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Song S, Feng L, Xi K, Sun Z, Kong D, Luo Z, Pei W, Zhang H. Single-cell profiling of the copy-number heterogeneity in colorectal cancer. Chin Med J (Engl) 2023; 136:707-718. [PMID: 36914941 PMCID: PMC10129169 DOI: 10.1097/cm9.0000000000002469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND With functionally heterogeneous cells, tumors comprise a complex ecosystem to promote tumor adaptability and evolution under strong selective pressure from the given microenvironment. Diversifying tumor cells or intra-tumor heterogeneity is essential for tumor growth, invasion, and immune evasion. However, no reliable method to classify tumor cell subtypes is yet available. In this study, we introduced the single-cell sequencing combined with copy number characteristics to identify the types of tumor cells in microsatellite stable (MSS) colorectal cancer (CRC). METHODS To characterize the somatic copy number alteration (SCNA) of MSS CRC in a single cell profile, we analyzed 26 tissue samples from 19 Korean patients (GSE132465, the Samsung Medical Center [SMC] dataset) and then verified our findings with 15 tissue samples from five Belgian patients (GSE144735, the Katholieke Universiteit Leuven 3 [KUL3] dataset). The Cancer Genome Atlas (TCGA) cohort, GSE39582 cohort, and National Cancer Center (NCC) cohort (24 MSS CRC patients were enrolled in this study between March 2017 and October 2017) were used to validate the clinical features of prognostic signatures. RESULTS We employed single cell RNA-sequencing data to identify three types of tumor cells in MSS CRC by their SCNA characteristics. Among these three types of tumor cells, C1 and C3 had a higher SCNA burden; C1 had significant chromosome 13 and 20 amplification, whereas C3 was the polar opposite of C1, which exhibited deletion in chromosome 13 and 20. The three types of tumor cells exhibited various functions in the tumor microenvironment and harbored different mutations. C1 and C2 were linked to the immune response and hypoxia, respectively, while C3 was critical for cell adhesion activity and tumor angiogenesis. Additionally, one gene ( OLFM4 ) was identified as epithelium-specific biomarker of better prognosis of CRC (TCGA cohort: P = 0.0110; GSE39582 cohort: P = 0.0098; NCC cohort: P = 0.0360). CONCLUSIONS On the basis of copy number characteristics, we illustrated tumor heterogeneity in MSS CRC and identified three types of tumor cells with distinct roles in tumor microenvironment. By understanding heterogeneity in the intricate tumor microenvironment, we gained an insight into the mechanisms of tumor evolution, which may support the development of therapeutic strategies.
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Affiliation(s)
- Shiyu Song
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kexing Xi
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhigang Sun
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Deyang Kong
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhenkai Luo
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wei Pei
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Haizeng Zhang
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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Chauss D, Freiwald T, McGregor R, Yan B, Wang L, Nova-Lamperti E, Kumar D, Zhang Z, Teague H, West EE, Vannella KM, Ramos-Benitez MJ, Bibby J, Kelly A, Malik A, Freeman AF, Schwartz DM, Portilla D, Chertow DS, John S, Lavender P, Kemper C, Lombardi G, Mehta NN, Cooper N, Lionakis MS, Laurence A, Kazemian M, Afzali B. Autocrine vitamin D signaling switches off pro-inflammatory programs of T H1 cells. Nat Immunol 2022; 23:62-74. [PMID: 34764490 PMCID: PMC7612139 DOI: 10.1038/s41590-021-01080-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The molecular mechanisms governing orderly shutdown and retraction of CD4+ type 1 helper T (TH1) cell responses remain poorly understood. Here we show that complement triggers contraction of TH1 responses by inducing intrinsic expression of the vitamin D (VitD) receptor and the VitD-activating enzyme CYP27B1, permitting T cells to both activate and respond to VitD. VitD then initiated the transition from pro-inflammatory interferon-γ+ TH1 cells to suppressive interleukin-10+ cells. This process was primed by dynamic changes in the epigenetic landscape of CD4+ T cells, generating super-enhancers and recruiting several transcription factors, notably c-JUN, STAT3 and BACH2, which together with VitD receptor shaped the transcriptional response to VitD. Accordingly, VitD did not induce interleukin-10 expression in cells with dysfunctional BACH2 or STAT3. Bronchoalveolar lavage fluid CD4+ T cells of patients with COVID-19 were TH1-skewed and showed de-repression of genes downregulated by VitD, from either lack of substrate (VitD deficiency) and/or abnormal regulation of this system.
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Affiliation(s)
- Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Tilo Freiwald
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA,Medic Clinic III, Department of Nephrology, University Hospital Frankfurt, Goethe-University, Frankfurt, Hesse, Germany
| | - Reuben McGregor
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA,Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Estefania Nova-Lamperti
- Molecular and Translational Immunology Laboratory, Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy; Universidad de Concepcion, Concepcion, Chile
| | - Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA,Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Zonghao Zhang
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette IN, USA
| | - Heather Teague
- Laboratory of Inflammation & Cardiometabolic diseases, Cardiovascular Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Erin E West
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kevin M Vannella
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA,Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, NIH, Bethesda, MD, USA
| | - Marcos J Ramos-Benitez
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA,Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, NIH, Bethesda, MD, USA
| | - Jack Bibby
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Audrey Kelly
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Amna Malik
- Department of Medicine, Imperial College London, London, UK
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Daniella M Schwartz
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Didier Portilla
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA,Division of Nephrology and the Center for Immunity, Inflammation and Regenerative Medicine, University of Virginia, VA, USA
| | - Daniel S Chertow
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA,Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, NIH, Bethesda, MD, USA
| | - Susan John
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Paul Lavender
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Claudia Kemper
- Complement and Inflammation Research Section, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA,Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Giovanna Lombardi
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Nehal N Mehta
- Laboratory of Inflammation & Cardiometabolic diseases, Cardiovascular Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nichola Cooper
- Department of Medicine, Imperial College London, London, UK
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Arian Laurence
- Nuffield Department of Medicine, University of Oxford, UK
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA. .,Department of Computer Science, Purdue University, West Lafayette, IN, USA.
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD, USA.
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3
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Ligon MM, Wang C, DeJong EN, Schulz C, Bowdish DME, Mysorekar IU. Single cell and tissue-transcriptomic analysis of murine bladders reveals age- and TNFα-dependent but microbiota-independent tertiary lymphoid tissue formation. Mucosal Immunol 2020; 13:908-918. [PMID: 32366865 PMCID: PMC7572484 DOI: 10.1038/s41385-020-0290-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/02/2020] [Accepted: 03/31/2020] [Indexed: 02/04/2023]
Abstract
Aging has multifaceted effects on the immune system, but how aging affects tissue-specific immunity is not well-defined. Bladder diseases characterized by chronic inflammation are highly prevalent in older women, but mechanisms by which aging promotes these pathologies remain unknown. Tissue transcriptomics of unperturbed, young and aged bladders identified a highly altered immune landscape as a fundamental feature of the aging female bladder. Detailed mapping of immune cells using single cell RNA-sequencing revealed novel subsets of macrophages and dendritic cells and unique changes to the immune repertoire in the aged bladder. B and T cells are highly enriched in aged bladders and spontaneously form organized bladder tertiary lymphoid tissues (bTLTs). Naïve, activated, and germinal center B cells and IgA+ plasma cells are found within bTLT and associated with increased urinary IgA concentrations. bTLTs form with increasing age and their formation is dependent on TNFα. Microbiota are not required to form bTLT, as aged germfree mice also harbor them. Thus, bTLTs require age-dependent TNFα but are independent of the microbiota. Our results indicate that chronic, age-associated inflammation underlies a fundamental alteration to the bladder and establishes a resource for further investigation of the bladder immune system in homeostasis, aging, and disease.
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Affiliation(s)
- Marianne M. Ligon
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Caihong Wang
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Erica N. DeJong
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Christian Schulz
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Dawn M. E. Bowdish
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Indira U. Mysorekar
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.,To whom correspondence should be addressed: Indira U. Mysorekar, Ph.D., Washington University School of Medicine, Depts. of Obstetrics and Gynecology & Pathology and Immunology, 660 S. Euclid Ave., St. Louis, MO 63110, Phone: 314-747-1329, Fax: 314-747-1350,
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4
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Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, Miao Z, Dixon D, Rowell R, McDonald D, Fletcher J, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young MD, Meyer KB, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chédotal A, Roberts I, Göttgens B, Behjati S, Laurenti E, Teichmann SA, Haniffa M. Decoding human fetal liver haematopoiesis. Nature 2019; 574:365-371. [PMID: 31597962 PMCID: PMC6861135 DOI: 10.1038/s41586-019-1652-y] [Citation(s) in RCA: 310] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 09/09/2019] [Indexed: 11/09/2022]
Abstract
Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.
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Affiliation(s)
- Dorin-Mirel Popescu
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Kile Green
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Simone Webb
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Emily F Calderbank
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Meghan Acres
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Maunder
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Peter Vegh
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhichao Miao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - David Dixon
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Rowell
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - David McDonald
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - James Fletcher
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Elizabeth Poyner
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Michael Mather
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Pathology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frankie Greig
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Steven Lisgo
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew Fuller
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ben Millar
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Barbara Innes
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Monika S Kowalczyk
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Bo Li
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marcin Tabaka
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Timothy L Tickle
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Haematology Department, Royal Victoria Infirmary, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Andrew Filby
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Peter Carey
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
- Data Sciences Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit and Department of Paediatrics, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | - Elisa Laurenti
- Department of Haematology and Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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