johansson A, Sommerkamp P, Yamashita M, Lin DS. Expanding hematopoietic stem cell ex vivo: recent advances and technical considerations. Exp Hematol 2023; 125-126:6-15. [PMID: 37543237 DOI: 10.1016/j.exphem.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/07/2023]
Abstract
Hematopoietic stem cells (HSCs) are the most primitive cell type in the hematopoietic hierarchy, which are responsible for sustaining the lifelong production of mature blood and immune cells. Due to their superior long-term regenerative capacity, HSC therapies such as stem cell transplantation have been used in a broad range of hematologic disorders. However, the rarity of this population in vivo considerably limits its clinical applications and large-scale analyses such as screening and safety studies. Therefore, ex vivo culture methods that allow long-term expansion and maintenance of functional HSCs are instrumental in overcoming the difficulties in studying HSC biology and improving HSC therapies. In this perspective, we discuss recent advances and technical considerations for three ex vivo HSC expansion methods including 1) polyvinyl alcohol-based HSC expansion, 2) mesenchymal stromal cell-HSC co-culture, and 3) two-/three-dimensional hydrogel HSC culture. This review summarizes the presentations and discussions from the 2022 International Society for Experimental Hematology (ISEH) Annual Meeting New Investigator Technology Session.
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Affiliation(s)
| | - Kyomi J Igarashi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Shubhankar Sood
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Inflammatory Stress in Stem Cells, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alban Johansson
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Pia Sommerkamp
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Masayuki Yamashita
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Dawn S Lin
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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7
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Tavakoli S, Garcia V, Gähwiler E, Adatto I, Rangan A, Messemer KA, Kakhki SA, Yang S, Chan VS, Manning ME, Fotowat H, Zhou Y, Wagers AJ, Zon LI. Transplantation-based screen identifies inducers of muscle progenitor cell engraftment across vertebrate species. Cell Rep 2023; 42:112365. [PMID: 37018075 PMCID: PMC10548355 DOI: 10.1016/j.celrep.2023.112365] [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: 10/21/2022] [Revised: 01/06/2023] [Accepted: 03/22/2023] [Indexed: 04/06/2023] Open
Abstract
Stem cell transplantation presents a potentially curative strategy for genetic disorders of skeletal muscle, but this approach is limited by the deleterious effects of cell expansion in vitro and consequent poor engraftment efficiency. In an effort to overcome this limitation, we sought to identify molecular signals that enhance the myogenic activity of cultured muscle progenitors. Here, we report the development and application of a cross-species small-molecule screening platform employing zebrafish and mice, which enables rapid, direct evaluation of the effects of chemical compounds on the engraftment of transplanted muscle precursor cells. Using this system, we screened a library of bioactive lipids to discriminate those that could increase myogenic engraftment in vivo in zebrafish and mice. This effort identified two lipids, lysophosphatidic acid and niflumic acid, both linked to the activation of intracellular calcium-ion flux, which showed conserved, dose-dependent, and synergistic effects in promoting muscle engraftment across these vertebrate species.
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Affiliation(s)
- Sahar Tavakoli
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vivian Garcia
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Eric Gähwiler
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Institute for Regenerative Medicine, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Isaac Adatto
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Apoorva Rangan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Stanford Medicine, Stanford University, Stanford, CA 94305, USA
| | - Kathleen A Messemer
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sara Ashrafi Kakhki
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Victoria S Chan
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Margot E Manning
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Haleh Fotowat
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA.
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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8
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Charlesworth CT, Hsu I, Wilkinson AC, Nakauchi H. Immunological barriers to haematopoietic stem cell gene therapy. Nat Rev Immunol 2022; 22:719-733. [PMID: 35301483 PMCID: PMC8929255 DOI: 10.1038/s41577-022-00698-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2022] [Indexed: 12/12/2022]
Abstract
Cell and gene therapies using haematopoietic stem cells (HSCs) epitomize the transformative potential of regenerative medicine. Recent clinical successes for gene therapies involving autologous HSC transplantation (HSCT) demonstrate the potential of genetic engineering in this stem cell type for curing disease. With recent advances in CRISPR gene-editing technologies, methodologies for the ex vivo expansion of HSCs and non-genotoxic conditioning protocols, the range of clinical indications for HSC-based gene therapies is expected to significantly expand. However, substantial immunological challenges need to be overcome. These include pre-existing immunity to gene-therapy reagents, immune responses to neoantigens introduced into HSCs by genetic engineering, and unique challenges associated with next-generation and off-the-shelf HSC products. By synthesizing these factors in this Review, we hope to encourage more research to address the immunological issues associated with current and next-generation HSC-based gene therapies to help realize the full potential of this field.
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Affiliation(s)
- Carsten T Charlesworth
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian Hsu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adam C Wilkinson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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9
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A cardioimmunologist's toolkit: genetic tools to dissect immune cells in cardiac disease. Nat Rev Cardiol 2022; 19:395-413. [PMID: 35523863 DOI: 10.1038/s41569-022-00701-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
Cardioimmunology is a field that encompasses the immune cells and pathways that modulate cardiac function in homeostasis and regulate the temporal balance between tissue injury and repair in disease. Over the past two decades, genetic fate mapping and high-dimensional sequencing techniques have defined increasing functional heterogeneity of innate and adaptive immune cell populations in the heart and other organs, revealing a complexity not previously appreciated and challenging established frameworks for the immune system. Given these rapid advances, understanding how to use these tools has become crucial. However, cardiovascular biologists without immunological expertise might not be aware of the strengths and caveats of immune-related tools and how they can be applied to examine the pathogenesis of myocardial diseases. In this Review, we guide readers through case-based examples to demonstrate how tool selection can affect data quality and interpretation and we provide critical analysis of the experimental tools that are currently available, focusing on their use in models of ischaemic heart injury and heart failure. The goal is to increase the use of relevant immunological tools and strategies among cardiovascular researchers to improve the precision, translatability and consistency of future studies of immune cells in cardiac disease.
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10
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Research Highlights. Transplantation 2021. [DOI: 10.1097/tp.0000000000003906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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