51
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Brandstadter JD, De Martin A, Lϋtge M, Ferreira A, Gaudette BT, Stanossek Y, Wang S, Gonzalez MV, Camiolo E, Wertheim G, Austin B, Allman D, Bagg A, Lim MS, Fajgenbaum DC, Aster JC, Ludewig B, Maillard I. A novel cryopreservation and biobanking strategy to study lymphoid tissue stromal cells in human disease. Eur J Immunol 2023; 53:e2250362. [PMID: 37366295 PMCID: PMC10529925 DOI: 10.1002/eji.202250362] [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: 12/29/2022] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
Nonhematopoietic lymph node stromal cells (LNSCs) regulate lymphocyte trafficking, survival, and function for key roles in host defense, autoimmunity, alloimmunity, and lymphoproliferative disorders. However, the study of LNSCs in human diseases is complicated by a dependence on viable lymphoid tissues, which are most often excised prior to establishment of a specific diagnosis. Here, we demonstrate that cryopreservation can be used to bank lymphoid tissue for the study of LNSCs in human disease. Using human tonsils and lymph nodes (LN), lymphoid tissue fragments were cryopreserved for subsequent enzymatic digestion and recovery of viable nonhematopoietic cells. Flow cytometry and single-cell transcriptomics identified comparable proportions of LN stromal cell types in fresh and cryopreserved tissue. Moreover, cryopreservation had little effect on transcriptional profiles, which showed significant overlap between tonsils and LN. The presence and spatial distribution of transcriptionally defined cell types were confirmed by in situ analyses. Our broadly applicable approach promises to greatly enable research into the roles of LNSCs in human disease.
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Affiliation(s)
- Joshua D Brandstadter
- Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angelina De Martin
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Mechthild Lϋtge
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Antonio Ferreira
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian T Gaudette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yves Stanossek
- Department of Otorhinolaryngology, Head and Neck Surgery, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Shumei Wang
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael V Gonzalez
- Center for Cytokine Storm Treatment and Laboratory, Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edward Camiolo
- Children’s Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, Philadelphia, PA, USA
| | - Gerald Wertheim
- Children’s Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, Philadelphia, PA, USA
| | - Bridget Austin
- Center for Cytokine Storm Treatment and Laboratory, Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan S Lim
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David C Fajgenbaum
- Center for Cytokine Storm Treatment and Laboratory, Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Burkhard Ludewig
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Ivan Maillard
- Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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52
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Mass E, Nimmerjahn F, Kierdorf K, Schlitzer A. Tissue-specific macrophages: how they develop and choreograph tissue biology. Nat Rev Immunol 2023; 23:563-579. [PMID: 36922638 PMCID: PMC10017071 DOI: 10.1038/s41577-023-00848-y] [Citation(s) in RCA: 80] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 03/17/2023]
Abstract
Macrophages are innate immune cells that form a 3D network in all our tissues, where they phagocytose dying cells and cell debris, immune complexes, bacteria and other waste products. Simultaneously, they produce growth factors and signalling molecules - such activities not only promote host protection in response to invading microorganisms but are also crucial for organ development and homeostasis. There is mounting evidence of macrophages orchestrating fundamental physiological processes, such as blood vessel formation, adipogenesis, metabolism and central and peripheral neuronal function. In parallel, novel methodologies have led to the characterization of tissue-specific macrophages, with distinct subpopulations of these cells showing different developmental trajectories, transcriptional programmes and life cycles. Here, we summarize our growing knowledge of macrophage diversity and how macrophage subsets orchestrate tissue development and function. We further interrelate macrophage ontogeny with their core functions across tissues, that is, the signalling events within the macrophage niche that may control organ functionality during development, homeostasis and ageing. Finally, we highlight the open questions that will need to be addressed by future studies to better understand the tissue-specific functions of distinct macrophage subsets.
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Affiliation(s)
- Elvira Mass
- Developmental Biology of the Immune System, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Falk Nimmerjahn
- Division of Genetics, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Katrin Kierdorf
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Centre for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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53
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Cho SJ, Oh JH, Baek J, Shin Y, Kim W, Ko J, Jun E, Lee D, Kim SH, Sohn I, Sung CO. Intercellular cross-talk through lineage-specific gap junction of cancer-associated fibroblasts related to stromal fibrosis and prognosis. Sci Rep 2023; 13:14230. [PMID: 37648762 PMCID: PMC10469165 DOI: 10.1038/s41598-023-40957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
Stromal fibrosis in cancer is usually associated with poor prognosis and chemotherapy resistance. It is thought to be caused by fibroblasts; however, the exact mechanism is not yet well understood. The study aimed to identify lineage-specific cancer-associated fibroblast (CAF) subgroup and their associations with extracellular matrix remodeling and clinical significances in various tumor types using single-cell and bulk RNA sequencing data. Through unsupervised clustering, six subclusters of CAFs were identified, including a cluster with exclusively high gap junction protein beta-2 (GJB2) expression. This cluster was named GJB2-positive CAF. It was found to be a unique subgroup of terminally differentiated CAFs associated with collagen gene expression and extracellular matrix remodeling. GJB2-positive CAFs showed higher communication frequency with vascular endothelial cells and cancer cells than GJB2-negative CAFs. Moreover, GJB2 was poorly expressed in normal tissues, indicating that its expression is dependent on interaction with other cells, including vascular endothelial cells and cancer cells. Finally, the study investigated the clinical significance of GJB2 signature score for GJB2-positive CAFs in cancer and found a correlation with poor prognosis. These results suggest that GJB2-positive CAF is a unique fibroblast subtype involved in extracellular matrix remodeling, with significant clinical implications in cancer.
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Affiliation(s)
- Seong Ju Cho
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Arontier Inc., Gangnam-Daero 241, Seocho-Gu, Seoul, Republic of Korea
| | - Ji-Hye Oh
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olymphic-Ro 43-Gil, Seoul, 05505, South Korea
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jaehoon Baek
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Arontier Inc., Gangnam-Daero 241, Seocho-Gu, Seoul, Republic of Korea
| | - Yunsu Shin
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Arontier Inc., Gangnam-Daero 241, Seocho-Gu, Seoul, Republic of Korea
| | - Wonkyung Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olymphic-Ro 43-Gil, Seoul, 05505, South Korea
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Junsu Ko
- Arontier Inc., Gangnam-Daero 241, Seocho-Gu, Seoul, Republic of Korea
| | - Eunsung Jun
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Ulsan University College of Medicine and Asan Medical Center, Seoul, Korea
| | - Dakeun Lee
- Department of Pathology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Seok-Hyung Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea.
| | - Insuk Sohn
- Arontier Inc., Gangnam-Daero 241, Seocho-Gu, Seoul, Republic of Korea.
| | - Chang Ohk Sung
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olymphic-Ro 43-Gil, Seoul, 05505, South Korea.
- Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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54
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Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Londoño MQ, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar M, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M. Yolk sac cell atlas reveals multiorgan functions during human early development. Science 2023; 381:eadd7564. [PMID: 37590359 PMCID: PMC7614978 DOI: 10.1126/science.add7564] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/03/2023] [Indexed: 08/19/2023]
Abstract
The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds.
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Affiliation(s)
- Issac Goh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Rachel A. Botting
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Antony Rose
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Simone Webb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Emily Stephenson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Michael Mather
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nicole Mende
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus,
CD2 0QH, UK
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Dave Horsfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Daniela Basurto-Lozada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Victoria Rook
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Mai-Linh Ton
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Daniel Keitley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Zoology, University of Cambridge, Cambridge UK
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - M.S. Vijayabaskar
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Laure Gambardella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kile Green
- Translational and Clinical Research Institute, Newcastle University,
NE2 4HH, UK
| | - Stephane Ballereau
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Valentina Lorenzi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Clara Alsinet
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Centre Nacional d’Analisi Genomica-Centre de Regulacio
Genomica (CNAG-CRG), Barcelona Institute of Science and Technology (BIST),
Barcelona, Spain
| | - Bayanne Olabi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Mohi Miah
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Chloe Admane
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Meghan Acres
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Thomas Ness
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Rowen Coulthard
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Sarah J. Kinston
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Jong-eun Park
- Korea Advanced Institute of Science and Technology, Daejeon, South
Korea
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - John Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- EMBL-EBI, Wellcome Genome Campus, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Marella de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of
Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS,
UK
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center,
Rochester, 14642, NY, USA
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge,
UK
| | - Elisa Laurenti
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Nicola K. Wilson
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, OX3 9DS, UK
| | - Laura Jardine
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department
of Physics, University of Cambridge, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research
Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP,
UK
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55
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Calvanese V, Mikkola HKA. The genesis of human hematopoietic stem cells. Blood 2023; 142:519-532. [PMID: 37339578 PMCID: PMC10447622 DOI: 10.1182/blood.2022017934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/27/2023] [Accepted: 05/13/2023] [Indexed: 06/22/2023] Open
Abstract
Developmental hematopoiesis consists of multiple, partially overlapping hematopoietic waves that generate the differentiated blood cells required for embryonic development while establishing a pool of undifferentiated hematopoietic stem cells (HSCs) for postnatal life. This multilayered design in which active hematopoiesis migrates through diverse extra and intraembryonic tissues has made it difficult to define a roadmap for generating HSCs vs non-self-renewing progenitors, especially in humans. Recent single-cell studies have helped in identifying the rare human HSCs at stages when functional assays are unsuitable for distinguishing them from progenitors. This approach has made it possible to track the origin of human HSCs to the unique type of arterial endothelium in the aorta-gonad-mesonephros region and document novel benchmarks for HSC migration and maturation in the conceptus. These studies have delivered new insights into the intricate process of HSC generation and provided tools to inform the in vitro efforts to replicate the physiological developmental journey from pluripotent stem cells via distinct mesodermal and endothelial intermediates to HSCs.
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Affiliation(s)
- Vincenzo Calvanese
- Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
| | - Hanna K. A. Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA
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56
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Abstract
Organismal aging exhibits wide-ranging hallmarks in divergent cell types across tissues, organs, and systems. The advancement of single-cell technologies and generation of rich datasets have afforded the scientific community the opportunity to decode these hallmarks of aging at an unprecedented scope and resolution. In this review, we describe the technological advancements and bioinformatic methodologies enabling data interpretation at the cellular level. Then, we outline the application of such technologies for decoding aging hallmarks and potential intervention targets and summarize common themes and context-specific molecular features in representative organ systems across the body. Finally, we provide a brief summary of available databases relevant for aging research and present an outlook on the opportunities in this emerging field.
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Affiliation(s)
- Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Xu Chi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
| | - Yusheng Cai
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Zhejun Ji
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jie Ren
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; ,
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China;
- University of Chinese Academy of Sciences, Beijing, China
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57
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De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, Kohler TN, Amadei G, Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun 2023; 14:4788. [PMID: 37553326 PMCID: PMC10409775 DOI: 10.1038/s41467-023-40322-w] [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: 01/05/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023] Open
Abstract
Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.
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Affiliation(s)
- Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - David B Morse
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte E Handford
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, USA
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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58
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Lagattuta KA, Nathan A, Rumker L, Birnbaum ME, Raychaudhuri S. The T cell receptor sequence influences the likelihood of T cell memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549939. [PMID: 37502994 PMCID: PMC10370203 DOI: 10.1101/2023.07.20.549939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
T cell differentiation depends on activation through the T cell receptor (TCR), whose amino acid sequence varies cell to cell. Particular TCR amino acid sequences nearly guarantee Mucosal-Associated Invariant T (MAIT) and Natural Killer T (NKT) cell fates. To comprehensively define how TCR amino acids affects all T cell fates, we analyze the paired αβTCR sequence and transcriptome of 819,772 single cells. We find that hydrophobic CDR3 residues promote regulatory T cell transcriptional states in both the CD8 and CD4 lineages. Most strikingly, we find a set of TCR sequence features, concentrated in CDR2α, that promotes positive selection in the thymus as well as transition from naïve to memory in the periphery. Even among T cells that recognize the same antigen, these TCR sequence features help to explain which T cells form immunological memory, which is essential for effective pathogen response.
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Affiliation(s)
- Kaitlyn A. Lagattuta
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael E. Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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59
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Zhang Y, Fan A, Li Y, Liu Z, Yu L, Guo J, Hou J, Li X, Chen W. Single-cell RNA sequencing reveals that HSD17B2 in cancer-associated fibroblasts promotes the development and progression of castration-resistant prostate cancer. Cancer Lett 2023; 566:216244. [PMID: 37244445 DOI: 10.1016/j.canlet.2023.216244] [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: 02/11/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
Castration-resistant prostate cancer (CRPC) responds poorly to existing therapy and appears as the lethal consequence of prostate cancer (PCa) progression. The tumour microenvironment (TME) has been thought to play a crucial role in CRPC progression. Here, we conducted single-cell RNA sequencing analysis on two CRPC and two hormone-sensitive prostate cancer (HSPC) samples to reveal potential leading roles in castration resistance. We described the single-cell transcriptional landscape of PCa. Higher cancer heterogeneity was explored in CRPC, with stronger cell cycling status and heavier copy number variant burden of luminal cells. Cancer-associated fibroblasts (CAFs), which are one of the most critical components of TME, demonstrated unique expression and cell-cell communication features in CRPC. A CAFs subtype with high expression of HSD17B2 in CRPC was identified with inflammatory features. HSD17B2 catalyses the conversion of testosterone and dihydrotestosterone to their less active forms, which was associated with steroid hormone metabolism in PCa tumour cells. However, the characteristics of HSD17B2 in PCa fibroblasts remained unknown. We found that HSD17B2 knockdown in CRPC-CAFs could inhibit migration, invasion, and castration resistance of PCa cells in vitro. Further study showed that HSD17B2 could regulate CAFs functions and promote PCa migration through the AR/ITGBL1 axis. Overall, our study revealed the important role of CAFs in the formation of CRPC. HSD17B2 in CAFs regulated AR activation and subsequent ITGBL1 secretion to promote the malignant behaviour of PCa cells. HSD17B2 in CAFs could serve as a promising therapeutic target for CRPC.
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Affiliation(s)
- Yunyan Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Aoyu Fan
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunpeng Li
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhuolin Liu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Liu Yu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Hou
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaobo Li
- School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Wei Chen
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, China.
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60
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Strobl J, Haniffa M. Functional heterogeneity of human skin-resident memory T cells in health and disease. Immunol Rev 2023; 316:104-119. [PMID: 37144705 PMCID: PMC10952320 DOI: 10.1111/imr.13213] [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: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The human skin is populated by a diverse pool of memory T cells, which can act rapidly in response to pathogens and cancer antigens. Tissue-resident memory T cells (TRM ) have been implicated in range of allergic, autoimmune and inflammatory skin diseases. Clonal expansion of cells with TRM properties is also known to contribute to cutaneous T-cell lymphoma. Here, we review the heterogeneous phenotypes, transcriptional programs, and effector functions of skin TRM . We summarize recent studies on TRM formation, longevity, plasticity, and retrograde migration and contextualize the findings to skin TRM and their role in maintaining skin homeostasis and altered functions in skin disease.
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Affiliation(s)
- Johanna Strobl
- Department of DermatologyMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular MedicineViennaAustria
| | - Muzlifah Haniffa
- Wellcome Sanger InstituteCambridgeUK
- Department of Dermatology and NIHR Newcastle Biomedical Research CentreNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUK
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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61
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Ke H, Li Z, Li P, Ye S, Huang J, Hu T, Zhang C, Yuan M, Chen Y, Wu X, Lan P. Dynamic heterogeneity of colorectal cancer during progression revealed clinical risk-associated cell types and regulations in single-cell resolution and spatial context. Gastroenterol Rep (Oxf) 2023; 11:goad034. [PMID: 37360193 PMCID: PMC10290555 DOI: 10.1093/gastro/goad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 06/28/2023] Open
Abstract
Background Tumor heterogeneity is contributed by tumor cells and the microenvironment. Dynamics of tumor heterogeneity during colorectal cancer (CRC) progression have not been elucidated. Methods Eight single-cell RNA sequencing (scRNA-seq) data sets of CRC were included. Milo was utilized to reveal the differential abundance of cell clusters during progression. The differentiation trajectory was imputed by using the Palantir algorithm and metabolic states were assessed by using scMetabolism. Three spatial transcription sequencing (ST-seq) data sets of CRC were used to validate cell-type abundances and colocalization. Cancer-associated regulatory hubs were defined as communication networks affecting tumor biological behaviors. Finally, quantitative reverse transcription polymerase chain reaction and immunohistochemistry staining were performed for validation. Results TM4SF1+, SOX4+, and MKI67+ tumor cells; CXCL12+ cancer-associated fibroblasts; CD4+ resident memory T cells; Treg; IgA+ plasma cells; and several myeloid subsets were enriched in stage IV CRC, most of which were associated with overall survival of patients. Trajectory analysis indicated that tumor cells from patients with advanced-stage CRC were less differentiated, when metabolic heterogeneity showed a highest metabolic signature in terminal states of stromal cells, T cells, and myeloid cells. Moreover, ST-seq validated cell-type abundance in a spatial context and also revealed the correlation of immune infiltration between tertiary lymphoid structures and tumors followed by validation in our cohort. Importantly, analysis of cancer-associated regulatory hubs revealed a cascade of activated pathways including leukocyte apoptotic process, MAPK pathway, myeloid leukocyte differentiation, and angiogenesis during CRC progression. Conclusions Tumor heterogeneity was dynamic during progression, with the enrichment of immunosuppressive Treg, myeloid cells, and fibrotic cells. The differential state of tumor cells was associated with cancer staging. Assessment of cancer-associated regulatory hubs suggested impaired antitumor immunity and increased metastatic ability during CRC progression.
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Affiliation(s)
| | | | | | - Shubiao Ye
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Junfeng Huang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Tuo Hu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Chi Zhang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Ming Yuan
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Yuan Chen
- School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, P. R. China
| | - Xianrui Wu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology ,The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Ping Lan
- Corresponding author. Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, No. 26 Yuancun Erheng Road, Guangzhou, Guangdong 510655, China. Tel: +86-20-38254009;
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62
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Combes AJ, Samad B, Krummel MF. Defining and using immune archetypes to classify and treat cancer. Nat Rev Cancer 2023:10.1038/s41568-023-00578-2. [PMID: 37277485 DOI: 10.1038/s41568-023-00578-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2023] [Indexed: 06/07/2023]
Abstract
Tumours are surrounded by a host immune system that can suppress or promote tumour growth. The tumour microenvironment (TME) has often been framed as a singular entity, suggesting a single type of immune state that is defective and in need of therapeutic intervention. By contrast, the past few years have highlighted a plurality of immune states that can surround tumours. In this Perspective, we suggest that different TMEs have 'archetypal' qualities across all cancers - characteristic and repeating collections of cells and gene-expression profiles at the level of the bulk tumour. We discuss many studies that together support a view that tumours typically draw from a finite number (around 12) of 'dominant' immune archetypes. In considering the likely evolutionary origin and roles of these archetypes, their associated TMEs can be predicted to have specific vulnerabilities that can be leveraged as targets for cancer treatment with expected and addressable adverse effects for patients.
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Affiliation(s)
- Alexis J Combes
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA.
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Bushra Samad
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA.
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA.
- UCSF Immunoprofiler Initiative, University of California San Francisco, San Francisco, CA, USA.
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63
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Yang F, Nourse C, Helgason GV, Kirschner K. Unraveling Heterogeneity in the Aging Hematopoietic Stem Cell Compartment: An Insight From Single-cell Approaches. Hemasphere 2023; 7:e895. [PMID: 37304939 PMCID: PMC10256339 DOI: 10.1097/hs9.0000000000000895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/18/2023] [Indexed: 06/13/2023] Open
Abstract
Specific cell types and, therefore, organs respond differently during aging. This is also true for the hematopoietic system, where it has been demonstrated that hematopoietic stem cells alter a variety of features, such as their metabolism, and accumulate DNA damage, which can lead to clonal outgrowth over time. In addition, profound changes in the bone marrow microenvironment upon aging lead to senescence in certain cell types such as mesenchymal stem cells and result in increased inflammation. This heterogeneity makes it difficult to pinpoint the molecular drivers of organismal aging gained from bulk approaches, such as RNA sequencing. A better understanding of the heterogeneity underlying the aging process in the hematopoietic compartment is, therefore, needed. With the advances of single-cell technologies in recent years, it is now possible to address fundamental questions of aging. In this review, we discuss how single-cell approaches can and indeed are already being used to understand changes observed during aging in the hematopoietic compartment. We will touch on established and novel methods for flow cytometric detection, single-cell culture approaches, and single-cell omics.
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Affiliation(s)
- Fei Yang
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - Craig Nourse
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
| | - G. Vignir Helgason
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kristina Kirschner
- School of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
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64
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Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, Bécavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-López C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Bossé Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med 2023; 29:1563-1577. [PMID: 37291214 PMCID: PMC10287567 DOI: 10.1038/s41591-023-02327-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 03/30/2023] [Indexed: 06/10/2023]
Abstract
Single-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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Grants
- R01 HL153375 NHLBI NIH HHS
- R01 HL127349 NHLBI NIH HHS
- U54 HL165443 NHLBI NIH HHS
- P01 HL107202 NHLBI NIH HHS
- U01 HL148856 NHLBI NIH HHS
- R21 HL156124 NHLBI NIH HHS
- U54 AG075931 NIA NIH HHS
- Wellcome Trust
- R01 HL146557 NHLBI NIH HHS
- R01 HL123766 NHLBI NIH HHS
- U01 HL148861 NHLBI NIH HHS
- R01 HL141852 NHLBI NIH HHS
- R01 ES034350 NIEHS NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 HL126176 NHLBI NIH HHS
- R21 HL161760 NHLBI NIH HHS
- R01 HL145372 NHLBI NIH HHS
- P01 AG049665 NIA NIH HHS
- K12 HD105271 NICHD NIH HHS
- U19 AI135964 NIAID NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 HL142568 NHLBI NIH HHS
- R01 HL153312 NHLBI NIH HHS
- U54 AG079754 NIA NIH HHS
- R56 HL157632 NHLBI NIH HHS
- R01 HL158139 NHLBI NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL153045 NHLBI NIH HHS
- U54 HL145608 NHLBI NIH HHS
- P50 AR060780 NIAMS NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL146519 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R01 HL068702 NHLBI NIH HHS
- U01 HL145567 NHLBI NIH HHS
- P01 HL132821 NHLBI NIH HHS
- MR/R015635/1 Medical Research Council
- R01 MD010443 NIMHD NIH HHS
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” NIH 1U54HL145608-01 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- ESPOD fellowship of EMBL-EBI and Sanger Institute
- 3IA Cote d’Azur PhD program
- The Ministry of Economic Affairs and Climate Policy by means of the PPP
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- Joachim Herz Stiftung (Joachim Herz Foundation)
- P50 AR060780-06A1
- University College London, Birkbeck MRC Doctoral Training Programme
- Jikei University School of Medicine (Jikei University)
- 5R01HL14254903, 4UH3CA25513503
- R01HL127349, R01HL141852, U01HL145567 and CZI
- MRC Clinician Scientist Fellowship (MR/W00111X/1)
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” 2R01HL068702
- R01 HL135156, R01 MD010443, R01 HL128439, P01 HL132821, P01 HL107202, R01 HL117004, and DOD Grant W81WH-16-2-0018
- HL142568 and HL14507 from the NHLBI
- Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”, 2R01HL068702
- Wellcome (WT211276/Z/18/Z) Sanger core grant WT206194 CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- R21HL156124, R56HL157632, and R21HL161760
- CZI, 5U01HL148856
- CZI, 5U01HL148856, R01 HL153045
- U.S. Department of Defense (United States Department of Defense)
- The National Institute of Health R01HL145372
- Fondation pour la Recherche Médicale (Foundation for Medical Research in France)
- Conseil Départemental des Alpes Maritimes
- Inserm Cross-cutting Scientific Program HuDeCA 2018, ANR SAHARRA (ANR-19-CE14–0027), ANR-19-P3IA-0002–3IA, the National Infrastructure France Génomique (ANR-10-INBS-09-03), PPIA 4D-OMICS (21-ESRE-0052), and the Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0”.
- Wellcome Trust (Wellcome)
- Sanger core grant WT206194 Chan Zuckerberg Initiative, LLC Seed Network grant (CZF2019-002438) “Lung Cell Atlas 1.0” CZIF2022-007488 from the Chan Zuckerberg Initiative Foundation
- Doris Duke Charitable Foundation (DDCF)
- The National Institute of Health R01HL145372 Department of Defense W81XWH-19-1-0416
- The National Institute of Health R01HL146557 and R01HL153375 and funds from Chan Zuckerberg Initiative - Human Lung Cell Atlas-pilot award
- 1U54HL145608-01
- CZI Deep Visual Proteomics
- 1U54HL145608-01, U01HL148861-03
- 1) the Chan Zuckerberg Initiative, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”; 2) R01 HL153312; 3) U19 AI135964; 4) P01 AG049665
- Netherlands Lung Foundation project nos. 5.1.14.020 and 4.1.18.226, LLC Seed Network grant CZF2019-002438 “Lung Cell Atlas 1.0”
- grant number 2019-002438 from the Chan Zuckerberg Foundation, by the Helmholtz Association’s Initiative and Networking Fund through Helmholtz AI [ZT-I-PF-5-01] and by the Bavarian Ministry of Science and the Arts in the framework of the Bavarian Research Association “ForInter” (Interaction of human brain cells)
- 1 U01 HL14555-01, R01 HL123766-04
- NIH U54 AG075931, 5R01 HL146519
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Affiliation(s)
- Lisa Sikkema
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ciro Ramírez-Suástegui
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Daniel C Strobl
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Tessa E Gillett
- Experimental Pulmonary and Inflammatory Research, Department of Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Luke Zappia
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Department of Mathematics, Technical University of Munich, Garching, Germany
| | | | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Laure-Emmanuelle Zaragosi
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Yuge Ji
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Meshal Ansari
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Marie-Jeanne Arguel
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Leonie Apperloo
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Martin Banchero
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Christophe Bécavin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
| | - Marijn Berg
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Mei-I Chung
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Antoine Collin
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Aurore C A Gay
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Janine Gote-Schniering
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Baharak Hooshiar Kashani
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Kemal Inecik
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Theodore S Kapellos
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Tessa M Kole
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sylvie Leroy
- Pulmonology Department, Fédération Hospitalo-Universitaire OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France
| | - Christoph H Mayr
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | | | - Lance Peter
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Chase J Taylor
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Chuan Xu
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Linh T Bui
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Carlo De Donno
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Leander Dony
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry and International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- School of Life Sciences, Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Sydney, Australia
| | - Minzhe Guo
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, US
| | | | - Lukas Heumos
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | - Ni Huang
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Ignacio L Ibarra
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Preetish Kadur Lakshminarasimha Murthy
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois Chicago, Chicago, IL, USA
| | - Mohammad Lotfollahi
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carlos Talavera-López
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Klinikum der Lüdwig-Maximilians-Universität, Munich, Germany
| | - Kyle J Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kaylee B Worlock
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Tushar J Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mark A Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marko Z Nikolic
- Department of Respiratory Medicine, Division of Medicine, University College London, London, UK
| | - Joseph E Powell
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Jayaraj Rajagopal
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cellular and Tissue Genomics, Genentech, South San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dean Sheppard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Douglas P Shepherd
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Whitsett
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yan Xu
- Division of Neonatology and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and Centre National de la Recherche Scientifique, Valbonne, France
- 3IA Côte d'Azur, Nice, France
| | - Thu Elizabeth Duong
- Department of Pediatrics, Division of Respiratory Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christine S Falk
- Institute for Transplant Immunology, Hannover Medical School, Hannover, Germany
| | | | - Jonathan A Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Dana Pe'er
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany
| | | | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen and University of Bonn, Bonn, Germany
| | - Sara A Teichmann
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Malte D Luecken
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- Institute of Lung Health and Immunity (a member of the German Center for Lung Research) and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Center Munich, Munich, Germany.
| | - Fabian J Theis
- Department of Computational Health, Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
- Department of Mathematics, Technical University of Munich, Garching, Germany.
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Huang S, Wang X, Wang Y, Wang Y, Fang C, Wang Y, Chen S, Chen R, Lei T, Zhang Y, Xu X, Li Y. Deciphering and advancing CAR T-cell therapy with single-cell sequencing technologies. Mol Cancer 2023; 22:80. [PMID: 37149643 PMCID: PMC10163813 DOI: 10.1186/s12943-023-01783-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has made remarkable progress in cancer immunotherapy, but several challenges with unclear mechanisms hinder its wide clinical application. Single-cell sequencing technologies, with the powerful unbiased analysis of cellular heterogeneity and molecular patterns at unprecedented resolution, have greatly advanced our understanding of immunology and oncology. In this review, we summarize the recent applications of single-cell sequencing technologies in CAR T-cell therapy, including the biological characteristics, the latest mechanisms of clinical response and adverse events, promising strategies that contribute to the development of CAR T-cell therapy and CAR target selection. Generally, we propose a multi-omics research mode to guide potential future research on CAR T-cell therapy.
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Affiliation(s)
- Shengkang Huang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyu Wang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Wang
- The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yajing Wang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chenglong Fang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yazhuo Wang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- School of Rehabilitation Sciences, Southern Medical University, Guangzhou, China
| | - Sifei Chen
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Runkai Chen
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tao Lei
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yuchen Zhang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xinjie Xu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China.
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66
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Chia SL, Kapoor S, Carvalho C, Bajénoff M, Gentek R. Mast cell ontogeny: From fetal development to life-long health and disease. Immunol Rev 2023; 315:31-53. [PMID: 36752151 PMCID: PMC10952628 DOI: 10.1111/imr.13191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mast cells (MCs) are evolutionarily ancient innate immune cells with important roles in protective immunity against bacteria, parasites, and venomous animals. They can be found in most organs of the body, where they also contribute to normal tissue functioning, for example by engaging in crosstalk with nerves. Despite this, they are most widely known for their detrimental roles in allergy, anaphylaxis, and atopic disease. Just like macrophages, mast cells were conventionally thought to originate from the bone marrow. However, they are already present in fetal tissues before the onset of bone marrow hematopoiesis, questioning this dogma. In recent years, our view of myeloid cell ontogeny has been revised. We now know that the first mast cells originate from progenitors made in the extra-embryonic yolk sac, and later get supplemented with mast cells produced from subsequent waves of hematopoiesis. In most connective tissues, sizeable populations of fetal-derived mast cells persist into adulthood, where they self-maintain largely independently from the bone marrow. These developmental origins are highly reminiscent of macrophages, which are known to have critical functions in development. Mast cells too may thus support healthy development. Their fetal origins and longevity also make mast cells susceptible to genetic and environmental perturbations, which may render them pathological. Here, we review our current understanding of mast cell biology from a developmental perspective. We first summarize how mast cell populations are established from distinct hematopoietic progenitor waves, and how they are subsequently maintained throughout life. We then discuss what functions mast cells may normally have at early life stages, and how they may be co-opted to cause, worsen, or increase susceptibility to disease.
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Affiliation(s)
- Shin Li Chia
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Simran Kapoor
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Cyril Carvalho
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
| | - Marc Bajénoff
- Centre d'Immunologie de Marseille‐Luminy (CIML)MarseilleFrance
| | - Rebecca Gentek
- Institute for Regeneration and Repair, Centre for Inflammation Research & Centre for Reproductive HealthThe University of EdinburghEdinburghUK
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67
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Li Y, He M, Zhang W, Liu W, Xu H, Yang M, Zhang H, Liang H, Li W, Wu Z, Fu W, Xu S, Liu X, Fan S, Zhou L, Wang C, Zhang L, Li Y, Gu J, Yin J, Zhang Y, Xia Y, Mao X, Cheng T, Shi J, Du Y, Gao Y. Expansion of human megakaryocyte-biased hematopoietic stem cells by biomimetic Microniche. Nat Commun 2023; 14:2207. [PMID: 37072407 PMCID: PMC10113370 DOI: 10.1038/s41467-023-37954-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/04/2023] [Indexed: 04/20/2023] Open
Abstract
Limited numbers of available hematopoietic stem cells (HSCs) limit the widespread use of HSC-based therapies. Expansion systems for functional heterogenous HSCs remain to be optimized. Here, we present a convenient strategy for human HSC expansion based on a biomimetic Microniche. After demonstrating the expansion of HSC from different sources, we find that our Microniche-based system expands the therapeutically attractive megakaryocyte-biased HSC. We demonstrate scalable HSC expansion by applying this strategy in a stirred bioreactor. Moreover, we identify that the functional human megakaryocyte-biased HSCs are enriched in the CD34+CD38-CD45RA-CD90+CD49f lowCD62L-CD133+ subpopulation. Specifically, the expansion of megakaryocyte-biased HSCs is supported by a biomimetic niche-like microenvironment, which generates a suitable cytokine milieu and supplies the appropriate physical scaffolding. Thus, beyond clarifying the existence and immuno-phenotype of human megakaryocyte-biased HSC, our study demonstrates a flexible human HSC expansion strategy that could help realize the strong clinical promise of HSC-based therapies.
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Affiliation(s)
- Yinghui Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Mei He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wenshan Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Wei Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua-PKU Center for Life Sciences, Tsinghua University, 100084, Beijing, China
- Beijing CytoNiche Biotechnology Co. Ltd., 100195, Beijing, China
| | - Hui Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Ming Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Hexiao Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Haiwei Liang
- Department of Biomedical Engineering, School of Medicine, Tsinghua-PKU Center for Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Wenjing Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua-PKU Center for Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Zhaozhao Wu
- Department of Biomedical Engineering, School of Medicine, Tsinghua-PKU Center for Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Weichao Fu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Shiqi Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xiaolei Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Sibin Fan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Liwei Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Chaoqun Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Lele Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yafang Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jiali Gu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Jingjing Yin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yiran Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yonghui Xia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xuemei Mao
- Nankai Hospital, Tianjin Hospital of Integrated Traditional Chinese and Western Medicine, Tianjin, 300100, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Jun Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yanan Du
- Department of Biomedical Engineering, School of Medicine, Tsinghua-PKU Center for Life Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing CytoNiche Biotechnology Co. Ltd., 100195, Beijing, China.
| | - Yingdai Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, PUMC Department of Stem Cell and Regenerative Medicine, CAMS Key Laboratory of Gene Therapy for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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68
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Stankiewicz LN, Salim K, Flaschner EA, Wang YX, Edgar JM, Lin BZB, Bingham GC, Major MC, Jones RD, Blau HM, Rideout EJ, Levings MK, Zandstra PW, Rossi FMV. Sex biased human thymic architecture guides T cell development through spatially defined niches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536804. [PMID: 37090676 PMCID: PMC10120731 DOI: 10.1101/2023.04.13.536804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Within the thymus, regulation of the cellular cross-talk directing T cell development is dependent on spatial interactions within specialized niches. To create a holistic, spatially defined map of tissue niches guiding postnatal T cell development we employed the multidimensional imaging platform CO-detection by indEXing (CODEX), as well as CITE-seq and ATAC-seq. We generated age-matched 4-5-month-old postnatal thymus datasets for male and female donors, and identify significant sex differences in both T cell and thymus biology. We demonstrate a crucial role for JAG ligands in directing thymic-like dendritic cell development, reveal important functions of a novel population of ECM- fibroblasts, and characterize the medullary niches surrounding Hassall's corpuscles. Together, these data represent a unique age-matched spatial multiomic resource to investigate how sex-based differences in thymus regulation and T cell development arise, and provide an essential resource to understand the mechanisms underlying immune function and dysfunction in males and females.
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Affiliation(s)
| | - Kevin Salim
- Department of Surgery, University of British Columbia, Canada
- BC Children’s Hospital Research Institute, Canada
| | - Emily A Flaschner
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Yu Xin Wang
- Center for Genetic Disorders and Aging, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John M Edgar
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Bruce ZB Lin
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Grace C Bingham
- Department of Biomedical Engineering, University of Virginia, USA
| | - Matthew C Major
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Ross D Jones
- School of Biomedical Engineering, University of British Columbia, Canada
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, USA
| | | | - Megan K Levings
- School of Biomedical Engineering, University of British Columbia, Canada
- Department of Surgery, University of British Columbia, Canada
- BC Children’s Hospital Research Institute, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Canada
- These authors contributed equally
- Lead contact
| | - Fabio MV Rossi
- School of Biomedical Engineering, University of British Columbia, Canada
- These authors contributed equally
- Lead contact
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69
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Molofsky AB, Locksley RM. The ins and outs of innate and adaptive type 2 immunity. Immunity 2023; 56:704-722. [PMID: 37044061 PMCID: PMC10120575 DOI: 10.1016/j.immuni.2023.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023]
Abstract
Type 2 immunity is orchestrated by a canonical group of cytokines primarily produced by innate lymphoid cells, group 2, and their adaptive counterparts, CD4+ helper type 2 cells, and elaborated by myeloid cells and antibodies that accumulate in response. Here, we review the cytokine and cellular circuits that mediate type 2 immunity. Building from insights in cytokine evolution, we propose that innate type 2 immunity evolved to monitor the status of microbe-rich epithelial barriers (outside) and sterile parenchymal borders (inside) to meet the functional demands of local tissue, and, when necessary, to relay information to the adaptive immune system to reinforce demarcating borders to sustain these efforts. Allergic pathology likely results from deviations in local sustaining units caused by alterations imposed by environmental effects during postnatal developmental windows and exacerbated by mutations that increase vulnerabilities. This framework positions T2 immunity as central to sustaining tissue repair and regeneration and provides a context toward understanding allergic disease.
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Affiliation(s)
- Ari B Molofsky
- Department of Lab Medicine, University of California, San Francisco, San Francisco, CA 94143-0451, USA
| | - Richard M Locksley
- Howard Hughes Medical Institute and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-0795, USA.
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70
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Smith FL, Savage HP, Luo Z, Tipton CM, Lee FEH, Apostol AC, Beaudin AE, Lopez DA, Jensen I, Keller S, Baumgarth N. B-1 plasma cells require non-cognate CD4 T cell help to generate a unique repertoire of natural IgM. J Exp Med 2023; 220:e20220195. [PMID: 36811605 PMCID: PMC9960156 DOI: 10.1084/jem.20220195] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/01/2022] [Accepted: 01/27/2023] [Indexed: 02/24/2023] Open
Abstract
Evolutionarily conserved, "natural" (n)IgM is broadly reactive to both self and foreign antigens. Its selective deficiency leads to increases in autoimmune diseases and infections. In mice, nIgM is secreted independent of microbial exposure to bone marrow (BM) and spleen B-1 cell-derived plasma cells (B-1PC), generating the majority of nIgM, or by B-1 cells that remain non-terminally differentiated (B-1sec). Thus, it has been assumed that the nIgM repertoire is broadly reflective of the repertoire of body cavity B-1 cells. Studies here reveal, however, that B-1PC generate a distinct, oligoclonal nIgM repertoire, characterized by short CDR3 variable immunoglobulin heavy chain regions, 7-8 amino acids in length, some public, many arising from convergent rearrangements, while specificities previously associated with nIgM were generated by a population of IgM-secreting B-1 (B-1sec). BM, but not spleen B-1PC, or B-1sec also required the presence of TCRαβ CD4 T cells for their development from fetal precursors. Together, the studies identify important previously unknown characteristics of the nIgM pool.
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Affiliation(s)
- Fauna L. Smith
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA, USA
- Integrated Pathobiology Graduate Group, University of California, Davis, Davis, CA, USA
| | - Hannah P. Savage
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA, USA
- Graduate Group in Immunology, University of California, Davis, Davis, CA, USA
| | - Zheng Luo
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - F. Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
| | - April C. Apostol
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Anna E. Beaudin
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Diego A. Lopez
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, UT, USA
| | - Ingvill Jensen
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA, USA
| | - Stefan Keller
- Department Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Nicole Baumgarth
- Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA, USA
- Integrated Pathobiology Graduate Group, University of California, Davis, Davis, CA, USA
- Graduate Group in Immunology, University of California, Davis, Davis, CA, USA
- Department Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
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71
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Michaels YS, Durland LJ, Zandstra PW. Engineering T Cell Development for the Next Generation of Stem Cell-Derived Immunotherapies. GEN BIOTECHNOLOGY 2023; 2:106-119. [PMID: 37928777 PMCID: PMC10624212 DOI: 10.1089/genbio.2023.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 11/07/2023]
Abstract
Engineered T cells are at the leading edge of clinical cell therapy. T cell therapies have had a remarkable impact on patient care for a subset of hematological malignancies. This foundation has motivated the development of off-the-shelf engineered cell therapies for a broad range of devastating indications. Achieving this vision will require cost-effective manufacturing of precision cell products capable of addressing multiple process and clinical-design challenges. Pluripotent stem cell (PSC)-derived engineered T cells are emerging as a solution of choice. To unleash the full potential of PSC-derived T cell therapies, the field will require technologies capable of robustly orchestrating the complex series of time- and dose-dependent signaling events needed to recreate functional T cell development in the laboratory. In this article, we review the current state of allogenic T cell therapies, focusing on strategies to generate engineered lymphoid cells from PSCs. We highlight exciting recent progress in this field and outline timely opportunities for advancement with an emphasis on niche engineering and synthetic biology.
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Affiliation(s)
- Yale S. Michaels
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada; University of British Columbia, Vancouver, Canada
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Canada; and University of British Columbia, Vancouver, Canada
| | - Lauren J. Durland
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
| | - Peter W. Zandstra
- School of Biomedical Engineering, University of British Columbia, Vancouver, Canada; University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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72
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Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
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Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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73
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Bosticardo M, Notarangelo LD. Human thymus in health and disease: Recent advances in diagnosis and biology. Semin Immunol 2023; 66:101732. [PMID: 36863139 PMCID: PMC10134747 DOI: 10.1016/j.smim.2023.101732] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/30/2023] [Accepted: 02/14/2023] [Indexed: 03/04/2023]
Abstract
The thymus is the crucial tissue where thymocytes develop from hematopoietic precursors that originate from the bone marrow and differentiate to generate a repertoire of mature T cells able to respond to foreign antigens while remaining tolerant to self-antigens. Until recently, most of the knowledge on thymus biology and its cellular and molecular complexity have been obtained through studies in animal models, because of the difficulty to gain access to thymic tissue in humans and the lack of in vitro models able to faithfully recapitulate the thymic microenvironment. This review focuses on recent advances in the understanding of human thymus biology in health and disease obtained through the use of innovative experimental techniques (eg. single cell RNA sequencing, scRNAseq), diagnostic tools (eg. next generation sequencing), and in vitro models of T-cell differentiation (artificial thymic organoids) and thymus development (eg. thymic epithelial cell differentiation from embryonic stem cells or induced pluripotent stem cells).
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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74
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Kim IS. Single-Cell Molecular Barcoding to Decode Multimodal Information Defining Cell States. Mol Cells 2023; 46:74-85. [PMID: 36859472 PMCID: PMC9982054 DOI: 10.14348/molcells.2023.2168] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 03/03/2023] Open
Abstract
Single-cell research has provided a breakthrough in biology to understand heterogeneous cell groups, such as tissues and organs, in development and disease. Molecular barcoding and subsequent sequencing technology insert a singlecell barcode into isolated single cells, allowing separation cell by cell. Given that multimodal information from a cell defines precise cellular states, recent technical advances in methods focus on simultaneously extracting multimodal data recorded in different biological materials (DNA, RNA, protein, etc.). This review summarizes recently developed singlecell multiomics approaches regarding genome, epigenome, and protein profiles with the transcriptome. In particular, we focus on how to anchor or tag molecules from a cell, improve throughputs with sample multiplexing, and record lineages, and we further discuss the future developments of the technology.
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Affiliation(s)
- Ik Soo Kim
- Department of Microbiology, Gachon University College of Medicine, Incheon 21999, Korea
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75
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Brandstadter JD, De Martin A, Lütge M, Ferreira A, Gaudette BT, Stanossek Y, Wang S, Gonzalez MV, Camiolo E, Wertheim G, Austin B, Allman D, Lim MS, Fajgenbaum DC, Aster JC, Ludewig B, Maillard I. A novel cryopreservation and biobanking strategy to study lymphoid tissue stromal cells in human disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.525604. [PMID: 36798373 PMCID: PMC9934566 DOI: 10.1101/2023.02.06.525604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Non-hematopoietic lymph node stromal cells (LNSCs) regulate lymphocyte trafficking, survival, and function for key roles in host defense, autoimmunity, alloimmunity, and lymphoproliferative disorders. However, study of LNSCs in human diseases is complicated by a dependence on viable lymphoid tissues, which are most often excised prior to establishment of a specific diagnosis. Here, we demonstrate that cryopreservation can be used to bank lymphoid tissue for the study of LNSCs in human disease. Using human tonsils, lymphoid tissue fragments were cryopreserved for subsequent enzymatic digestion and recovery of viable non-hematopoietic cells. Flow cytometry and single-cell transcriptomics identified comparable proportions of LNSC cell types in fresh and cryopreserved tissue. Moreover, cryopreservation had little effect on transcriptional profiles, which showed significant overlap between tonsils and lymph nodes. The presence and spatial distribution of transcriptionally defined cell types was confirmed by in situ analyses. Our broadly applicable approach promises to greatly enable research into the roles of LNSC in human disease.
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76
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Wang S, Sun ST, Zhang XY, Ding HR, Yuan Y, He JJ, Wang MS, Yang B, Li YB. The Evolution of Single-Cell RNA Sequencing Technology and Application: Progress and Perspectives. Int J Mol Sci 2023; 24:ijms24032943. [PMID: 36769267 PMCID: PMC9918030 DOI: 10.3390/ijms24032943] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/01/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
As an emerging sequencing technology, single-cell RNA sequencing (scRNA-Seq) has become a powerful tool for describing cell subpopulation classification and cell heterogeneity by achieving high-throughput and multidimensional analysis of individual cells and circumventing the shortcomings of traditional sequencing for detecting the average transcript level of cell populations. It has been applied to life science and medicine research fields such as tracking dynamic cell differentiation, revealing sensitive effector cells, and key molecular events of diseases. This review focuses on the recent technological innovations in scRNA-Seq, highlighting the latest research results with scRNA-Seq as the core technology in frontier research areas such as embryology, histology, oncology, and immunology. In addition, this review outlines the prospects for its innovative application in traditional Chinese medicine (TCM) research and discusses the key issues currently being addressed by scRNA-Seq and its great potential for exploring disease diagnostic targets and uncovering drug therapeutic targets in combination with multiomics technologies.
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Affiliation(s)
| | | | | | | | | | | | | | - Bin Yang
- Correspondence: (B.Y.); (Y.-B.L.)
| | - Yu-Bo Li
- Correspondence: (B.Y.); (Y.-B.L.)
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77
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Jardine L, Schim van der Loeff I, Haq IJ, Sproat TDR. Gestational Development of the Human Immune System. Immunol Allergy Clin North Am 2023; 43:1-15. [PMID: 36410996 DOI: 10.1016/j.iac.2022.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Building an immune system is a monumental task critical to the survival of the fetus and newborn. A functional fetal immune system must complement the maternal immune system in handling in utero infection; abstain from damaging non-self-reactions that would compromise the materno-fetal interface; mobilize in response to infection and equip mucosal tissues for pathogen exposure at birth. There is growing appreciation that immune cells also have noncanonical roles in development and specifically may contribute to tissue morphogenesis. In this review we detail how hematopoietic and lymphoid organs jointly establish cellular constituents of the immune system; how these constituents are organized in 2 mucosal sites-gut and lung-where early life immune function has long-term consequences for health; and how exemplar diseases of prematurity and inborn errors of immunity reveal dominant pathways in prenatal immunity.
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Affiliation(s)
- Laura Jardine
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom; Haematology Department, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom.
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom
| | - Iram J Haq
- Translational and Clinical Research Institute, Newcastle University, Faculty of Medical Sciences, Newcastle Upon Tyne NE2 4HH, United Kingdom; Department of Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, United Kingdom
| | - Thomas D R Sproat
- Neonatal Unit, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Richardson Road, Newcastle Upon Tyne NE1 4LP, United Kingdom
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78
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Heimli M, Flåm ST, Hjorthaug HS, Trinh D, Frisk M, Dumont KA, Ribarska T, Tekpli X, Saare M, Lie BA. Multimodal human thymic profiling reveals trajectories and cellular milieu for T agonist selection. Front Immunol 2023; 13:1092028. [PMID: 36741401 PMCID: PMC9895842 DOI: 10.3389/fimmu.2022.1092028] [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: 11/07/2022] [Accepted: 12/22/2022] [Indexed: 01/22/2023] Open
Abstract
To prevent autoimmunity, thymocytes expressing self-reactive T cell receptors (TCRs) are negatively selected, however, divergence into tolerogenic, agonist selected lineages represent an alternative fate. As thymocyte development, selection, and lineage choices are dependent on spatial context and cell-to-cell interactions, we have performed Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) and spatial transcriptomics on paediatric human thymus. Thymocytes expressing markers of strong TCR signalling diverged from the conventional developmental trajectory prior to CD4+ or CD8+ lineage commitment, while markers of different agonist selected T cell populations (CD8αα(I), CD8αα(II), T(agonist), Treg(diff), and Treg) exhibited variable timing of induction. Expression profiles of chemokines and co-stimulatory molecules, together with spatial localisation, supported that dendritic cells, B cells, and stromal cells contribute to agonist selection, with different subsets influencing thymocytes at specific developmental stages within distinct spatial niches. Understanding factors influencing agonist T cells is needed to benefit from their immunoregulatory effects in clinical use.
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Affiliation(s)
- Marte Heimli
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Siri Tennebø Flåm
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Don Trinh
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Michael Frisk
- Institute for Experimental Medical Research, Oslo University Hospital, University of Oslo, Oslo, Norway,KG Jebsen Centre for Cardiac Research, University of Oslo, Oslo, Norway
| | - Karl-Andreas Dumont
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | - Teodora Ribarska
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Mario Saare
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Benedicte Alexandra Lie
- Department of Medical Genetics, Oslo University Hospital, University of Oslo, Oslo, Norway,*Correspondence: Benedicte Alexandra Lie,
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79
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Han J, Sheng T, Zhang Y, Cheng H, Gao J, Yu J, Gu Z. Bioresponsive Immunotherapeutic Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2209778. [PMID: 36639983 DOI: 10.1002/adma.202209778] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/31/2022] [Indexed: 06/17/2023]
Abstract
The human immune system is an interaction network of biological processes, and its dysfunction is closely associated with a wide array of diseases, such as cancer, infectious diseases, tissue damage, and autoimmune diseases. Manipulation of the immune response network in a desired and controlled fashion has been regarded as a promising strategy for maximizing immunotherapeutic efficacy and minimizing side effects. Integration of "smart" bioresponsive materials with immunoactive agents including small molecules, biomacromolecules, and cells can achieve on-demand release of agents at targeted sites to reduce overdose-related toxicity and alleviate off-target effects. This review highlights the design principles of bioresponsive immunotherapeutic materials and discusses the critical roles of controlled release of immunoactive agents from bioresponsive materials in recruiting, housing, and manipulating immune cells for evoking desired immune responses. Challenges and future directions from the perspective of clinical translation are also discussed.
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Affiliation(s)
- Jinpeng Han
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Tao Sheng
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuqi Zhang
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Department of Burns and Wound Center, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Hao Cheng
- Department of Materials Science and Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Jianqing Gao
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Cancer Center, Zhejiang University, Hangzhou, 310058, China
- Jinhua Institute of Zhejiang University, Jinhua, 321299, China
| | - Jicheng Yu
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Jinhua Institute of Zhejiang University, Jinhua, 321299, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
- Department of General Surgery, Sir Run Run Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Zhen Gu
- Zhejiang Provincial Key Laboratory for Advanced Drug Delivery Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Jinhua Institute of Zhejiang University, Jinhua, 321299, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
- Department of General Surgery, Sir Run Run Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, China
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80
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Sanchez Sanchez G, Tafesse Y, Papadopoulou M, Vermijlen D. Surfing on the waves of the human γδ T cell ontogenic sea. Immunol Rev 2023; 315:89-107. [PMID: 36625367 DOI: 10.1111/imr.13184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
While γδ T cells are present virtually in all vertebrates, there is a remarkable lack of conservation of the TRG and TRD loci underlying the generation of the γδ T cell receptor (TCR), which is associated with the generation of species-specific γδ T cells. A prominent example is the human phosphoantigen-reactive Vγ9Vδ2 T cell subset that is absent in mice. Murine γδ thymocyte cells were among the first immune cells identified to follow a wave-based layered development during embryonic and early life, and since this initial observation, in-depth insight has been obtained in their thymic ontogeny. By contrast, less is known about the development of human γδ T cells, especially regarding the generation of γδ thymocyte waves. Here, after providing an overview of thymic γδ wave generation in several vertebrate classes, we review the evidence for γδ waves in the human fetal thymus, where single-cell technologies have allowed the breakdown of human γδ thymocytes into functional waves with important TCR associations. Finally, we discuss the possible mechanisms contributing to the generation of waves of γδ thymocytes and their possible significance in the periphery.
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Affiliation(s)
- Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Yohannes Tafesse
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Maria Papadopoulou
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Gosselies, Belgium.,ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium.,WELBIO Department, WEL Research Institute, Wavre, Belgium
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81
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Patil AR, Schug J, Naji A, Kaestner KH, Faryabi RB, Vahedi G. Computational workflow and interactive analysis of single-cell expression profiling of islets generated by the Human Pancreas Analysis Program. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522578. [PMID: 36711819 PMCID: PMC9881881 DOI: 10.1101/2023.01.03.522578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Type 1 and Type 2 diabetes are distinct genetic diseases of the pancreas which are defined by the abnormal level of blood glucose. Understanding the initial molecular perturbations that occur during the pathogenesis of diabetes is of critical importance in understanding these disorders. The inability to biopsy the human pancreas of living donors hampers insights into early detection, as the majority of diabetes studies have been performed on peripheral leukocytes from the blood, which is not the site of pathogenesis. Therefore, efforts have been made by various teams including the Human Pancreas Analysis Program (HPAP) to collect pancreatic tissues from deceased organ donors with different clinical phenotypes. HPAP is designed to define the molecular pathogenesis of islet dysfunction by generating detailed datasets of functional, cellular, and molecular information in pancreatic tissues of clinically well-defined organ donors with Type 1 and Type 2 diabetes. Moreover, data generated by HPAP continously become available through a centralized database, PANC-DB, thus enabling the diabetes research community to access these multi-dimensional data prepublication. Here, we present the computational workflow for single-cell RNA-seq data analysis of 258,379 high-quality cells from the pancreatic islets of 67 human donors generated by HPAP, the largest existing scRNA-seq dataset of human pancreatic tissues. We report various computational steps including preprocessing, doublet removal, clustering and cell type annotation across single-cell RNA-seq data from islets of four distintct classes of organ donors, i.e. non-diabetic control, autoantibody positive but normoglycemic, Type 1 diabetic, and Type 2 diabetic individuals. Moreover, we present an interactive tool, called CellxGene developed by the Chan Zuckerberg initiative, to navigate these high-dimensional datasets. Our data and interactive tools provide a reliable reference for singlecell pancreatic islet biology studies, especially diabetes-related conditions.
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82
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Ospina O, Soupir A, Fridley BL. A Primer on Preprocessing, Visualization, Clustering, and Phenotyping of Barcode-Based Spatial Transcriptomics Data. Methods Mol Biol 2023; 2629:115-140. [PMID: 36929076 DOI: 10.1007/978-1-0716-2986-4_7] [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: 03/18/2023]
Abstract
Recent developments in spatially resolved transcriptomics (ST) have resulted in a large number of studies characterizing the architecture of tissues, the spatial distribution of cell types, and their interactions. Furthermore, ST promises to enable the discovery of more accurate drug targets while also providing a better understanding of the etiology and evolution of complex diseases. The analysis of ST brings similar challenges as seen in other gene expression assays such as scRNA-seq; however, there is the additional spatial information that warrants the development of suitable algorithms for the quality control, preprocessing, visualization, and other discovery-enabling approaches (e.g., clustering, cell phenotyping). In this chapter, we review some of the existing algorithms to perform these analytical tasks and highlight some of the unmet analytical challenges in the analysis of ST data. Given the diversity of available ST technologies, we focus this chapter on the analysis of barcode-based RNA quantitation techniques.
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Affiliation(s)
- Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Alex Soupir
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Brooke L Fridley
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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83
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Hou S, Liu C, Yao Y, Bai Z, Gong Y, Wang C, He J, You G, Zhang G, Liu B, Lan Y. Hematopoietic Stem Cell Development in Mammalian Embryos. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1442:1-16. [PMID: 38228955 DOI: 10.1007/978-981-99-7471-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Hematopoietic stem cells (HSCs) are situated at the top of the adult hematopoietic hierarchy in mammals and give rise to the majority of blood cells throughout life. Recently, with the advance of multiple single-cell technologies, researchers have unprecedentedly deciphered the cellular and molecular evolution, the lineage relationships, and the regulatory mechanisms underlying HSC emergence in mammals. In this review, we describe the precise vascular origin of HSCs in mouse and human embryos, emphasizing the conservation in the unambiguous arterial characteristics of the HSC-primed hemogenic endothelial cells (HECs). Serving as the immediate progeny of some HECs, functional pre-HSCs of mouse embryos can now be isolated at single-cell level using defined surface marker combinations. Heterogeneity regrading cell cycle status or lineage differentiation bias within HECs, pre-HSCs, or emerging HSCs in mouse embryos has been figured out. Several epigenetic regulatory mechanisms of HSC generation, including long noncoding RNA, DNA methylation modification, RNA splicing, and layered epigenetic modifications, have also been recently uncovered. In addition to that of HSCs, the cellular and molecular events underlying the development of multiple hematopoietic progenitors in human embryos/fetus have been unraveled with the use of series of single-cell technologies. Specifically, yolk sac-derived myeloid-biased progenitors have been identified as the earliest multipotent hematopoietic progenitors in human embryo, serving as an important origin of fetal liver monocyte-derived macrophages. Moreover, the development of multiple hematopoietic lineages in human embryos such as T and B lymphocytes, innate lymphoid cells, as well as myeloid cells like monocytes, macrophages, erythrocytes, and megakaryocytes has also been depicted and reviewed here.
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Affiliation(s)
- Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chen Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yingpeng Yao
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Zhijie Bai
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chaojie Wang
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jian He
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Guoju You
- State Key Laboratory of Primate Biomedical Research, State Key Laboratory of Experimental Hematology, School of Medicine, Tsinghua University, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bing Liu
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
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84
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Chen D, Luo Y, Cheng G. Single cell and immunity: Better understanding immune cell heterogeneities with single cell sequencing. Clin Transl Med 2023; 13:e1159. [PMID: 36579366 PMCID: PMC9797918 DOI: 10.1002/ctm2.1159] [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: 12/10/2022] [Accepted: 12/14/2022] [Indexed: 12/30/2022] Open
Abstract
Single-cell sequencing has scientific impacts on better understanding the immunity. There is a rapid development in single cell-based databases and analytic tools to provide the potential of clinical and translational discovery. The understanding of single-cell based immunity needs a strong program and solid evidence of preclinical and clinical validation and evaluation. The current special topic issue on single cell and immunity aimed to provide a strong communication for the progress of single cell-based studies on immune cell functional diversity in development and disease. The topic has a clear scope on the application of single cell sequencing to better understand immune cell heterogeneities, functions, cell-cell interactions, responses and regulatory roles in systems immunology and diseases.
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Affiliation(s)
- Dongsheng Chen
- Institute of Systems MedicineChinese Academy of Medical Sciences & Peking Union Medical CollegeBeijingChina
- Suzhou Institute of Systems MedicineSuzhouChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesBGI‐Qingdao, BGI‐ShenzhenQingdaoChina
- Department of BiomedicineAarhus UniversityAarhusDenmark
| | - Genhong Cheng
- Department of MicrobiologyImmunology & Molecular GeneticsUniversity of California Los Angeles (UCLA), Los Angeles, California, USA
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85
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Lasry A, Nadorp B, Fornerod M, Nicolet D, Wu H, Walker CJ, Sun Z, Witkowski MT, Tikhonova AN, Guillamot-Ruano M, Cayanan G, Yeaton A, Robbins G, Obeng EA, Tsirigos A, Stone RM, Byrd JC, Pounds S, Carroll WL, Gruber TA, Eisfeld AK, Aifantis I. An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia. NATURE CANCER 2023; 4:27-42. [PMID: 36581735 PMCID: PMC9986885 DOI: 10.1038/s43018-022-00480-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022]
Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric patients with AML. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B-cell subtype enriched in patients with high-inflammation AML, as well as an increase in CD8+GZMK+ and regulatory T cells, accompanied by a reduction in T-cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in patients with AML. Addition of the iScore refines current risk stratifications for patients with AML and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying patients with AML based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.
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Affiliation(s)
- Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Bettina Nadorp
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Maarten Fornerod
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Huiyun Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher J Walker
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Zhengxi Sun
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anastasia N Tikhonova
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Maria Guillamot-Ruano
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Geraldine Cayanan
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Anna Yeaton
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Gabriel Robbins
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY, USA
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Tanja A Gruber
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, USA.
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY, USA.
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
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86
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Velounias RL, Tull TJ. Human B-cell subset identification and changes in inflammatory diseases. Clin Exp Immunol 2022; 210:201-216. [PMID: 36617261 PMCID: PMC9985170 DOI: 10.1093/cei/uxac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/19/2022] [Accepted: 11/15/2022] [Indexed: 01/09/2023] Open
Abstract
Our understanding of the B-cell subsets found in human blood and their functional significance has advanced greatly in the past decade. This has been aided by the evolution of high dimensional phenotypic tools such as mass cytometry and single-cell RNA sequencing which have revealed heterogeneity in populations that were previously considered homogenous. Despite this, there is still uncertainty and variation between studies as to how B-cell subsets are identified and named. This review will focus on the most commonly encountered subsets of B cells in human blood and will describe gating strategies for their identification by flow and mass cytometry. Important changes to population frequencies and function in common inflammatory and autoimmune diseases will also be described.
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Affiliation(s)
- Rebekah L Velounias
- Department of Immunobiology, King’s College London, Guy’s Hospital Campus, London, UK
| | - Thomas J Tull
- St John’s Institute of Dermatology, King’s College London, Guy’s Hospital Campus, London, UK
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87
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Spencer J, Bemark M, Tull TJ. Human B cells. Clin Exp Immunol 2022; 210:199-200. [PMID: 36512653 PMCID: PMC9985144 DOI: 10.1093/cei/uxac110] [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: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The importance of B cells and their critical role in the maintenance of health through generation of antibody-mediated immune protection is undoubted. However, the differences between the responses of B cells with different surface phenotypes in different microanatomical sites as well as diversity in B-cell function outside antibody production are just starting to be acknowledged and resolved. This series of reviews and papers that focus on human B cells will be divided across two issues. The first part of the review series in this issue captures practical information on identifying B-cell subtypes in blood in health and inflammatory diseases as well as describing aspects of B-cell diversity depending on immunoglobulin isotype and microanatomical context. It also explores our current understanding of cytokine production by human B cells and the effect of obesity on the B-cell response. The last review in this issue will reflect on the important lessons learned from the SARS-CoV-2 pandemic; in particular the role of antigen availability and its effect on B-cell memory and antibody production.
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Affiliation(s)
- Jo Spencer
- Correspondence: School of Immunology and Microbial Sciences, King’s College London, Guy’s Campus, London, UK.
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE 405 30 Gothenburg, Sweden, and Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas J Tull
- St John’s Institute of Dermatology, King’s College London, Guy’s Hospital Campus, London, UK
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88
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Montorsi L, Siu JHY, Spencer J. B cells in human lymphoid structures. Clin Exp Immunol 2022; 210:240-252. [PMID: 36370126 PMCID: PMC9985168 DOI: 10.1093/cei/uxac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/30/2022] [Accepted: 11/11/2022] [Indexed: 11/13/2022] Open
Abstract
Most B cells in the human body are present in tissues where they support immune responses to pathogens, vaccines, autoantigens, and tumours. Despite their clear importance, they are very difficult to study and there are many areas of uncertainty that are difficult to resolve because of limited tissue access. In this review, we consider the zonal structure of lymphoid tissues, the B cell subsets they contain, and how these are regulated. We also discuss the impact that methods of deep interrogation have made on our current knowledge base, especially with respect to studies of cells from dissociated tissues. We discuss in some detail the controversial B cells with marginal zone distribution that some consider being archived memory B cells. We anticipate that more we understand of B cells in tissues and the niches they create, the more opportunities will be identified to harness their potential for therapeutic benefit.
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Affiliation(s)
- Lucia Montorsi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Jacqueline H Y Siu
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, UK
| | - Jo Spencer
- Correspondence: Jo Spencer, Peter Gorer Department of Immunobiology, King’s College London, Second Floor Borough Wing, Guy’s Hospital Campus, St Thomas’ St, London SE1 9RT, UK.
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89
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Chen S, Chang Y, Li L, Acosta D, Li Y, Guo Q, Wang C, Turkes E, Morrison C, Julian D, Hester ME, Scharre DW, Santiskulvong C, Song SX, Plummer JT, Serrano GE, Beach TG, Duff KE, Ma Q, Fu H. Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer's disease. Acta Neuropathol Commun 2022; 10:188. [PMID: 36544231 PMCID: PMC9773466 DOI: 10.1186/s40478-022-01494-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/11/2022] [Indexed: 12/24/2022] Open
Abstract
Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer's disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10 × Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identify unique marker genes for cortical layers and the white matter, and layer-specific differentially expressed genes (DEGs) in human AD compared to CT. Deconvolution of the Visium spots showcases the significant difference in particular cell types among cortical layers and the white matter. Gene co-expression analyses reveal eight gene modules, four of which have significantly altered co-expression patterns in the presence of AD pathology. The co-expression patterns of hub genes and enriched pathways in the presence of AD pathology indicate an important role of cell-cell-communications among microglia, oligodendrocytes, astrocytes, and neurons, which may contribute to the cellular and regional vulnerability in early AD. Using single-molecule fluorescent in situ hybridization, we validated the cell-type-specific expression of three novel DEGs (e.g., KIF5A, PAQR6, and SLC1A3) and eleven previously reported DEGs associated with AD pathology (i.e., amyloid beta plaques and intraneuronal neurofibrillary tangles or neuropil threads) at the single cell level. Our results may contribute to the understanding of the complex architecture and neuronal and glial response to AD pathology of this vulnerable brain region.
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Affiliation(s)
- Shuo Chen
- grid.261331.40000 0001 2285 7943Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH 43210 USA
| | - Yuzhou Chang
- grid.261331.40000 0001 2285 7943Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Liangping Li
- grid.261331.40000 0001 2285 7943Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Diana Acosta
- grid.261331.40000 0001 2285 7943Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Yang Li
- grid.261331.40000 0001 2285 7943Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Qi Guo
- grid.261331.40000 0001 2285 7943Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Cankun Wang
- grid.261331.40000 0001 2285 7943Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Emir Turkes
- grid.83440.3b0000000121901201UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Cody Morrison
- grid.261331.40000 0001 2285 7943Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Dominic Julian
- grid.240344.50000 0004 0392 3476The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205 USA
| | - Mark E. Hester
- grid.240344.50000 0004 0392 3476The Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205 USA
| | - Douglas W. Scharre
- grid.261331.40000 0001 2285 7943Department of Neurology, Center for Cognitive and Memory Disorders, Center for Neuromodulation, Ohio State University, Columbus, OH 43210 USA
| | - Chintda Santiskulvong
- grid.50956.3f0000 0001 2152 9905Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Sarah XueYing Song
- grid.50956.3f0000 0001 2152 9905Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Jasmine T. Plummer
- grid.50956.3f0000 0001 2152 9905Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Geidy E. Serrano
- grid.414208.b0000 0004 0619 8759Banner Sun Health Research Institute, Sun City, AZ 85351 USA
| | - Thomas G. Beach
- grid.414208.b0000 0004 0619 8759Banner Sun Health Research Institute, Sun City, AZ 85351 USA
| | - Karen E. Duff
- grid.83440.3b0000000121901201UK Dementia Research Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Qin Ma
- grid.261331.40000 0001 2285 7943Department of Biomedical Informatics, College of Medicine, Ohio State University, Columbus, OH 43210 USA
| | - Hongjun Fu
- grid.261331.40000 0001 2285 7943Department of Neuroscience, College of Medicine, Ohio State University, Columbus, OH 43210 USA
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90
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Hernández-Torres DC, Stehle C. Embryonic ILC-poiesis across tissues. Front Immunol 2022; 13:1040624. [PMID: 36605193 PMCID: PMC9807749 DOI: 10.3389/fimmu.2022.1040624] [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: 09/09/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The family of innate lymphoid cells (ILCs), consisting of Group 1 ILCs (natural killer cells and ILC1), ILC2, and ILC3, are critical effectors of innate immunity, inflammation, and homeostasis post-natally, but also exert essential functions before birth. Recent studies during critical developmental periods in the embryo have hinted at complex waves of tissue colonization, and highlighted the breadth of multipotent and committed ILC progenitors from both classic fetal hematopoietic organs such as the liver, as well as tissue sites such as the lung, thymus, and intestine. Assessment of the mechanisms driving cell fate and function of the ILC family in the embryo will be vital to the understanding ILC biology throughout fetal life and beyond.
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Affiliation(s)
- Daniela Carolina Hernández-Torres
- Innate Immunity, German Rheumatism Research Center (DRFZ), Leibniz Association, Berlin, Germany,Medical Department I, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Daniela Carolina Hernández-Torres, ; Christina Stehle,
| | - Christina Stehle
- Innate Immunity, German Rheumatism Research Center (DRFZ), Leibniz Association, Berlin, Germany,Medical Department I, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Daniela Carolina Hernández-Torres, ; Christina Stehle,
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91
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Chen S, Duan B, Zhu C, Tang C, Wang S, Gao Y, Fu S, Fan L, Yang Q, Liu Q. Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy. SCIENCE CHINA. LIFE SCIENCES 2022; 66:1183-1195. [PMID: 36543995 PMCID: PMC9771767 DOI: 10.1007/s11427-022-2224-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022]
Abstract
The rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses. However, the privacy issue has existed but being ignored, since we are limited to access and utilize all the reference datasets distributed in different institutions globally due to the prohibited data transmission across institutions by data regulation laws. To this end, we present scPrivacy, which is the first and generalized automatically single-cell type identification prototype to facilitate single cell annotations in a data privacy-preserving collaboration manner. We evaluated scPrivacy on a comprehensive set of publicly available benchmark datasets for single-cell type identification to stimulate the scenario that the reference datasets are rapidly generated and distributed in multiple institutions, while they are prohibited to be integrated directly or exposed to each other due to the data privacy regulations, demonstrating its effectiveness, time efficiency and robustness for privacy-preserving integration of multiple institutional datasets in single cell annotations.
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Affiliation(s)
- Shaoqi Chen
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Bin Duan
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Chenyu Zhu
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Chen Tang
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Shuguang Wang
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Yicheng Gao
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Shaliu Fu
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Lixin Fan
- Department of AI, WeBank, Shenzhen, 518055 China
| | - Qiang Yang
- Department of AI, WeBank, Shenzhen, 518055 China
| | - Qi Liu
- grid.24516.340000000123704535Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department of Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China ,grid.24516.340000000123704535Translational Medical Center for Stem Cell Therapy and Institution for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China ,Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210 China
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92
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Machlin JH, Shikanov A. Single-cell RNA-sequencing of retrieved human oocytes and eggs in clinical practice and for human ovarian cell atlasing. Mol Reprod Dev 2022; 89:597-607. [PMID: 36264989 PMCID: PMC9805491 DOI: 10.1002/mrd.23648] [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: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 01/18/2023]
Abstract
With the advancement of single-cell separation techniques and high-throughput sequencing platforms, single-cell RNA-sequencing (scRNA-seq) has emerged as a vital technology for understanding tissue and organ systems at cellular resolution. Through transcriptional analysis, it is possible to characterize unique or rare cell types, interpret their interactions, and reveal novel functional states or shifts in developmental stages. As such, this technology is uniquely suited for studying the cells within the human ovary. The ovary is a cellularly heterogeneous organ that houses follicles, the reproductive and endocrine unit that consists of an oocyte surrounded by hormone-producing support cells, as well as many other cell populations constituting stroma, vasculature, lymphatic, and immune components. Here we review studies that have utilized scRNA-seq technology to analyze cells from healthy human ovaries and discuss the single-cell isolation techniques used. We identified two overarching applications for scRNA-seq in the human ovary. The first applies this technology to investigate transcriptional differences in oocytes/eggs from patients undergoing in vitro fertilization treatments to ultimately improve clinical outcomes. The second utilizes scRNA-seq for the pursuit of creating a comprehensive single-cell atlas of the human ovary. The knowledge gained from these studies underscores the importance of scRNA-seq technologies in unlocking a new biological understanding of the human ovary.
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Affiliation(s)
- Jordan H. Machlin
- Program in Cellular and Molecular BiologyUniversity of MichiganAnn ArborMichiganUSA
| | - Ariella Shikanov
- Program in Cellular and Molecular BiologyUniversity of MichiganAnn ArborMichiganUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Department of Obstetrics and GynecologyUniversity of MichiganAnn ArborMichiganUSA
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93
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Rood JE, Maartens A, Hupalowska A, Teichmann SA, Regev A. Impact of the Human Cell Atlas on medicine. Nat Med 2022; 28:2486-2496. [PMID: 36482102 DOI: 10.1038/s41591-022-02104-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/24/2022] [Indexed: 12/13/2022]
Abstract
Single-cell atlases promise to provide a 'missing link' between genes, diseases and therapies. By identifying the specific cell types, states, programs and contexts where disease-implicated genes act, we will understand the mechanisms of disease at the cellular and tissue levels and can use this understanding to develop powerful disease diagnostics; identify promising new drug targets; predict their efficacy, toxicity and resistance mechanisms; and empower new kinds of therapies, from cancer therapies to regenerative medicine. Here, we lay out a vision for the potential of cell atlases to impact the future of medicine, and describe how advances over the past decade have begun to realize this potential in common complex diseases, infectious diseases (including COVID-19), rare diseases and cancer.
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Affiliation(s)
| | - Aidan Maartens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
| | - Aviv Regev
- Genentech, South San Francisco, CA, USA.
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94
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Zhou Z, Tan C, Chau M, Jiang X, Ke Z, Chen X, Cao Y, Kwok YK, Bellgard M, Leung T, Choy K, Dong Z. TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms. Nucleic Acids Res 2022; 51:D1168-D1178. [PMID: 36350663 PMCID: PMC9825605 DOI: 10.1093/nar/gkac978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/06/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.
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Affiliation(s)
| | | | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Xiaosen Jiang
- BGI-Shenzhen, Shenzhen 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyuan Ke
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoyan Chen
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Maternal-Fetal Medicine Institute, Shenzhen Baoan Women's and Children's Hospital, Shenzhen University, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Bellgard
- eResearch Office, Queensland University of Technology, Brisbane, QLD, Australia
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Correspondence may also be addressed to Kwong Wai Choy. Tel: +852 3505 3099; Fax: +852 2636 0008;
| | - Zirui Dong
- To whom correspondence should be addressed. Tel: +852 3505 3099; Fax: +852 2636 0008;
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95
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Tanemoto S, Sujino T, Miyamoto K, Moody J, Yoshimatsu Y, Ando Y, Koya I, Harada Y, Tojo AO, Ono K, Hayashi Y, Takabayashi K, Okabayashi K, Teratani T, Mikami Y, Nakamoto N, Hosoe N, Ogata H, Hon CC, Shin JW, Kanai T. Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4 +CD8A + T cells related to mouse CD4 cytotoxic T cells. Front Immunol 2022; 13:977117. [PMID: 36353619 PMCID: PMC9639511 DOI: 10.3389/fimmu.2022.977117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/07/2022] [Indexed: 08/21/2023] Open
Abstract
Cytotoxic CD4+ T cells (CD4-CTLs) show the presence of cytolytic granules, which include the enzymes granzyme and perforin. The cells have a pathogenic and protective role in various diseases, including cancer, viral infection, and autoimmune disease. In mice, cytotoxic CD4+ T cells express CD8αα+ and reside in the intestine (mouse CD4+CTLs; mCD4-CTLs). The population of cytotoxic CD4+ T cells in the human intestine is currently unknown. Moreover, it is unclear how cytotoxic CD4 T cells change in patients with inflammatory bowel disease (IBD). Here, we aimed to identify cytotoxic CD4+ T cells in the human intestine and analyze the characteristics of the population in patients with IBD using single-cell RNA-seq (scRNA-seq). In CD4+ T cells, granzyme and perforin expression was high in humanMAIT (hMAIT) cells and hCD4+CD8A+ T cell cluster. Both CD4 and CD8A were expressed in hTreg, hMAIT, and hCD4+CD8A+ T cell clusters. Next we performed fast gene set enrichment analysis to identify cell populations that showed homology to mCD4CTLs. The analysis identified the hCD4+CD8A+ T cell cluster (hCTL-like population; hCD4-CTL) similar to mouse CTLs. The percentage of CD4+CD8A+ T cells among the total CD4+ T cells in the inflamed intestine of the patients with Crohn's disease was significantly reduced compared with that in the noninflamed intestine of the patients. In summary, we identified cytotoxic CD4+CD8+ T cells in the small intestine of humans. The integration of the mouse and human sc-RNA-seq data analysis highlight an approach to identify human cell populations related to mouse cell populations, which may help determine the functional properties of several human cell populations in mice.
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Affiliation(s)
- Shun Tanemoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
- Research Laboratory, Miyarisan Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Jonathan Moody
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Ikuko Koya
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Anna Okuzawa Tojo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukie Hayashi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Koji Okabayashi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Ogata
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
- Laboratory of Regulatory Genomics, Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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96
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Gao F, Wang T. Two-sample testing of high-dimensional linear regression coefficients via complementary sketching. Ann Stat 2022. [DOI: 10.1214/22-aos2216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Fengnan Gao
- School of Data Science, Shanghai Center for Mathematical Sciences, Fudan University
| | - Tengyao Wang
- Department of Statistics, London School of Economics
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97
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Drouin-Ouellet J, Li D, Lu YR, Echegaray CV. The 2022 International Society for Stem Cell Research (ISSCR) Annual Meeting: Celebrating 20 Years of Achievements. Cell Reprogram 2022; 24:212-222. [DOI: 10.1089/cell.2022.0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Dan Li
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Massachusetts General Hospital, Harvard University, Boston, Massachusetts, USA
| | - Yuancheng Ryan Lu
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Camila Vazquez Echegaray
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Centre, Wallenberg Centre for Molecular Medicine, Lund University, Lund, Sweden
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98
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Neuwirth T, Knapp K, Stary G. (Not) Home alone: Antigen presenting cell - T Cell communication in barrier tissues. Front Immunol 2022; 13:984356. [PMID: 36248804 PMCID: PMC9556809 DOI: 10.3389/fimmu.2022.984356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Priming of T cells by antigen presenting cells (APCs) is essential for T cell fate decisions, enabling T cells to migrate to specific tissues to exert their effector functions. Previously, these interactions were mainly explored using blood-derived cells or animal models. With great advances in single cell RNA-sequencing techniques enabling analysis of tissue-derived cells, it has become clear that subsets of APCs are responsible for priming and modulating heterogeneous T cell effector responses in different tissues. This composition of APCs and T cells in tissues is essential for maintaining homeostasis and is known to be skewed in infection and inflammation, leading to pathological T cell responses. This review highlights the commonalities and differences of T cell priming and subsequent effector function in multiple barrier tissues such as the skin, intestine and female reproductive tract. Further, we provide an overview of how this process is altered during tissue-specific infections which are known to cause chronic inflammation and how this knowledge could be harnessed to modify T cell responses in barrier tissue.
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Affiliation(s)
- Teresa Neuwirth
- Department of Dermatology, Medical University of Vienna, Vienna, Austria,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Katja Knapp
- Department of Dermatology, Medical University of Vienna, Vienna, Austria,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Georg Stary
- Department of Dermatology, Medical University of Vienna, Vienna, Austria,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria,*Correspondence: Georg Stary,
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99
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Jiang S, Qian Q, Zhu T, Zong W, Shang Y, Jin T, Zhang Y, Chen M, Wu Z, Chu Y, Zhang R, Luo S, Jing W, Zou D, Bao Y, Xiao J, Zhang Z. Cell Taxonomy: a curated repository of cell types with multifaceted characterization. Nucleic Acids Res 2022; 51:D853-D860. [PMID: 36161321 PMCID: PMC9825571 DOI: 10.1093/nar/gkac816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/24/2022] [Indexed: 01/12/2023] Open
Abstract
Single-cell studies have delineated cellular diversity and uncovered increasing numbers of previously uncharacterized cell types in complex tissues. Thus, synthesizing growing knowledge of cellular characteristics is critical for dissecting cellular heterogeneity, developmental processes and tumorigenesis at single-cell resolution. Here, we present Cell Taxonomy (https://ngdc.cncb.ac.cn/celltaxonomy), a comprehensive and curated repository of cell types and associated cell markers encompassing a wide range of species, tissues and conditions. Combined with literature curation and data integration, the current version of Cell Taxonomy establishes a well-structured taxonomy for 3,143 cell types and houses a comprehensive collection of 26,613 associated cell markers in 257 conditions and 387 tissues across 34 species. Based on 4,299 publications and single-cell transcriptomic profiles of ∼3.5 million cells, Cell Taxonomy features multifaceted characterization for cell types and cell markers, involving quality assessment of cell markers and cell clusters, cross-species comparison, cell composition of tissues and cellular similarity based on markers. Taken together, Cell Taxonomy represents a fundamentally useful reference to systematically and accurately characterize cell types and thus lays an important foundation for deeply understanding and exploring cellular biology in diverse species.
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Affiliation(s)
| | | | | | - Wenting Zong
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunfei Shang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Jin
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansheng Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Chen
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zishan Wu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Chu
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongqin Zhang
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sicheng Luo
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Jing
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China
| | - Yiming Bao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- Correspondence may also be addressed to Jingfa Xiao.
| | - Zhang Zhang
- To whom correspondence should be addressed. Tel: +86 10 84097261; Fax: +86 10 84097720;
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100
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Yao H, Tang G. Macrophages in intestinal fibrosis and regression. Cell Immunol 2022; 381:104614. [PMID: 36182587 DOI: 10.1016/j.cellimm.2022.104614] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 11/03/2022]
Abstract
Intestinal macrophages are heterogenous cell populations with different developmental ontogeny and tissue anatomy. The concerted actions of intestinal macrophage subsets are critical to maintaining tissue homeostasis. However, the dysregulation of macrophages following tissue injury or chronic inflammation could also lead to intestinal fibrosis, with few treatment options in the clinic. In this review, we will characterize the features of intestinal macrophages in light of the latest advances in lineage tracing and single-cell sequencing technology. The roles of macrophages in distinct stages of intestinal fibrosis would be also elaborated. Finally, based on the reciprocal interaction between macrophages and intestinal fibrosis, we will propose the potential macrophage targeting anti-intestinal fibrosis therapies.
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Affiliation(s)
- Hui Yao
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China; National Center for Stomatology, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Guoyao Tang
- Department of Oral Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; College of Stomatology, Shanghai Jiao Tong University, Shanghai 200011, China; National Center for Stomatology, Shanghai 200011, China; National Clinical Research Center for Oral Diseases, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
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