151
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Huo Y, Wu L, Pang A, Li Q, Hong F, Zhu C, Yang Z, Dai W, Zheng Y, Meng Q, Sun J, Ma S, Hu L, Zhu P, Dong F, Gao X, Jiang E, Hao S, Cheng T. Single-cell dissection of human hematopoietic reconstitution after allogeneic hematopoietic stem cell transplantation. Sci Immunol 2023; 8:eabn6429. [PMID: 36930730 DOI: 10.1126/sciimmunol.abn6429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
Abstract
Hematopoietic stem cell transplantation is an effective regenerative therapy for many malignant, inherited, or autoimmune diseases. However, our understanding of reconstituted hematopoiesis in transplant patients remains limited. Here, we uncover the reconstitution dynamics of human allogeneic hematopoietic stem and progenitor cells (HSPCs) at single-cell resolution after transplantation. Transplanted HSPCs underwent rapid and measurable changes during the first 30 days after transplantation, characterized by a strong proliferative response on the first day. Transcriptomic analysis of HSPCs enabled us to observe that immunoregulatory neutrophil progenitors expressing high levels of the S100A gene family were enriched in granulocyte colony-stimulating factor-mobilized peripheral blood stem cells. Transplant recipients who developed acute graft-versus-host disease (aGVHD) infused fewer S100Ahigh immunoregulatory neutrophil progenitors, immunophenotyped as Lin-CD34+CD66b+CD177+, than those who did not develop aGVHD. Therefore, our study provides insights into the regenerative process of transplanted HSPCs in human patients and identifies a potential criterion for identifying patients at high risk for developing aGVHD early after transplant.
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Affiliation(s)
- Yingying Huo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Linjie Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Aiming Pang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qing Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Zining Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Weiqian Dai
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yawei Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qianqian Meng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jiali Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shihui Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Linping Hu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Fang Dong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Sha Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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152
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Friedrich MJ, Neri P, Kehl N, Michel J, Steiger S, Kilian M, Leblay N, Maity R, Sankowski R, Lee H, Barakat E, Ahn S, Weinhold N, Rippe K, Bunse L, Platten M, Goldschmidt H, Müller-Tidow C, Raab MS, Bahlis NJ. The pre-existing T cell landscape determines the response to bispecific T cell engagers in multiple myeloma patients. Cancer Cell 2023; 41:711-725.e6. [PMID: 36898378 DOI: 10.1016/j.ccell.2023.02.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 11/02/2022] [Accepted: 02/08/2023] [Indexed: 03/11/2023]
Abstract
Bispecific T cell engagers (TCEs) have shown promise in the treatment of various cancers, but the immunological mechanism and molecular determinants of primary and acquired resistance to TCEs remain poorly understood. Here, we identify conserved behaviors of bone marrow-residing T cells in multiple myeloma patients undergoing BCMAxCD3 TCE therapy. We show that the immune repertoire reacts to TCE therapy with cell state-dependent clonal expansion and find evidence supporting the coupling of tumor recognition via major histocompatibility complex class I (MHC class I), exhaustion, and clinical response. We find the abundance of exhausted-like CD8+ T cell clones to be associated with clinical response failure, and we describe loss of target epitope and MHC class I as tumor-intrinsic adaptations to TCEs. These findings advance our understanding of the in vivo mechanism of TCE treatment in humans and provide the rationale for predictive immune-monitoring and conditioning of the immune repertoire to guide future immunotherapy in hematological malignancies.
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Affiliation(s)
- Mirco J Friedrich
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Paola Neri
- Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada; Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Niklas Kehl
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Julius Michel
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Simon Steiger
- Division of Chromatin Networks, BioQuant Center & German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Michael Kilian
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Noémie Leblay
- Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Ranjan Maity
- Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Roman Sankowski
- Department of Neuropathology, Freiburg University Hospital, Freiburg, Germany
| | - Holly Lee
- Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada; Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Elie Barakat
- Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Sungwoo Ahn
- Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada
| | - Niels Weinhold
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, BioQuant Center & German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lukas Bunse
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Neurology, MCTN, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Helmholtz Institute of Translational Oncology (HI-TRON), Mainz, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany; DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim Germany
| | - Hartmut Goldschmidt
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Carsten Müller-Tidow
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Marc-Steffen Raab
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany; Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, Canada; Tom Baker Cancer Center, Department of Hematology and Oncology, Calgary, Canada.
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153
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Raths F, Karimzadeh M, Ing N, Martinez A, Yang Y, Qu Y, Lee TY, Mulligan B, Devkota S, Tilley WT, Hickey TE, Wang B, Giuliano AE, Bose S, Goodarzi H, Ray EC, Cui X, Knott SR. The molecular consequences of androgen activity in the human breast. CELL GENOMICS 2023; 3:100272. [PMID: 36950379 PMCID: PMC10025454 DOI: 10.1016/j.xgen.2023.100272] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/20/2022] [Accepted: 01/30/2023] [Indexed: 03/24/2023]
Abstract
Estrogen and progesterone have been extensively studied in the mammary gland, but the molecular effects of androgen remain largely unexplored. Transgender men are recorded as female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single-cell-resolution transcriptome, chromatin, and spatial profiling of breast tissues from transgender men following androgen therapy. We find canonical androgen receptor gene targets are upregulated in cells expressing the androgen receptor and that paracrine signaling likely drives sex-relevant androgenic effects in other cell types. We also observe involution of the epithelium and a spatial reconfiguration of immune, fibroblast, and vascular cells, and identify a gene regulatory network associated with androgen-induced fat loss. This work elucidates the molecular consequences of androgen activity in the human breast at single-cell resolution.
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Affiliation(s)
- Florian Raths
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mehran Karimzadeh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan Ing
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrew Martinez
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yoona Yang
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Qu
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tian-Yu Lee
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brianna Mulligan
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Suzanne Devkota
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wayne T. Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
| | - Theresa E. Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Bo Wang
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | - Shikha Bose
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Edward C. Ray
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Transgender Surgery and Health Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon R.V. Knott
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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154
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Maniyadath B, Zhang Q, Gupta RK, Mandrup S. Adipose tissue at single-cell resolution. Cell Metab 2023; 35:386-413. [PMID: 36889280 PMCID: PMC10027403 DOI: 10.1016/j.cmet.2023.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 03/09/2023]
Abstract
Adipose tissue exhibits remarkable plasticity with capacity to change in size and cellular composition under physiological and pathophysiological conditions. The emergence of single-cell transcriptomics has rapidly transformed our understanding of the diverse array of cell types and cell states residing in adipose tissues and has provided insight into how transcriptional changes in individual cell types contribute to tissue plasticity. Here, we present a comprehensive overview of the cellular atlas of adipose tissues focusing on the biological insight gained from single-cell and single-nuclei transcriptomics of murine and human adipose tissues. We also offer our perspective on the exciting opportunities for mapping cellular transitions and crosstalk, which have been made possible by single-cell technologies.
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Affiliation(s)
- Babukrishna Maniyadath
- Center for Functional Genomics and Tissue Plasticity, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Qianbin Zhang
- Department of Internal Medicine, Touchstone Diabetes Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rana K Gupta
- Department of Internal Medicine, Touchstone Diabetes Center, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Susanne Mandrup
- Center for Functional Genomics and Tissue Plasticity, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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155
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Gurtner A, Borrelli C, Gonzalez-Perez I, Bach K, Acar IE, Núñez NG, Crepaz D, Handler K, Vu VP, Lafzi A, Stirm K, Raju D, Gschwend J, Basler K, Schneider C, Slack E, Valenta T, Becher B, Krebs P, Moor AE, Arnold IC. Active eosinophils regulate host defence and immune responses in colitis. Nature 2023; 615:151-157. [PMID: 36509106 PMCID: PMC9977678 DOI: 10.1038/s41586-022-05628-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
In the past decade, single-cell transcriptomics has helped to uncover new cell types and states and led to the construction of a cellular compendium of health and disease. Despite this progress, some difficult-to-sequence cells remain absent from tissue atlases. Eosinophils-elusive granulocytes that are implicated in a plethora of human pathologies1-5-are among these uncharted cell types. The heterogeneity of eosinophils and the gene programs that underpin their pleiotropic functions remain poorly understood. Here we provide a comprehensive single-cell transcriptomic profiling of mouse eosinophils. We identify an active and a basal population of intestinal eosinophils, which differ in their transcriptome, surface proteome and spatial localization. By means of a genome-wide CRISPR inhibition screen and functional assays, we reveal a mechanism by which interleukin-33 (IL-33) and interferon-γ (IFNγ) induce the accumulation of active eosinophils in the inflamed colon. Active eosinophils are endowed with bactericidal and T cell regulatory activity, and express the co-stimulatory molecules CD80 and PD-L1. Notably, active eosinophils are enriched in the lamina propria of a small cohort of patients with inflammatory bowel disease, and are closely associated with CD4+ T cells. Our findings provide insights into the biology of eosinophils and highlight the crucial contribution of this cell type to intestinal homeostasis, immune regulation and host defence. Furthermore, we lay a framework for the characterization of eosinophils in human gastrointestinal diseases.
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Affiliation(s)
- Alessandra Gurtner
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | | | - Karsten Bach
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nicolás G Núñez
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Daniel Crepaz
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Vivian P Vu
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Kristin Stirm
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Deeksha Raju
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Julia Gschwend
- Institute of Physiology, University of Zürich, Zürich, Switzerland
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
| | | | - Emma Slack
- Institute for Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
- Botnar Research Center for Child Health, Basel, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Isabelle C Arnold
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland.
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156
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The early neutrophil-committed progenitors aberrantly differentiate into immunoregulatory monocytes during emergency myelopoiesis. Cell Rep 2023; 42:112165. [PMID: 36862552 DOI: 10.1016/j.celrep.2023.112165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/08/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Inflammatory stimuli cause a state of emergency myelopoiesis leading to neutrophil-like monocyte expansion. However, their function, the committed precursors, or growth factors remain elusive. In this study we find that Ym1+Ly6Chi monocytes, an immunoregulatory entity of neutrophil-like monocytes, arise from progenitors of neutrophil 1 (proNeu1). Granulocyte-colony stimulating factor (G-CSF) favors the production of neutrophil-like monocytes through previously unknown CD81+CX3CR1lo monocyte precursors. GFI1 promotes the differentiation of proNeu2 from proNeu1 at the cost of producing neutrophil-like monocytes. The human counterpart of neutrophil-like monocytes that also expands in response to G-CSF is found in CD14+CD16- monocyte fraction. The human neutrophil-like monocytes are discriminated from CD14+CD16- classical monocytes by CXCR1 expression and the capacity to suppress T cell proliferation. Collectively, our findings suggest that the aberrant expansion of neutrophil-like monocytes under inflammatory conditions is a process conserved between mouse and human, which may be beneficial for the resolution of inflammation.
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157
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McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS. The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR + CD8 + effector state and its deletion improves checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528833. [PMID: 36824931 PMCID: PMC9948998 DOI: 10.1101/2023.02.16.528833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
T cell exhaustion (T EX ) impairs the ability of T cells to clear chronic infection or cancer. While exhausted T cells are hypofunctional, some exhausted T cells retain effector gene signatures, a feature that is associated with expression of KLRs (killer lectin-like receptors). Although KLR + T cells may improve control of chronic antigen, the signaling molecules regulating this population are poorly understood. Using scRNA-seq, flow cytometry, RNA velocity, and scTCR-seq, we demonstrate that deleting the pseudokinase Trib1 shifts T EX towards CX3CR1 + intermediates (T INT ) with robust enrichment of KLR + CD8 + T cells (T KLR ) via clonal T cell expansion. These changes are associated with globally increased KLR gene expression throughout the exhaustion program. Further, Trib1 loss augments anti-PD-L1 blockade to improve viral clearance by expanding the T KLR population. Together, these data identify Trib1 as an important regulator of T cell exhaustion whose targeting enhances the KLR + effector state and improves the response to checkpoint inhibitor therapy.
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Affiliation(s)
- Susan E. McClory
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oishi Bardhan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly S. Rome
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert B. Faryabi
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martha S. Jordan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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158
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Salta E, Lazarov O, Fitzsimons CP, Tanzi R, Lucassen PJ, Choi SH. Adult hippocampal neurogenesis in Alzheimer's disease: A roadmap to clinical relevance. Cell Stem Cell 2023; 30:120-136. [PMID: 36736288 PMCID: PMC10082636 DOI: 10.1016/j.stem.2023.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Adult hippocampal neurogenesis (AHN) drops sharply during early stages of Alzheimer's disease (AD), via unknown mechanisms, and correlates with cognitive status in AD patients. Understanding AHN regulation in AD could provide a framework for innovative pharmacological interventions. We here combine molecular, behavioral, and clinical data and critically discuss the multicellular complexity of the AHN niche in relation to AD pathophysiology. We further present a roadmap toward a better understanding of the role of AHN in AD by probing the promises and caveats of the latest technological advancements in the field and addressing the conceptual and methodological challenges ahead.
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Affiliation(s)
- Evgenia Salta
- Laboratory of Neurogenesis and Neurodegeneration, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA, Amsterdam, The Netherlands
| | - Orly Lazarov
- Department of Anatomy and Cell Biology, College of Medicine, The University of Illinois at Chicago, 808 S Wood St., Chicago, IL 60612, USA
| | - Carlos P Fitzsimons
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Rudolph Tanzi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
| | - Paul J Lucassen
- Brain Plasticity group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands; Center for Urban Mental Health, University of Amsterdam, Kruislaan 404, 1098 SM, Amsterdam, The Netherlands.
| | - Se Hoon Choi
- Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, McCance Center for Brain Health, 114 16th Street, Boston, MA 02129, USA.
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159
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Song H, Morrow BE. Tbx2 and Tbx3 regulate cell fate progression of the otic vesicle for inner ear development. Dev Biol 2023; 494:71-84. [PMID: 36521641 PMCID: PMC9870991 DOI: 10.1016/j.ydbio.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/05/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
The morphogenesis of the otic vesicle (OV) to form inner ear organs serves as an excellent model system to understand cell fate acquisition on a single cell level. Tbx2 and Tbx3 (Tbx2/3) encode closely related T-box transcription factors that are expressed widely in the mammalian OV. Inactivation of both genes in the OV (Tbx2/3cKO) results in failed morphogenesis into inner ear organs. To understand the basis of these defects, single cell RNA-sequencing (scRNA-seq) was performed on the OV lineage, in controls versus Tbx2/3cKO embryos. We identified a multipotent population termed otic progenitors in controls that are marked by expression of the known otic placode markers Eya1, Sox2, and Sox3 as well as new markers Fgf18, Cxcl12, and Pou3f3. The otic progenitor population was increased three-fold in Tbx2/3cKO embryos, concomitant with dysregulation of genes in these cells as well as reduced progression to more differentiated states of prosensory and nonsensory cells. An ectopic neural population of cells was detected in the posterior OV of Tbx2/3cKO embryos but had reduced maturation to delaminated neural cells. As all three cell fates were affected in Tbx2/3cKO embryos, we suggest that Tbx2/3 promotes progression of multipotent otic progenitors to more differentiated cell types in the OV.
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Affiliation(s)
- Hansoo Song
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY, USA.
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160
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Miao Y, Djeffal Y, De Simone A, Zhu K, Lee JG, Lu Z, Silberfeld A, Rao J, Tarazona OA, Mongera A, Rigoni P, Diaz-Cuadros M, Song LMS, Di Talia S, Pourquié O. Reconstruction and deconstruction of human somitogenesis in vitro. Nature 2023; 614:500-508. [PMID: 36543321 PMCID: PMC10018515 DOI: 10.1038/s41586-022-05655-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The vertebrate body displays a segmental organization that is most conspicuous in the periodic organization of the vertebral column and peripheral nerves. This metameric organization is first implemented when somites, which contain the precursors of skeletal muscles and vertebrae, are rhythmically generated from the presomitic mesoderm. Somites then become subdivided into anterior and posterior compartments that are essential for vertebral formation and segmental patterning of the peripheral nervous system1-4. How this key somitic subdivision is established remains poorly understood. Here we introduce three-dimensional culture systems of human pluripotent stem cells called somitoids and segmentoids, which recapitulate the formation of somite-like structures with anteroposterior identity. We identify a key function of the segmentation clock in converting temporal rhythmicity into the spatial regularity of anterior and posterior somitic compartments. We show that an initial 'salt and pepper' expression of the segmentation gene MESP2 in the newly formed segment is transformed into compartments of anterior and posterior identity through an active cell-sorting mechanism. Our research demonstrates that the major patterning modules that are involved in somitogenesis, including the clock and wavefront, anteroposterior polarity patterning and somite epithelialization, can be dissociated and operate independently in our in vitro systems. Together, we define a framework for the symmetry-breaking process that initiates somite polarity patterning. Our work provides a platform for decoding general principles of somitogenesis and advancing knowledge of human development.
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Affiliation(s)
- Yuchuan Miao
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yannis Djeffal
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Kongju Zhu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jong Gwan Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziqi Lu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Andrew Silberfeld
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jyoti Rao
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar A Tarazona
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alessandro Mongera
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Pietro Rigoni
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Min Sook Song
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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161
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Haghverdi L, Ludwig LS. Single-cell multi-omics and lineage tracing to dissect cell fate decision-making. Stem Cell Reports 2023; 18:13-25. [PMID: 36630900 PMCID: PMC9860164 DOI: 10.1016/j.stemcr.2022.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
The concept of cell fate relates to the future identity of a cell, and its daughters, which is obtained via cell differentiation and division. Understanding, predicting, and manipulating cell fate has been a long-sought goal of developmental and regenerative biology. Recent insights obtained from single-cell genomic and integrative lineage-tracing approaches have further aided to identify molecular features predictive of cell fate. In this perspective, we discuss these approaches with a focus on theoretical concepts and future directions of the field to dissect molecular mechanisms underlying cell fate.
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Affiliation(s)
- Laleh Haghverdi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
| | - Leif S. Ludwig
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany,Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany,Corresponding author
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162
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Zhu Q, Ge J, Liu Y, Xu JW, Yan S, Zhou F. Decoding anterior-posterior axis emergence among mouse, monkey, and human embryos. Dev Cell 2023; 58:63-79.e4. [PMID: 36626872 DOI: 10.1016/j.devcel.2022.12.004] [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] [Received: 02/03/2022] [Revised: 08/23/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Anterior-posterior axis formation regulated by the distal visceral endoderm (DVE) and anterior visceral endoderm (AVE) is essential for peri-implantation embryogenesis. However, the principles of the origin and specialization of DVE and AVE remain elusive. Here, with single-cell transcriptome analysis and pseudotime prediction, we show that DVE and AVE independently originate from the specialized primary endoderm in mouse blastocysts. Along distinct developmental paths, these two lineages, respectively, undergo four representative states with stage-specific transcriptional patterns around implantation. Further comparative analysis shows that AVE, but not DVE, is detected in human and non-human primate embryos, defining differences in polarity formation across species. Moreover, stem cell-assembled human blastoids lack DVE or AVE precursors, implying that additional induction of stem cells with DVE/AVE potential could promote the current embryo-like models and their post-implantation growth. Our work provides insight into understanding of embryonic polarity formation and early mammalian development.
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Affiliation(s)
- Qingyuan Zhu
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jitao Ge
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ying Liu
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jia-Wen Xu
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shengyi Yan
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fan Zhou
- Haihe Laboratory of Cell Ecosystem, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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163
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Sun ED, Ma R, Zou J. Dynamic visualization of high-dimensional data. NATURE COMPUTATIONAL SCIENCE 2023; 3:86-100. [PMID: 38177955 DOI: 10.1038/s43588-022-00380-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/16/2022] [Indexed: 01/06/2024]
Abstract
Dimensionality reduction (DR) is commonly used to project high-dimensional data into lower dimensions for visualization, which could then generate new insights and hypotheses. However, DR algorithms introduce distortions in the visualization and cannot faithfully represent all relations in the data. Thus, there is a need for methods to assess the reliability of DR visualizations. Here we present DynamicViz, a framework for generating dynamic visualizations that capture the sensitivity of DR visualizations to perturbations in the data resulting from bootstrap sampling. DynamicViz can be applied to all commonly used DR methods. We show the utility of dynamic visualizations in diagnosing common interpretative pitfalls of static visualizations and extending existing single-cell analyses. We introduce the variance score to quantify the dynamic variability of observations in these visualizations. The variance score characterizes natural variability in the data and can be used to optimize DR algorithm implementations.
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Affiliation(s)
- Eric D Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Rong Ma
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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164
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Faure L, Soldatov R, Kharchenko PV, Adameyko I. scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data. Bioinformatics 2023; 39:btac746. [PMID: 36394263 PMCID: PMC9805561 DOI: 10.1093/bioinformatics/btac746] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/30/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
SUMMARY scFates provides an extensive toolset for the analysis of dynamic trajectories comprising tree learning, feature association testing, branch differential expression and with a focus on cell biasing and fate splits at the level of bifurcations. It is meant to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g. RNA and ATAC). AVAILABILITY AND IMPLEMENTATION scFates is released as open-source software under the BSD 3-Clause 'New' License and is available from the Python Package Index at https://pypi.org/project/scFates/. The source code is available on GitHub at https://github.com/LouisFaure/scFates/. Code reproduction and tutorials on published datasets are available on GitHub at https://github.com/LouisFaure/scFates_notebooks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Louis Faure
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
| | - Ruslan Soldatov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- Altos Labs, San Diego, CA 92121, USA
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, 1090 Vienna, Austria
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165
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Sountoulidis A, Marco Salas S, Braun E, Avenel C, Bergenstråhle J, Theelke J, Vicari M, Czarnewski P, Liontos A, Abalo X, Andrusivová Ž, Mirzazadeh R, Asp M, Li X, Hu L, Sariyar S, Martinez Casals A, Ayoglu B, Firsova A, Michaëlsson J, Lundberg E, Wählby C, Sundström E, Linnarsson S, Lundeberg J, Nilsson M, Samakovlis C. A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nat Cell Biol 2023; 25:351-365. [PMID: 36646791 PMCID: PMC9928586 DOI: 10.1038/s41556-022-01064-x] [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: 03/18/2022] [Accepted: 11/23/2022] [Indexed: 01/18/2023]
Abstract
The lung contains numerous specialized cell types with distinct roles in tissue function and integrity. To clarify the origins and mechanisms generating cell heterogeneity, we created a comprehensive topographic atlas of early human lung development. Here we report 83 cell states and several spatially resolved developmental trajectories and predict cell interactions within defined tissue niches. We integrated single-cell RNA sequencing and spatially resolved transcriptomics into a web-based, open platform for interactive exploration. We show distinct gene expression programmes, accompanying sequential events of cell differentiation and maturation of the secretory and neuroendocrine cell types in proximal epithelium. We define the origin of airway fibroblasts associated with airway smooth muscle in bronchovascular bundles and describe a trajectory of Schwann cell progenitors to intrinsic parasympathetic neurons controlling bronchoconstriction. Our atlas provides a rich resource for further research and a reference for defining deviations from homeostatic and repair mechanisms leading to pulmonary diseases.
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Affiliation(s)
- Alexandros Sountoulidis
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sergio Marco Salas
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emelie Braun
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Christophe Avenel
- grid.8993.b0000 0004 1936 9457Department of Information Technology, Uppsala University, Uppsala, Sweden ,grid.452834.c0000 0004 5911 2402BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Joseph Bergenstråhle
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonas Theelke
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marco Vicari
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Paulo Czarnewski
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Andreas Liontos
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Xesus Abalo
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Žaneta Andrusivová
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Reza Mirzazadeh
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Michaela Asp
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Xiaofei Li
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lijuan Hu
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Sanem Sariyar
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Martinez Casals
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Burcu Ayoglu
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Alexandra Firsova
- grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Solna, Sweden ,grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jakob Michaëlsson
- grid.4714.60000 0004 1937 0626Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Emma Lundberg
- grid.5037.10000000121581746Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Carolina Wählby
- grid.8993.b0000 0004 1936 9457Department of Information Technology, Uppsala University, Uppsala, Sweden ,grid.452834.c0000 0004 5911 2402BioImage Informatics Facility, Science for Life Laboratory, SciLifeLab, Sweden
| | - Erik Sundström
- grid.4714.60000 0004 1937 0626Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Sten Linnarsson
- grid.4714.60000 0004 1937 0626Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Joakim Lundeberg
- grid.5037.10000000121581746Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Solna, Sweden. .,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Christos Samakovlis
- Science for Life Laboratory, Solna, Sweden. .,Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden. .,Molecular Pneumology, Cardiopulmonary Institute, Justus Liebig University, Giessen, Germany.
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166
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Wu S, Schmitz U. Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination. Comput Struct Biotechnol J 2023; 21:2373-2380. [PMID: 37066125 PMCID: PMC10091034 DOI: 10.1016/j.csbj.2023.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Single-cell sequencing technologies have revolutionised the life sciences and biomedical research. Single-cell sequencing provides high-resolution data on cell heterogeneity, allowing high-fidelity cell type identification, and lineage tracking. Computational algorithms and mathematical models have been developed to make sense of the data, compensate for errors and simulate the biological processes, which has led to breakthroughs in our understanding of cell differentiation, cell-fate determination and tissue cell composition. The development of long-read (a.k.a. third-generation) sequencing technologies has produced powerful tools for investigating alternative splicing, isoform expression (at the RNA level), genome assembly and the detection of complex structural variants (at the DNA level). In this review, we provide an overview of the recent advancements in single-cell and long-read sequencing technologies, with a particular focus on the computational algorithms that help in correcting, analysing, and interpreting the resulting data. Additionally, we review some mathematical models that use single-cell and long-read sequencing data to study cell-fate determination and alternative splicing, respectively. Moreover, we highlight the emerging opportunities in modelling cell-fate determination that result from the combination of single-cell and long-read sequencing technologies.
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167
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Singh A, Tiwari VK. Transcriptional networks of transient cell states during human prefrontal cortex development. Front Mol Neurosci 2023; 16:1126438. [PMID: 37138706 PMCID: PMC10150774 DOI: 10.3389/fnmol.2023.1126438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/15/2023] [Indexed: 05/05/2023] Open
Abstract
The human brain is divided into various anatomical regions that control and coordinate unique functions. The prefrontal cortex (PFC) is a large brain region that comprises a range of neuronal and non-neuronal cell types, sharing extensive interconnections with subcortical areas, and plays a critical role in cognition and memory. A timely appearance of distinct cell types through embryonic development is crucial for an anatomically perfect and functional brain. Direct tracing of cell fate development in the human brain is not possible, but single-cell transcriptome sequencing (scRNA-seq) datasets provide the opportunity to dissect cellular heterogeneity and its molecular regulators. Here, using scRNA-seq data of human PFC from fetal stages, we elucidate distinct transient cell states during PFC development and their underlying gene regulatory circuitry. We further identified that distinct intermediate cell states consist of specific gene regulatory modules essential to reach terminal fate using discrete developmental paths. Moreover, using in silico gene knock-out and over-expression analysis, we validated crucial gene regulatory components during the lineage specification of oligodendrocyte progenitor cells. Our study illustrates unique intermediate states and specific gene interaction networks that warrant further investigation for their functional contribution to typical brain development and discusses how this knowledge can be harvested for therapeutic intervention in challenging neurodevelopmental disorders.
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Affiliation(s)
- Aditi Singh
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University, Belfast, United Kingdom
| | - Vijay K. Tiwari
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University, Belfast, United Kingdom
- Institute of Molecular Medicine, University of Southern Denmark, Odense C, Denmark
- Danish Institute for Advanced Study (DIAS), Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- *Correspondence: Vijay K. Tiwari, ;
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168
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Gupta R, Cerletti D, Gut G, Oxenius A, Claassen M. Simulation-based inference of differentiation trajectories from RNA velocity fields. CELL REPORTS METHODS 2022; 2:100359. [PMID: 36590685 PMCID: PMC9795361 DOI: 10.1016/j.crmeth.2022.100359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/02/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022]
Abstract
We report Cytopath, a method for trajectory inference that takes advantage of transcriptional activity information from the RNA velocity of single cells to perform trajectory inference. Cytopath performs this task by defining a Markov chain model, simulating an ensemble of possible differentiation trajectories, and constructing a consensus trajectory. We show that Cytopath can recapitulate the topological and molecular characteristics of the differentiation process under study. In our analysis, we include differentiation trajectories with varying bifurcated, circular, convergent, and mixed topologies studied in single-snapshot as well as time-series single-cell RNA sequencing experiments. We demonstrate the capability to reconstruct differentiation trajectories, assess the association of RNA velocity-based pseudotime with actually elapsed process time, and identify drawbacks in current state-of-the art trajectory inference approaches.
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Affiliation(s)
- Revant Gupta
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Dario Cerletti
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gilles Gut
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
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169
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Mohanty SK, Maryam S, Gautam V, Mittal A, Gupta K, Arora R, Bhadra W, Mishra T, Sengupta D, Ahuja G. Transcriptional advantage influence odorant receptor gene choice. Brief Funct Genomics 2022; 22:281-290. [DOI: 10.1093/bfgp/elac052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/13/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Abstract
Odorant receptors (ORs) obey mutual exclusivity and monoallelic mode of expression. Efforts are ongoing to decipher the molecular mechanism that drives the ‘one-neuron-one-receptor’ rule of olfaction. Recently, single-cell profiling of olfactory sensory neurons (OSNs) revealed the expression of multiple ORs in the immature neurons, suggesting that the OR gene choice mechanism is much more complex than previously described by the silence-all-and-activate-one model. These results also led to the genesis of two possible mechanistic models i.e. winner-takes-all and stochastic selection. We developed Reverse Cell Tracking (RCT), a novel computational framework that facilitates OR-guided cellular backtracking by leveraging Uniform Manifold Approximation and Projection embeddings from RNA Velocity Workflow. RCT-based trajectory backtracking, coupled with statistical analysis, revealed the OR gene choice bias for the transcriptionally advanced (highest expressed) OR during neuronal differentiation. Interestingly, the observed selection bias was uniform for all ORs across different spatial zones or their relative expression within the olfactory organ. We validated these findings on independent datasets and further confirmed that the OR gene selection may be regulated by Upf3b. Lastly, our RNA dynamics-based tracking of the differentiation cascade revealed a transition cell state that harbors mixed molecular identities of immature and mature OSNs, and their relative abundance is regulated by Upf3b.
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Affiliation(s)
- Sanjay Kumar Mohanty
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Sidrah Maryam
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Vishakha Gautam
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Aayushi Mittal
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Krishan Gupta
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computer Science and Engineering, , Okhla, Phase III, New Delhi 110020, India
| | - Radhika Arora
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Wrik Bhadra
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
| | - Tripti Mishra
- Pathfinder Research and Training Foundation , Uttar Pradesh 201308, India
| | - Debarka Sengupta
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computer Science and Engineering, , Okhla, Phase III, New Delhi 110020, India
| | - Gaurav Ahuja
- Indraprastha Institute of Information Technology-Delhi (IIIT-Delhi) Department of Computational Biology, , Okhla, Phase III, New Delhi 110020, India
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170
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Single-cell microglial transcriptomics during demyelination defines a microglial state required for lytic carcass clearance. Mol Neurodegener 2022; 17:82. [PMID: 36514132 PMCID: PMC9746011 DOI: 10.1186/s13024-022-00584-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Microglia regulate the response to injury and disease in the brain and spinal cord. In white matter diseases microglia may cause demyelination. However, how microglia respond and regulate demyelination is not fully understood. METHODS To understand how microglia respond during demyelination, we fed mice cuprizone-a potent demyelinating agent-and assessed the dynamics of genetically fate-mapped microglia. We then used single-cell RNA sequencing to identify and track the microglial subpopulations that arise during demyelination. To understand how microglia contribute to the clearance of dead oligodendrocytes, we ablated microglia starting at the peak of cuprizone-induced cell death and used the viability dye acridine orange to monitor apoptotic and lytic cell morphologies after microglial ablation. Lastly, we treated serum-free primary microglial cultures to model distinct aspects of cuprizone-induced demyelination and assessed the response. RESULTS The cuprizone diet generated a robust microglial response by week 4 of the diet. Single-cell RNA sequencing at this time point revealed the presence of several cuprizone-associated microglia (CAM) clusters. These clusters expressed a transcriptomic signature indicative of cytokine regulation and reactive oxygen species production with altered lysosomal and metabolic changes consistent with ongoing phagocytosis. Using acridine orange to monitor apoptotic and lytic cell death after microglial ablation, we found that microglia preferentially phagocytose lytic carcasses. In culture, microglia exposed to lytic carcasses partially recapitulated the CAM state, suggesting that phagocytosis contributes to this distinct microglial state during cuprizone demyelination. CONCLUSIONS Microglia serve multiple roles during demyelination, yet their transcriptomic state resembles other neurodegenerative conditions. The phagocytosis of cellular debris is likely a universal cause for a common neurodegenerative microglial state.
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171
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Liu Z, Shi H, Xu J, Yang Q, Ma Q, Mao X, Xu Z, Zhou Y, Da Q, Cai Y, Fulton DJ, Dong Z, Sodhi A, Caldwell RB, Huo Y. Single-cell transcriptome analyses reveal microglia types associated with proliferative retinopathy. JCI Insight 2022; 7:160940. [PMID: 36264636 PMCID: PMC9746914 DOI: 10.1172/jci.insight.160940] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/18/2022] [Indexed: 01/14/2023] Open
Abstract
Pathological angiogenesis is a major cause of irreversible blindness in individuals of all age groups with proliferative retinopathy (PR). Mononuclear phagocytes (MPs) within neovascular areas contribute to aberrant retinal angiogenesis. Due to their cellular heterogeneity, defining the roles of MP subsets in PR onset and progression has been challenging. Here, we aimed to investigate the heterogeneity of microglia associated with neovascularization and to characterize the transcriptional profiles and metabolic pathways of proangiogenic microglia in a mouse model of oxygen-induced PR (OIR). Using transcriptional single-cell sorting, we comprehensively mapped all microglia populations in retinas of room air (RA) and OIR mice. We have unveiled several unique types of PR-associated microglia (PRAM) and identified markers, signaling pathways, and regulons associated with these cells. Among these microglia subpopulations, we found a highly proliferative microglia subset with high self-renewal capacity and a hypermetabolic microglia subset that expresses high levels of activating microglia markers, glycolytic enzymes, and proangiogenic Igf1. IHC staining shows that these PRAM were spatially located within or around neovascular tufts. These unique types of microglia have the potential to promote retinal angiogenesis, which may have important implications for future treatment of PR and other pathological ocular angiogenesis-related diseases.
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Affiliation(s)
- Zhiping Liu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Huidong Shi
- Georgia Cancer Center and,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Jiean Xu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qiuhua Yang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qian Ma
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Xiaoxiao Mao
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Zhimin Xu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Yaqi Zhou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qingen Da
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongfeng Cai
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - David J.R. Fulton
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia, USA
| | - Akrit Sodhi
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ruth B. Caldwell
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Yuqing Huo
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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172
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Sinha S, Sparks HD, Labit E, Robbins HN, Gowing K, Jaffer A, Kutluberk E, Arora R, Raredon MSB, Cao L, Swanson S, Jiang P, Hee O, Pope H, Workentine M, Todkar K, Sharma N, Bharadia S, Chockalingam K, de Almeida LGN, Adam M, Niklason L, Potter SS, Seifert AW, Dufour A, Gabriel V, Rosin NL, Stewart R, Muench G, McCorkell R, Matyas J, Biernaskie J. Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer. Cell 2022; 185:4717-4736.e25. [PMID: 36493752 PMCID: PMC9888357 DOI: 10.1016/j.cell.2022.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 08/24/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022]
Abstract
Adult mammalian skin wounds heal by forming fibrotic scars. We report that full-thickness injuries of reindeer antler skin (velvet) regenerate, whereas back skin forms fibrotic scar. Single-cell multi-omics reveal that uninjured velvet fibroblasts resemble human fetal fibroblasts, whereas back skin fibroblasts express inflammatory mediators mimicking pro-fibrotic adult human and rodent fibroblasts. Consequently, injury elicits site-specific immune responses: back skin fibroblasts amplify myeloid infiltration and maturation during repair, whereas velvet fibroblasts adopt an immunosuppressive phenotype that restricts leukocyte recruitment and hastens immune resolution. Ectopic transplantation of velvet to scar-forming back skin is initially regenerative, but progressively transitions to a fibrotic phenotype akin to the scarless fetal-to-scar-forming transition reported in humans. Skin regeneration is diminished by intensifying, or enhanced by neutralizing, these pathologic fibroblast-immune interactions. Reindeer represent a powerful comparative model for interrogating divergent wound healing outcomes, and our results nominate decoupling of fibroblast-immune interactions as a promising approach to mitigate scar.
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Affiliation(s)
- Sarthak Sinha
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Holly D Sparks
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hayley N Robbins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kevin Gowing
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Arzina Jaffer
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Eren Kutluberk
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rohit Arora
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Micha Sam Brickman Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT, USA
| | - Leslie Cao
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Peng Jiang
- Morgridge Institute for Research, Madison, WI, USA
| | - Olivia Hee
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Hannah Pope
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Matt Workentine
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Kiran Todkar
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nilesh Sharma
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Shyla Bharadia
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Luiz G N de Almeida
- McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Mike Adam
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Laura Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Vascular Biology and Therapeutics, Yale University, New Haven, CT, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Antoine Dufour
- McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
| | - Vincent Gabriel
- Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; McCaig Institute, University of Calgary, Calgary, AB, Canada; Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Nicole L Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, USA
| | - Greg Muench
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Robert McCorkell
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - John Matyas
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; McCaig Institute, University of Calgary, Calgary, AB, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada; Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada; Hotchkiss Brain Institute, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, Calgary, AB, Canada.
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173
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Li H, Dixon EE, Wu H, Humphreys BD. Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis. Cell Metab 2022; 34:1977-1998.e9. [PMID: 36265491 PMCID: PMC9742301 DOI: 10.1016/j.cmet.2022.09.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/19/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
The underlying cellular events driving kidney fibrogenesis and metabolic dysfunction are incompletely understood. Here, we employed single-cell combinatorial indexing RNA sequencing to analyze 24 mouse kidneys from two fibrosis models. We profiled 309,666 cells in one experiment, representing 50 cell types/states encompassing epithelial, endothelial, immune, and stromal populations. Single-cell analysis identified diverse injury states of the proximal tubule, including two distinct early-phase populations with dysregulated lipid and amino acid metabolism, respectively. Lipid metabolism was defective in the chronic phase but was transiently activated in the very early stages of ischemia-induced injury, where we discovered increased lipid deposition and increased fatty acid β-oxidation. Perilipin 2 was identified as a surface marker of intracellular lipid droplets, and its knockdown in vitro disrupted cell energy state maintenance during lipid accumulation. Surveying epithelial cells across nephron segments identified shared and unique injury responses. Stromal cells exhibited high heterogeneity and contributed to fibrogenesis by epithelial-stromal crosstalk.
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Affiliation(s)
- Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA.
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174
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Zhou J, Wei A, Bertsch A, Renaud P. High precision, high throughput generation of droplets containing single cells. LAB ON A CHIP 2022; 22:4841-4848. [PMID: 36416090 DOI: 10.1039/d2lc00841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The Poisson limit is a major problem for the isolation of single cells in different single-cell technologies and applications. In droplet-based single-cell assays, a scheme that is increasingly popular, the intrinsic randomness during single-cell encapsulation in droplets requires most of the created droplets to be empty, which has a profound impact on the efficiency and throughput of such techniques, and on the predictability of the combinatory droplet assays. Here we present a simple passive microfluidic system overcoming this limitation with unprecedented efficacy, allowing the generation of single-cell droplets for a wide range of operating conditions, with extremely high throughput (more than 22 000 single-cell loaded droplets per minute) and with an extremely low fault ratio (doublets or empty droplets), applicable to any cells and deformable particles. This versatile technique will shift the paradigm of single-cell encapsulation and will impact single-cell sequencing, rare cell isolation, multicellular/bead studies in immunology or cancer biology, etc.
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Affiliation(s)
- Jiande Zhou
- Laboratory of Microsystems 4, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Amaury Wei
- Laboratory of Microsystems 4, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Arnaud Bertsch
- Laboratory of Microsystems 4, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Philippe Renaud
- Laboratory of Microsystems 4, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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175
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Hu H, Duan Y, Wang K, Fu H, Liao Y, Wang T, Zhang Z, Kang F, Zhang B, Zhang H, Huo F, Yin Y, Chen G, Hu H, Cai H, Tian W, Li Z. Dental niche cells directly contribute to tooth reconstitution and morphogenesis. Cell Rep 2022; 41:111737. [PMID: 36476878 DOI: 10.1016/j.celrep.2022.111737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/10/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Mammalian teeth develop from the inductive epithelial-mesenchymal interaction, an important mechanism shared by many organs. The cellular basis for such interaction remains elusive. Here, we generate a dual-fluorescence model to track and analyze dental cells from embryonic to postnatal stages, in which Pitx2+ epithelium and Msx1+ mesenchyme are sufficient for tooth reconstitution. Single-cell RNA sequencing and spatial mapping further revealed critical cellular dynamics during molar development, where tooth germs are organized by Msx1+Sdc1+ dental papilla and surrounding dental niche. Surprisingly, niche cells are more efficient in tooth reconstitution and can directly regenerate papilla cells through interaction with dental epithelium. Finally, from the dental niche, we identify a group of previously unappreciated migratory Msx1+ Sox9+ cells as the potential cell origin for dental papilla. Our results indicate that the dental niche cells directly contribute to tooth organogenesis and provide critical insights into the essential cell composition for tooth engineering.
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Affiliation(s)
- Hong Hu
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yufeng Duan
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China; National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China; National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kun Wang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Huancheng Fu
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuansong Liao
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tianshu Wang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Ziwei Zhang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fanchen Kang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China; National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Baiquan Zhang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haiying Zhang
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fangjun Huo
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China; National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China; National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yike Yin
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guoqing Chen
- National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China; School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongbo Hu
- Department of Rheumatology and Immunology, Department of Urology, Department of Pathology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Haoyang Cai
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Weidong Tian
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China; National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China; National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Zhonghan Li
- State Key Laboratory of Oral Disease, West China Hospital of Stomatology, Center of Growth Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu, China; National Engineering Laboratory for Oral Regenerative Medicine, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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176
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Su M, Pan T, Chen QZ, Zhou WW, Gong Y, Xu G, Yan HY, Li S, Shi QZ, Zhang Y, He X, Jiang CJ, Fan SC, Li X, Cairns MJ, Wang X, Li YS. Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications. Mil Med Res 2022; 9:68. [PMID: 36461064 PMCID: PMC9716519 DOI: 10.1186/s40779-022-00434-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications.
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Affiliation(s)
- Min Su
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tao Pan
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiu-Zhen Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Wei-Wei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yi Gong
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.,Department of Immunology, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Xu
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Huan-Yu Yan
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Si Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Qiao-Zhen Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ya Zhang
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Xiao He
- Department of Laboratory Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, 401174, China
| | | | - Shi-Cai Fan
- Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China, Shenzhen, 518110, Guangdong, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW, 2308, Australia. .,Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia.
| | - Xi Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Yong-Sheng Li
- College of Biomedical Information and Engineering, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, 571199, Hainan, China.
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177
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Jin JQ, Wu D, Spencer R, Elhage KG, Liu J, Davis M, Hakimi M, Kumar S, Huang ZM, Bhutani T, Liao W. Biologic insights from single-cell studies of psoriasis and psoriatic arthritis. Expert Opin Biol Ther 2022; 22:1449-1461. [PMID: 36317702 DOI: 10.1080/14712598.2022.2142465] [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
INTRODUCTION Psoriasis (PSO) and psoriatic arthritis (PSA) represent a large burden of global inflammatory disease, but sustained treatment response and early diagnosis remain challenging. Both conditions arise from complex immune cell dysregulation. Single-cell techniques, including single-cell RNA sequencing (scRNA-seq), have revolutionized our understanding of pathogenesis by illuminating heterogeneous cell populations and their interactions. AREAS COVERED We discuss the transcriptional profiles and cellular interactions unique to PSO/PSA affecting T cells, myeloid cells, keratinocytes, innate lymphoid cells, and stromal cells. We also review advances, limitations, and future challenges associated with single-cell studies. EXPERT OPINION Following analyses of 22 single-cell studies, several themes emerged. A small subpopulation of cells can have a large impact on disease pathogenesis. Multiple cell types identified via scRNA-seq play supporting roles in PSO pathogenesis, contrary to the traditional paradigm focusing on IL-23/IL-17 signaling among dendritic cells and T cells. Immune cell states are dynamic, with psoriatic subpopulations aberrantly re-activating and differentiating into inflammatory phenotypes depending on surrounding signaling cues. Comparison of circulating immune cells with resident skin/joint cells has uncovered specific T cell clonotypes associated with the disease. Finally, machine learning models demonstrate great promise in identifying biomarkers to diagnose clinically ambiguous rashes and PSA at earlier stages.
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Affiliation(s)
- Joy Q Jin
- Department of Medicine, UCSF School of Medicine, San Francisco, CA, USA.,Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - David Wu
- Department of Medicine, UCSF School of Medicine, San Francisco, CA, USA.,Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Riley Spencer
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Kareem G Elhage
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Jared Liu
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Mitchell Davis
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Marwa Hakimi
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Sugandh Kumar
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Zhi-Ming Huang
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Tina Bhutani
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Wilson Liao
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California at San Francisco, San Francisco, CA, USA
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178
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Xue R, Zhang Q, Cao Q, Kong R, Xiang X, Liu H, Feng M, Wang F, Cheng J, Li Z, Zhan Q, Deng M, Zhu J, Zhang Z, Zhang N. Liver tumour immune microenvironment subtypes and neutrophil heterogeneity. Nature 2022; 612:141-147. [PMID: 36352227 DOI: 10.1038/s41586-022-05400-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
Abstract
The heterogeneity of the tumour immune microenvironment (TIME), organized by various immune and stromal cells, is a major contributing factor of tumour metastasis, relapse and drug resistance1-3, but how different TIME subtypes are connected to the clinical relevance in liver cancer remains unclear. Here we performed single-cell RNA-sequencing (scRNA-seq) analysis of 189 samples collected from 124 patients and 8 mice with liver cancer. With more than 1 million cells analysed, we stratified patients into five TIME subtypes, including immune activation, immune suppression mediated by myeloid or stromal cells, immune exclusion and immune residence phenotypes. Different TIME subtypes were spatially organized and associated with chemokine networks and genomic features. Notably, tumour-associated neutrophil (TAN) populations enriched in the myeloid-cell-enriched subtype were associated with an unfavourable prognosis. Through in vitro induction of TANs and ex vivo analyses of patient TANs, we showed that CCL4+ TANs can recruit macrophages and that PD-L1+ TANs can suppress T cell cytotoxicity. Furthermore, scRNA-seq analysis of mouse neutrophil subsets revealed that they are largely conserved with those of humans. In vivo neutrophil depletion in mouse models attenuated tumour progression, confirming the pro-tumour phenotypes of TANs. With this detailed cellular heterogeneity landscape of liver cancer, our study illustrates diverse TIME subtypes, highlights immunosuppressive functions of TANs and sheds light on potential immunotherapies targeting TANs.
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Affiliation(s)
- Ruidong Xue
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Qiming Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China
| | - Qi Cao
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Ruirui Kong
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Xiao Xiang
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
| | - Hengkang Liu
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Mei Feng
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Fangyanni Wang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Jinghui Cheng
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China
| | - Zhao Li
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China
| | - Qimin Zhan
- International Cancer Institute, Peking University Health Science Center, Beijing, China
| | - Mi Deng
- International Cancer Institute, Peking University Health Science Center, Beijing, China
| | - Jiye Zhu
- Beijing Key Surgical Basic Research Laboratory of Liver Cirrhosis and Liver Cancer, Department of Hepatobiliary Surgery, Peking University People's Hospital, Beijing, China.
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing, China. .,Changping Laboratory, Beijing, China.
| | - Ning Zhang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, China. .,International Cancer Institute, Peking University Health Science Center, Beijing, China. .,Yunnan Baiyao Group, Kunming, China.
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179
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Matsushita Y, Chu AKY, Tsutsumi-Arai C, Orikasa S, Nagata M, Wong SY, Welch JD, Ono W, Ono N. The fate of early perichondrial cells in developing bones. Nat Commun 2022; 13:7319. [PMID: 36443296 PMCID: PMC9705540 DOI: 10.1038/s41467-022-34804-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/08/2022] [Indexed: 11/29/2022] Open
Abstract
In endochondral bone development, bone-forming osteoblasts and bone marrow stromal cells have dual origins in the fetal cartilage and its surrounding perichondrium. However, how early perichondrial cells distinctively contribute to developing bones remain unidentified. Here we show using in vivo cell-lineage analyses that Dlx5+ fetal perichondrial cells marked by Dlx5-creER do not generate cartilage but sustainably contribute to cortical bone and marrow stromal compartments in a manner complementary to fetal chondrocyte derivatives under the regulation of Hedgehog signaling. Postnatally, Dlx5+ fetal perichondrial cell derivatives preferentially populate the diaphyseal marrow stroma with a dormant adipocyte-biased state and are refractory to parathyroid hormone-induced bone anabolism. Therefore, early perichondrial cells of the fetal cartilage are destined to become an adipogenic subset of stromal cells in postnatal diaphyseal bone marrow, supporting the theory that the adult bone marrow stromal compartments are developmentally prescribed within the two distinct cells-of-origins of the fetal bone anlage.
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Affiliation(s)
- Yuki Matsushita
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA
- Department of Cell Biology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8588, Japan
| | - Angel Ka Yan Chu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chiaki Tsutsumi-Arai
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA
| | - Shion Orikasa
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA
| | - Mizuki Nagata
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA
| | - Sunny Y Wong
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Wanida Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA
| | - Noriaki Ono
- University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, 77054, USA.
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180
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Ishibashi K, Ikegami K, Shimbo T, Sasaki E, Kitayama T, Nakamura Y, Tsushima T, Ishibashi Y, Tamai K. Single-cell transcriptome analysis reveals cellular heterogeneity in mouse intra- and extra articular ligaments. Commun Biol 2022; 5:1233. [PMID: 36371589 PMCID: PMC9653455 DOI: 10.1038/s42003-022-04196-w] [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: 04/16/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Ligaments are collagenous connective tissues that connect bones. Injury of knee ligaments, namely anterior cruciate ligament (ACL) and medial collateral ligament (MCL), is common in athletes. Both ligaments have important functions, but distinct regeneration capacities. The capacity for recovery after injury also diminishes with age. However, cellular heterogeneity in the ligaments remains unclear. Here, we profiled the transcriptional signatures of ACL and MCL cells in mice using single-cell RNA sequencing. These ligaments comprise three fibroblast types expressing Col22a1, Col12a1, or Col14a1, but have distinct localizations in the tissue. We found substantial heterogeneity in Col12a1- and Col14a1-positive cells between ACL and MCL. Gene Ontology analysis revealed that angiogenesis- and collagen regulation-related genes were specifically enriched in MCL cells. Furthermore, we identified age-related changes in cell composition and gene expression in the ligaments. This study delineates cellular heterogeneity in ligaments, serving as a foundation for identifying potential therapeutic targets for ligament injuries. Cell heterogeneity in the mouse anterior cruciate ligament (ACL) and medial collateral ligament (MCL) is demonstrated using single-cell analysis with three types of fibroblasts identified, expressing Col14a1, Col12a1, or Col22a1.
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181
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Metastatic recurrence in colorectal cancer arises from residual EMP1+ cells. Nature 2022; 611:603-613. [DOI: 10.1038/s41586-022-05402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 09/30/2022] [Indexed: 11/10/2022]
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182
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Gao M, Qiao C, Huang Y. UniTVelo: temporally unified RNA velocity reinforces single-cell trajectory inference. Nat Commun 2022; 13:6586. [PMID: 36329018 PMCID: PMC9633790 DOI: 10.1038/s41467-022-34188-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The recent breakthrough of single-cell RNA velocity methods brings attractive promises to reveal directed trajectory on cell differentiation, states transition and response to perturbations. However, the existing RNA velocity methods are often found to return erroneous results, partly due to model violation or lack of temporal regularization. Here, we present UniTVelo, a statistical framework of RNA velocity that models the dynamics of spliced and unspliced RNAs via flexible transcription activities. Uniquely, it also supports the inference of a unified latent time across the transcriptome. With ten datasets, we demonstrate that UniTVelo returns the expected trajectory in different biological systems, including hematopoietic differentiation and those even with weak kinetics or complex branches.
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Affiliation(s)
- Mingze Gao
- grid.194645.b0000000121742757School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Chen Qiao
- grid.194645.b0000000121742757School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Yuanhua Huang
- grid.194645.b0000000121742757School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China ,grid.194645.b0000000121742757Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong SAR, China
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183
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Natoli M, Hatje K, Gulati P, Junker F, Herzig P, Jiang Z, Davydov II, Germann M, Trüb M, Marbach D, Zwick A, Weber P, Seeber S, Wiese M, Lardinois D, Heinzelmann-Schwarz V, Rosenberg R, Tietze L, Mertz KD, Umaña P, Klein C, Codarri-Deak L, Kao H, Zippelius A. Deciphering molecular and cellular ex vivo responses to bispecific antibodies PD1-TIM3 and PD1-LAG3 in human tumors. J Immunother Cancer 2022; 10:jitc-2022-005548. [PMID: 36319064 PMCID: PMC9628669 DOI: 10.1136/jitc-2022-005548] [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] [Accepted: 09/30/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Next-generation cancer immunotherapies are designed to broaden the therapeutic repertoire by targeting new immune checkpoints including lymphocyte-activation gene 3 (LAG-3) and T cell immunoglobulin and mucin-domain containing-3 (TIM-3). Yet, the molecular and cellular mechanisms by which either receptor functions to mediate its inhibitory effects are still poorly understood. Similarly, little is known on the differential effects of dual, compared with single, checkpoint inhibition. METHODS We here performed in-depth characterization, including multicolor flow cytometry, single cell RNA sequencing and multiplex supernatant analysis, using tumor single cell suspensions from patients with cancer treated ex vivo with novel bispecific antibodies targeting programmed cell death protein 1 (PD-1) and TIM-3 (PD1-TIM3), PD-1 and LAG-3 (PD1-LAG3), or with anti-PD-1. RESULTS We identified patient samples which were responsive to PD1-TIM3, PD1-LAG3 or anti-PD-1 using an in vitro approach, validated by the analysis of 659 soluble proteins and enrichment for an anti-PD-1 responder signature. We found increased abundance of an activated (HLA-DR+CD25+GranzymeB+) CD8+ T cell subset and of proliferating CD8+ T cells, in response to bispecific antibody or anti-PD-1 treatment. Bispecific antibodies, but not anti-PD-1, significantly increased the abundance of a proliferating natural killer cell subset, which exhibited enrichment for a tissue-residency signature. Key phenotypic and transcriptional changes occurred in a PD-1+CXCL13+CD4+ T cell subset, in response to all treatments, including increased interleukin-17 secretion and signaling toward plasma cells. Interestingly, LAG-3 protein upregulation was detected as a unique pharmacodynamic effect mediated by PD1-LAG3, but not by PD1-TIM3 or anti-PD-1. CONCLUSIONS Our in vitro system reliably assessed responses to bispecific antibodies co-targeting PD-1 together with LAG-3 or TIM-3 using patients' tumor infiltrating immune cells and revealed transcriptional and phenotypic imprinting by bispecific antibody formats currently tested in early clinical trials.
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Affiliation(s)
- Marina Natoli
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Klas Hatje
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Pratiksha Gulati
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Fabian Junker
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Petra Herzig
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Zhiwen Jiang
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Iakov I Davydov
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Markus Germann
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Marta Trüb
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Daniel Marbach
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Adrian Zwick
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Munich, F Hoffmann-La Roche Ltd, Penzberg, Germany
| | - Patrick Weber
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Stefan Seeber
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Munich, F Hoffmann-La Roche Ltd, Penzberg, Germany
| | - Mark Wiese
- Division of Thoracic Surgery, University Hospital Basel, Basel, Switzerland
| | - Didier Lardinois
- Division of Thoracic Surgery, University Hospital Basel, Basel, Switzerland
| | | | - Robert Rosenberg
- Department of Surgery, Cantonal Hospital Basel-Landschaft, Liestal, Switzerland
| | | | - Kirsten D Mertz
- Institute of Pathology, Cantonal Hospital Basel-Landschaft, Liestal, Switzerland
| | - Pablo Umaña
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Christian Klein
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Laura Codarri-Deak
- Roche Pharma Research and Early Development, Discovery Oncology, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Henry Kao
- Roche Pharma Research and Early Development, Early Biomarker Development Oncology, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Alfred Zippelius
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland,Medical Oncology, University Hospital Basel, Basel, Switzerland
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184
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Chandrasekaran P, Negretti NM, Sivakumar A, Liberti DC, Wen H, Peers de Nieuwburgh M, Wang JY, Michki NS, Chaudhry FN, Kaur S, Lu M, Jin A, Zepp JA, Young LR, Sucre JMS, Frank DB. CXCL12 defines lung endothelial heterogeneity and promotes distal vascular growth. Development 2022; 149:277385. [PMID: 36239312 PMCID: PMC9687018 DOI: 10.1242/dev.200909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
Abstract
There is a growing amount of data uncovering the cellular diversity of the pulmonary circulation and mechanisms governing vascular repair after injury. However, the molecular and cellular mechanisms contributing to the morphogenesis and growth of the pulmonary vasculature during embryonic development are less clear. Importantly, deficits in vascular development lead to significant pediatric lung diseases, indicating a need to uncover fetal programs promoting vascular growth. To address this, we used a transgenic mouse reporter for expression of Cxcl12, an arterial endothelial hallmark gene, and performed single-cell RNA sequencing on isolated Cxcl12-DsRed+ endothelium to assess cellular heterogeneity within pulmonary endothelium. Combining cell annotation with gene ontology and histological analysis allowed us to segregate the developing artery endothelium into functionally and spatially distinct subpopulations. Expression of Cxcl12 is highest in the distal arterial endothelial subpopulation, a compartment enriched in genes for vascular development. Accordingly, disruption of CXCL12 signaling led to, not only abnormal branching, but also distal vascular hypoplasia. These data provide evidence for arterial endothelial functional heterogeneity and reveal conserved signaling mechanisms essential for pulmonary vascular development.
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Affiliation(s)
- Prashant Chandrasekaran
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Nicholas M. Negretti
- Department of Pediatrics, Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Aravind Sivakumar
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Derek C. Liberti
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Hongbo Wen
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Maureen Peers de Nieuwburgh
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Joanna Y. Wang
- Department of Medicine, University of Pennsylvania, Penn-CHOP Lung Biology Institute, Philadelphia, PA 19104, USA
| | - Nigel S. Michki
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Fatima N. Chaudhry
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Philadelphia, PA 19104, USA
| | - Sukhmani Kaur
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - MinQi Lu
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Annabelle Jin
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA
| | - Jarod A. Zepp
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Philadelphia, PA 19104, USA
| | - Lisa R. Young
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Philadelphia, PA 19104, USA
| | - Jennifer M. S. Sucre
- Department of Pediatrics, Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Authors for correspondence (; )
| | - David B. Frank
- Department of Pediatrics, Division of Cardiology, University of Pennsylvania, Children's Hospital of Philadelphia, Penn-CHOP Lung Biology Institute, Penn Cardiovascular Institute, Philadelphia, PA 19104, USA,Authors for correspondence (; )
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185
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Avital G, Kuperwaser F, Pountain AW, Lacey KA, Zwack EE, Podkowik M, Shopsin B, Torres VJ, Yanai I. The tempo and mode of gene regulatory programs during bacterial infection. Cell Rep 2022; 41:111477. [PMID: 36223751 PMCID: PMC9741813 DOI: 10.1016/j.celrep.2022.111477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 06/10/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022] Open
Abstract
Innate immune recognition of bacterial pathogens is a key determinant of the ensuing systemic response, and host or pathogen heterogeneity in this early interaction can impact the course of infection. To gain insight into host response heterogeneity, we investigate macrophage inflammatory dynamics using primary human macrophages infected with Group B Streptococcus. Transcriptomic analysis reveals discrete cellular states within responding macrophages, one of which consists of four sub-states, reflecting inflammatory activation. Infection with six additional bacterial species-Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Yersinia pseudotuberculosis, Shigella flexneri, and Salmonella enterica-recapitulates these states, though at different frequencies. We show that modulating the duration of infection and the presence of a toxin impacts inflammatory trajectory dynamics. We provide evidence for this trajectory in infected macrophages in an in vivo model of Staphylococcus aureus infection. Our cell-state analysis defines a framework for understanding inflammatory activation dynamics in response to bacterial infection.
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Affiliation(s)
- Gal Avital
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,These authors contributed equally
| | - Felicia Kuperwaser
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,These authors contributed equally
| | - Andrew W. Pountain
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Keenan A. Lacey
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Erin E. Zwack
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA,Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Victor J. Torres
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York, NY, USA,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA,Lead contact,Correspondence:
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186
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Functional Heterogeneity of Bone Marrow Mesenchymal Stem Cell Subpopulations in Physiology and Pathology. Int J Mol Sci 2022; 23:ijms231911928. [PMID: 36233230 PMCID: PMC9570000 DOI: 10.3390/ijms231911928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Bone marrow mesenchymal stem cells (BMSCs) are multi-potent cell populations and are capable of maintaining bone and body homeostasis. The stemness and potential therapeutic effect of BMSCs have been explored extensively in recent years. However, diverse cell surface antigens and complex gene expression of BMSCs have indicated that BMSCs represent heterogeneous populations, and the natural characteristics of BMSCs make it difficult to identify the specific subpopulations in pathological processes which are often obscured by bulk analysis of the total BMSCs. Meanwhile, the therapeutic effect of total BMSCs is often less effective partly due to their heterogeneity. Therefore, understanding the functional heterogeneity of the BMSC subpopulations under different physiological and pathological conditions could have major ramifications for global health. Here, we summarize the recent progress of functional heterogeneity of BMSC subpopulations in physiology and pathology. Targeting tissue-resident single BMSC subpopulation offers a potentially innovative therapeutic strategy and improves BMSC effectiveness in clinical application.
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187
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Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V. Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Syst 2022; 13:690-710.e17. [PMID: 35981544 PMCID: PMC9615940 DOI: 10.1016/j.cels.2022.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/10/2022] [Accepted: 07/25/2022] [Indexed: 01/26/2023]
Abstract
Small cell lung cancer (SCLC) tumors comprise heterogeneous mixtures of cell states, categorized into neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. NE to non-NE state transitions, fueled by plasticity, likely underlie adaptability to treatment and dismal survival rates. Here, we apply an archetypal analysis to model plasticity by recasting SCLC phenotypic heterogeneity through multi-task evolutionary theory. Cell line and tumor transcriptomics data fit well in a five-dimensional convex polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterparts. These tasks, supported by knowledge and experimental data, include proliferation, slithering, metabolism, secretion, and injury repair, reflecting cancer hallmarks. SCLC subtypes, either at the population or single-cell level, can be positioned in archetypal space by bulk or single-cell transcriptomics, respectively, and characterized as task specialists or multi-task generalists by the distance from archetype vertex signatures. In the archetype space, modeling single-cell plasticity as a Markovian process along an underlying state manifold indicates that task trade-offs, in response to microenvironmental perturbations or treatment, may drive cell plasticity. Stifling phenotypic transitions and plasticity may provide new targets for much-needed translational advances in SCLC. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Sarah M Groves
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Geena V Ildefonso
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Caitlin O McAtee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Patricia M M Ozawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Abbie S Ireland
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Philip E Stauffer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Perry T Wasdin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Xiaomeng Huang
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Yi Qiao
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Jing Shan Lim
- Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jackie Bader
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Alan J Simmons
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Wade T Iams
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Doug P Hardin
- Department of Mathematics and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA
| | - Edward B Saff
- Department of Mathematics, Vanderbilt University, Nashville, TN 37235, USA
| | - William R Holmes
- Department of Mathematics, Vanderbilt University, Nashville, TN 37235, USA; Department of Physics, Vanderbilt University, Nashville, TN 37235, USA
| | - Darren R Tyson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA
| | - Christine M Lovly
- Department of Mathematics and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Jeffrey C Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gabor Marth
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Julien Sage
- Department of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Trudy G Oliver
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37235, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37235, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37235, USA.
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188
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Salomé B, Sfakianos JP, Ranti D, Daza J, Bieber C, Charap A, Hammer C, Banchereau R, Farkas AM, Ruan DF, Izadmehr S, Geanon D, Kelly G, de Real RM, Lee B, Beaumont KG, Shroff S, Wang YA, Wang YC, Thin TH, Garcia-Barros M, Hegewisch-Solloa E, Mace EM, Wang L, O'Donnell T, Chowell D, Fernandez-Rodriguez R, Skobe M, Taylor N, Kim-Schulze S, Sebra RP, Palmer D, Clancy-Thompson E, Hammond S, Kamphorst AO, Malmberg KJ, Marcenaro E, Romero P, Brody R, Viard M, Yuki Y, Martin M, Carrington M, Mehrazin R, Wiklund P, Mellman I, Mariathasan S, Zhu J, Galsky MD, Bhardwaj N, Horowitz A. NKG2A and HLA-E define an alternative immune checkpoint axis in bladder cancer. Cancer Cell 2022; 40:1027-1043.e9. [PMID: 36099881 PMCID: PMC9479122 DOI: 10.1016/j.ccell.2022.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/24/2022] [Accepted: 08/05/2022] [Indexed: 12/12/2022]
Abstract
Programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1)-blockade immunotherapies have limited efficacy in the treatment of bladder cancer. Here, we show that NKG2A associates with improved survival and responsiveness to PD-L1 blockade immunotherapy in bladder tumors that have high abundance of CD8+ T cells. In bladder tumors, NKG2A is acquired on CD8+ T cells later than PD-1 as well as other well-established immune checkpoints. NKG2A+ PD-1+ CD8+ T cells diverge from classically defined exhausted T cells through their ability to react to human leukocyte antigen (HLA) class I-deficient tumors using T cell receptor (TCR)-independent innate-like mechanisms. HLA-ABC expression by bladder tumors is progressively diminished as disease progresses, framing the importance of targeting TCR-independent anti-tumor functions. Notably, NKG2A+ CD8+ T cells are inhibited when HLA-E is expressed by tumors and partly restored upon NKG2A blockade in an HLA-E-dependent manner. Overall, our study provides a framework for subsequent clinical trials combining NKG2A blockade with other T cell-targeted immunotherapies, where tumors express higher levels of HLA-E.
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Affiliation(s)
- Bérengère Salomé
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John P Sfakianos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Ranti
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jorge Daza
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christine Bieber
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Charap
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christian Hammer
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA; Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Romain Banchereau
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA 94080, USA
| | - Adam M Farkas
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Fu Ruan
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sudeh Izadmehr
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Geanon
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Geoffrey Kelly
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ronaldo M de Real
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin G Beaumont
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjana Shroff
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuanshuo A Wang
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ying-Chih Wang
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tin Htwe Thin
- Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monica Garcia-Barros
- Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Li Wang
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, a Mount Sinai Venture, Stamford, CT 06902, USA
| | - Timothy O'Donnell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruben Fernandez-Rodriguez
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mihaela Skobe
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole Taylor
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seunghee Kim-Schulze
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert P Sebra
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, a Mount Sinai Venture, Stamford, CT 06902, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Doug Palmer
- AstraZeneca, Oncology R & D Unit, Gaithersburg, MD 20878, USA
| | | | - Scott Hammond
- AstraZeneca, Oncology R & D Unit, Gaithersburg, MD 20878, USA
| | - Alice O Kamphorst
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | | | - Pedro Romero
- Department of Oncology UNIL CHUV, University of Lausanne, Lausanne, Switzerland
| | - Rachel Brody
- Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Wiklund
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ira Mellman
- Department of Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Sanjeev Mariathasan
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA 94080, USA
| | - Jun Zhu
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Sema4, a Mount Sinai Venture, Stamford, CT 06902, USA
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nina Bhardwaj
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Amir Horowitz
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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189
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Ranek JS, Stanley N, Purvis JE. Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction. Genome Biol 2022; 23:186. [PMID: 36064614 PMCID: PMC9442962 DOI: 10.1186/s13059-022-02749-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/16/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Current methods for analyzing single-cell datasets have relied primarily on static gene expression measurements to characterize the molecular state of individual cells. However, capturing temporal changes in cell state is crucial for the interpretation of dynamic phenotypes such as the cell cycle, development, or disease progression. RNA velocity infers the direction and speed of transcriptional changes in individual cells, yet it is unclear how these temporal gene expression modalities may be leveraged for predictive modeling of cellular dynamics. RESULTS Here, we present the first task-oriented benchmarking study that investigates integration of temporal sequencing modalities for dynamic cell state prediction. We benchmark ten integration approaches on ten datasets spanning different biological contexts, sequencing technologies, and species. We find that integrated data more accurately infers biological trajectories and achieves increased performance on classifying cells according to perturbation and disease states. Furthermore, we show that simple concatenation of spliced and unspliced molecules performs consistently well on classification tasks and can be used over more memory intensive and computationally expensive methods. CONCLUSIONS This work illustrates how integrated temporal gene expression modalities may be leveraged for predicting cellular trajectories and sample-associated perturbation and disease phenotypes. Additionally, this study provides users with practical recommendations for task-specific integration of single-cell gene expression modalities.
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Affiliation(s)
- Jolene S. Ranek
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA ,grid.10698.360000000122483208Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Natalie Stanley
- grid.10698.360000000122483208Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, USA ,grid.10698.360000000122483208Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Jeremy E. Purvis
- grid.10698.360000000122483208Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA ,grid.10698.360000000122483208Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, USA
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190
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Lust K, Maynard A, Gomes T, Fleck JS, Camp JG, Tanaka EM, Treutlein B. Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration. Science 2022; 377:eabp9262. [PMID: 36048956 DOI: 10.1126/science.abp9262] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Salamanders are tetrapod models to study brain organization and regeneration; however, the identity and evolutionary conservation of brain cell types are largely unknown. We delineated the cell populations in the axolotl telencephalon during homeostasis and regeneration using single-cell genomic profiling. We identified glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved γ-aminobutyric acid-releasing (GABAergic) neuron classes. We inferred transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific neurogenesis and unraveled conserved differentiation signatures. After brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield insights into the organization, evolution, and regeneration of a tetrapod nervous system.
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Affiliation(s)
- Katharina Lust
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Ashley Maynard
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Tomás Gomes
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - J Gray Camp
- Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | - Elly M Tanaka
- Research Institute of Molecular Pathology, Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030 Vienna, Austria
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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191
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Franken A, Van Mol P, Vanmassenhove S, Donders E, Schepers R, Van Brussel T, Dooms C, Yserbyt J, De Crem N, Testelmans D, De Wever W, Nackaerts K, Vansteenkiste J, Vos R, Humblet-Baron S, Lambrechts D, Wauters E. Single-cell transcriptomics identifies pathogenic T-helper 17.1 cells and pro-inflammatory monocytes in immune checkpoint inhibitor-related pneumonitis. J Immunother Cancer 2022; 10:jitc-2022-005323. [PMID: 36171010 PMCID: PMC9528720 DOI: 10.1136/jitc-2022-005323] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/11/2022] Open
Abstract
Background Immune checkpoint inhibitor (ICI)-related pneumonitis is the most frequent fatal immune-related adverse event associated with programmed cell death protein-1/programmed death ligand-1 blockade. The pathophysiology however remains largely unknown, owing to limited and contradictory findings in existing literature pointing at either T-helper 1 or T-helper 17-mediated autoimmunity. In this study, we aimed to gain novel insights into the mechanisms of ICI-related pneumonitis, thereby identifying potential therapeutic targets. Methods In this prospective observational study, single-cell RNA and T-cell receptor sequencing was performed on bronchoalveolar lavage fluid of 11 patients with ICI-related pneumonitis and 6 demographically-matched patients with cancer without ICI-related pneumonitis. Single-cell transcriptomic immunophenotyping and cell fate mapping coupled to T-cell receptor repertoire analyses were performed. Results We observed enrichment of both CD4+ and CD8+ T cells in ICI-pneumonitis bronchoalveolar lavage fluid. The CD4+ T-cell compartment showed an increase of pathogenic T-helper 17.1 cells, characterized by high co-expression of TBX21 (encoding T-bet) and RORC (ROR-γ), IFN-G (IFN-γ), IL-17A, CSF2 (GM-CSF), and cytotoxicity genes. Type 1 regulatory T cells and naïve-like CD4+ T cells were also enriched. Within the CD8+ T-cell compartment, mainly effector memory T cells were increased. Correspondingly, myeloid cells in ICI-pneumonitis bronchoalveolar lavage fluid were relatively depleted of anti-inflammatory resident alveolar macrophages while pro-inflammatory ‘M1-like’ monocytes (expressing TNF, IL-1B, IL-6, IL-23A, and GM-CSF receptor CSF2RA, CSF2RB) were enriched compared with control samples. Importantly, a feedforward loop, in which GM-CSF production by pathogenic T-helper 17.1 cells promotes tissue inflammation and IL-23 production by pro-inflammatory monocytes and vice versa, has been well characterized in multiple autoimmune disorders but has never been identified in ICI-related pneumonitis. Conclusions Using single-cell transcriptomics, we identified accumulation of pathogenic T-helper 17.1 cells in ICI-pneumonitis bronchoalveolar lavage fluid—a phenotype explaining previous divergent findings on T-helper 1 versus T-helper 17 involvement in ICI-pneumonitis—, putatively engaging in detrimental crosstalk with pro-inflammatory ‘M1-like’ monocytes. This finding yields several novel potential therapeutic targets for the treatment of ICI-pneumonitis. Most notably repurposing anti-IL-23 merits further research as a potential efficacious and safe treatment for ICI-pneumonitis.
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Affiliation(s)
- Amelie Franken
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Pierre Van Mol
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Sam Vanmassenhove
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Elena Donders
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Rogier Schepers
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Thomas Van Brussel
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Christophe Dooms
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Jonas Yserbyt
- Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Nico De Crem
- Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Dries Testelmans
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Walter De Wever
- Department of Imaging & Pathology, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Kristiaan Nackaerts
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Johan Vansteenkiste
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Robin Vos
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium.,Pneumology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium
| | - Stéphanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Diether Lambrechts
- VIB - CCB Department of Human Genetics, KU Leuven, Leuven, Flemish Brabant, Belgium
| | - Els Wauters
- Pneumology - Respiratory Oncology, Katholieke Universiteit Leuven Universitaire Ziekenhuizen Leuven, Leuven, Flemish Brabant, Belgium.,Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Flemish Brabant, Belgium
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192
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Rukhlenko OS, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher NO, Kolch W, Kholodenko BN. Control of cell state transitions. Nature 2022; 609:975-985. [PMID: 36104561 PMCID: PMC9644236 DOI: 10.1038/s41586-022-05194-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment and regulation (cSTAR), an approach for mapping cell states, modelling transitions between them and predicting targeted interventions to convert cell fate decisions. cSTAR uses omics data as input, classifies cell states, and develops a workflow that transforms the input data into mechanistic models that identify a core signalling network, which controls cell fate transitions by influencing whole-cell networks. By integrating signalling and phenotypic data, cSTAR models how cells manoeuvre in Waddington's landscape1 and make decisions about which cell fate to adopt. Notably, cSTAR devises interventions to control the movement of cells in Waddington's landscape. Testing cSTAR in a cellular model of differentiation and proliferation shows a high correlation between quantitative predictions and experimental data. Applying cSTAR to different types of perturbation and omics datasets, including single-cell data, demonstrates its flexibility and scalability and provides new biological insights. The ability of cSTAR to identify targeted perturbations that interconvert cell fates will enable designer approaches for manipulating cellular development pathways and mechanistically underpinned therapeutic interventions.
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Affiliation(s)
- Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Thomas Prince
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Maher
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eugene Kashdan
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth MacLeod
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
- Department of Pharmacology, Yale University School of Medicine, New Haven, USA.
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193
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Hersbach BA, Fischer DS, Masserdotti G, Deeksha, Mojžišová K, Waltzhöni T, Rodriguez-Terrones D, Heinig M, Theis FJ, Götz M, Stricker SH. Probing cell identity hierarchies by fate titration and collision during direct reprogramming. Mol Syst Biol 2022; 18:e11129. [PMID: 36106915 PMCID: PMC9476893 DOI: 10.15252/msb.202211129] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the therapeutic promise of direct reprogramming, basic principles concerning fate erasure and the mechanisms to resolve cell identity conflicts remain unclear. To tackle these fundamental questions, we established a single‐cell protocol for the simultaneous analysis of multiple cell fate conversion events based on combinatorial and traceable reprogramming factor expression: Collide‐seq. Collide‐seq revealed the lack of a common mechanism through which fibroblast‐specific gene expression loss is initiated. Moreover, we found that the transcriptome of converting cells abruptly changes when a critical level of each reprogramming factor is attained, with higher or lower levels not contributing to major changes. By simultaneously inducing multiple competing reprogramming factors, we also found a deterministic system, in which titration of fates against each other yields dominant or colliding fates. By investigating one collision in detail, we show that reprogramming factors can disturb cell identity programs independent of their ability to bind their target genes. Taken together, Collide‐seq has shed light on several fundamental principles of fate conversion that may aid in improving current reprogramming paradigms.
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Affiliation(s)
- Bob A Hersbach
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,Graduate School of Systemic Neurosciences, Biocenter, Ludwig-Maximilians University, Munich, Germany
| | - David S Fischer
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Giacomo Masserdotti
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Deeksha
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
| | - Karolina Mojžišová
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Thomas Waltzhöni
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Core Facility Genomics, Helmholtz Zentrum München, Oberschleißheim, Germany
| | - Diego Rodriguez-Terrones
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany
| | - Matthias Heinig
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Department of Informatics, Technical University of Munich, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany.,German Excellence Cluster of Systems Neurology, Biomedical Center Munich, Munich, Germany
| | - Stefan H Stricker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Oberschleißheim, Germany.,Division of Physiological Genomics, Biomedical Center Munich, Ludwig-Maximilians University, Munich, Germany
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194
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Nagaharu K, Kojima Y, Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K. A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics. Cell Rep 2022; 40:111260. [PMID: 36044861 DOI: 10.1016/j.celrep.2022.111260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
Hematopoiesis was considered a hierarchical stepwise process but was revised to a continuous process following single-cell RNA sequencing. However, the uncertainty or fluctuation of single-cell transcriptome dynamics during differentiation was not considered, and the dendritic cell (DC) pathway in the lymphoid context remains unclear. Here, we identify human B-plasmacytoid DC (pDC) bifurcation as large fluctuating transcriptome dynamics in the putative B/NK progenitor region by dry and wet methods. By converting splicing kinetics into diffusion dynamics in a deep generative model, our original computational methodology reveals strong fluctuation at B/pDC bifurcation in IL-7Rα+ regions, and LFA-1 fluctuates positively in the pDC direction at the bifurcation. These expectancies are validated by the presence of B/pDC progenitors in the IL-7Rα+ fraction and preferential expression of LFA-1 in pDC-biased progenitors with a niche-like culture system. We provide a model of fluctuation-based differentiation, which reconciles continuous and discrete models and is applicable to other developmental systems.
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Affiliation(s)
- Keiki Nagaharu
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yasuhiro Kojima
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kodai Minoura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Hirohito Minami
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuki Kageyama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuka Sugimoto
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Masahiro Masuya
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Shigeru Nii
- Shiroko Women's Hospital, Suzuka 510-0235, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Isao Tawara
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Naoyuki Katayama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan; Division of Cancer Immunology, Research Institute, National Cancer Center, Tokyo 104-0045, Japan; Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba 277-8577, Japan.
| | - Kohshi Ohishi
- Department of Transfusion Medicine and Cell Therapy, Mie University Hospital, Tsu 514-8507, Japan.
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195
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Chen Y, Toth R, Chocarro S, Weichenhan D, Hey J, Lutsik P, Sawall S, Stathopoulos GT, Plass C, Sotillo R. Club cells employ regeneration mechanisms during lung tumorigenesis. Nat Commun 2022; 13:4557. [PMID: 35931677 PMCID: PMC9356049 DOI: 10.1038/s41467-022-32052-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 07/12/2022] [Indexed: 11/09/2022] Open
Abstract
The high plasticity of lung epithelial cells, has for many years, confounded the correct identification of the cell-of-origin of lung adenocarcinoma (LUAD), one of the deadliest malignancies worldwide. Here, we employ lineage-tracing mouse models to investigate the cell of origin of Eml4-Alk LUAD, and show that Club and Alveolar type 2 (AT2) cells give rise to tumours. We focus on Club cell originated tumours and find that Club cells experience an epigenetic switch by which they lose their lineage fidelity and gain an AT2-like phenotype after oncogenic transformation. Single-cell transcriptomic analyses identified two trajectories of Club cell evolution which are similar to the ones used during lung regeneration, suggesting that lung epithelial cells leverage on their plasticity and intrinsic regeneration mechanisms to give rise to a tumour. Together, this study highlights the role of Club cells in LUAD initiation, identifies the mechanism of Club cell lineage infidelity, confirms the presence of these features in human tumours, and unveils key mechanisms conferring LUAD heterogeneity.
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Affiliation(s)
- Yuanyuan Chen
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reka Toth
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Bioinformatics Platform, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,Ruprecht Karl University of Heidelberg, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan Sawall
- X-Ray Imaging and CT, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Georgios T Stathopoulos
- Comprehensive Pneumology Center (CPC) and Institute for Lung Biology and Disease (iLBD), Helmholtz Center Munich-German Research Center for Environmental Health (HMGU), Max-Lebsche-Platz 31, 81377, Munich, Bavaria, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TRLC), Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany. .,German Center for Lung Research (DZL), Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TRLC), Heidelberg, Germany. .,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany.
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196
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Vallelian F, Buzzi RM, Pfefferlé M, Yalamanoglu A, Dubach IL, Wassmer A, Gentinetta T, Hansen K, Humar R, Schulthess N, Schaer CA, Schaer DJ. Heme-stress activated NRF2 skews fate trajectories of bone marrow cells from dendritic cells towards red pulp-like macrophages in hemolytic anemia. Cell Death Differ 2022; 29:1450-1465. [PMID: 35031770 PMCID: PMC9345992 DOI: 10.1038/s41418-022-00932-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/28/2022] Open
Abstract
Heme is an erythrocyte-derived toxin that drives disease progression in hemolytic anemias, such as sickle cell disease. During hemolysis, specialized bone marrow-derived macrophages with a high heme-metabolism capacity orchestrate disease adaptation by removing damaged erythrocytes and heme-protein complexes from the blood and supporting iron recycling for erythropoiesis. Since chronic heme-stress is noxious for macrophages, erythrophagocytes in the spleen are continuously replenished from bone marrow-derived progenitors. Here, we hypothesized that adaptation to heme stress progressively shifts differentiation trajectories of bone marrow progenitors to expand the capacity of heme-handling monocyte-derived macrophages at the expense of the homeostatic generation of dendritic cells, which emerge from shared myeloid precursors. This heme-induced redirection of differentiation trajectories may contribute to hemolysis-induced secondary immunodeficiency. We performed single-cell RNA-sequencing with directional RNA velocity analysis of GM-CSF-supplemented mouse bone marrow cultures to assess myeloid differentiation under heme stress. We found that heme-activated NRF2 signaling shifted the differentiation of bone marrow cells towards antioxidant, iron-recycling macrophages, suppressing the generation of dendritic cells in heme-exposed bone marrow cultures. Heme eliminated the capacity of GM-CSF-supplemented bone marrow cultures to activate antigen-specific CD4 T cells. The generation of functionally competent dendritic cells was restored by NRF2 loss. The heme-induced phenotype of macrophage expansion with concurrent dendritic cell depletion was reproduced in hemolytic mice with sickle cell disease and spherocytosis and associated with reduced dendritic cell functions in the spleen. Our data provide a novel mechanistic underpinning of hemolytic stress as a driver of hyposplenism-related secondary immunodeficiency. ![]()
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Affiliation(s)
- Florence Vallelian
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland.
| | - Raphael M Buzzi
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Marc Pfefferlé
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Ayla Yalamanoglu
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Irina L Dubach
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - Kerstin Hansen
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Rok Humar
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja Schulthess
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
| | | | - Dominik J Schaer
- Division of Internal Medicine, University of Zurich, Zurich, Switzerland
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197
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Hardwick SA, Hu W, Joglekar A, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MM, Koopmans F, Prjibelski AD, Mikheenko A, Belchikov N, Jarroux J, Lucas AB, Palkovits M, Luo W, Milner TA, Ndhlovu LC, Smit AB, Trojanowski JQ, Lee VMY, Fedrigo O, Sloan SA, Tombácz D, Ross ME, Jarvis E, Boldogkői Z, Gan L, Tilgner HU. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol 2022; 40:1082-1092. [PMID: 35256815 PMCID: PMC9287170 DOI: 10.1038/s41587-022-01231-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/20/2022] [Indexed: 12/11/2022]
Abstract
Single-nuclei RNA sequencing characterizes cell types at the gene level. However, compared to single-cell approaches, many single-nuclei cDNAs are purely intronic, lack barcodes and hinder the study of isoforms. Here we present single-nuclei isoform RNA sequencing (SnISOr-Seq). Using microfluidics, PCR-based artifact removal, target enrichment and long-read sequencing, SnISOr-Seq increased barcoded, exon-spanning long reads 7.5-fold compared to naive long-read single-nuclei sequencing. We applied SnISOr-Seq to adult human frontal cortex and found that exons associated with autism exhibit coordinated and highly cell-type-specific inclusion. We found two distinct combination patterns: those distinguishing neural cell types, enriched in TSS-exon, exon-polyadenylation-site and non-adjacent exon pairs, and those with multiple configurations within one cell type, enriched in adjacent exon pairs. Finally, we observed that human-specific exons are almost as tightly coordinated as conserved exons, implying that coordination can be rapidly established during evolution. SnISOr-Seq enables cell-type-specific long-read isoform analysis in human brain and in any frozen or hard-to-dissociate sample.
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Affiliation(s)
- Simon A Hardwick
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Paul G Collier
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Careen Foord
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Samantha Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Frank Koopmans
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - Andrey D Prjibelski
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Natan Belchikov
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine, New York, NY, USA
| | - Julien Jarroux
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Wenjie Luo
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University, Amsterdam, The Netherlands
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Virginia M Y Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | | | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | | | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, Hungary
| | - Li Gan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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198
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Guerrero-Juarez CF, Lee GH, Liu Y, Wang S, Karikomi M, Sha Y, Chow RY, Nguyen TTL, Iglesias VS, Aasi S, Drummond ML, Nie Q, Sarin K, Atwood SX. Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment. SCIENCE ADVANCES 2022; 8:eabm7981. [PMID: 35687691 PMCID: PMC9187229 DOI: 10.1126/sciadv.abm7981] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/27/2022] [Indexed: 05/27/2023]
Abstract
How basal cell carcinoma (BCC) interacts with its tumor microenvironment to promote growth is unclear. We use singe-cell RNA sequencing to define the human BCC ecosystem and discriminate between normal and malignant epithelial cells. We identify spatial biomarkers of tumors and their surrounding stroma that reinforce the heterogeneity of each tissue type. Combining pseudotime, RNA velocity-PAGA, cellular entropy, and regulon analysis in stromal cells reveals a cancer-specific rewiring of fibroblasts, where STAT1, TGF-β, and inflammatory signals induce a noncanonical WNT5A program that maintains the stromal inflammatory state. Cell-cell communication modeling suggests that tumors respond to the sudden burst of fibroblast-specific inflammatory signaling pathways by producing heat shock proteins, whose expression we validated in situ. Last, dose-dependent treatment with an HSP70 inhibitor suppresses in vitro vismodegib-resistant BCC cell growth, Hedgehog signaling, and in vivo tumor growth in a BCC mouse model, validating HSP70's essential role in tumor growth and reinforcing the critical nature of tumor microenvironment cross-talk in BCC progression.
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Affiliation(s)
- Christian F. Guerrero-Juarez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Gun Ho Lee
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yingzi Liu
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Shuxiong Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
| | - Matthew Karikomi
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
| | - Yutong Sha
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
| | - Rachel Y. Chow
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Tuyen T. L. Nguyen
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Venus Sosa Iglesias
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Sumaira Aasi
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael L. Drummond
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Qing Nie
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Mathematics, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
| | - Kavita Sarin
- Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott X. Atwood
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA
- Department of Dermatology, University of California, Irvine, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
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199
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Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. Mapping the developing human immune system across organs. Science 2022; 376:eabo0510. [PMID: 35549310 PMCID: PMC7612819 DOI: 10.1126/science.abo0510] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell genomics studies have decoded the immune-cell composition of several human prenatal organs but were limited in understanding the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells prior to peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Paediatrics, Cambridge University Hospitals, Hills Road, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Haematology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadav Yayon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mohi Miah
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK.,Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, 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
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200
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van Bruggen D, Pohl F, Langseth CM, Kukanja P, Lee H, Albiach AM, Kabbe M, Meijer M, Linnarsson S, Hilscher MM, Nilsson M, Sundström E, Castelo-Branco G. Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis. Dev Cell 2022; 57:1421-1436.e5. [PMID: 35523173 DOI: 10.1016/j.devcel.2022.04.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 03/20/2022] [Accepted: 04/14/2022] [Indexed: 01/06/2023]
Abstract
Oligodendrogenesis in the human central nervous system has been observed mainly at the second trimester of gestation, a much later developmental stage compared to oligodendrogenesis in mice. Here, we characterize the transcriptomic neural diversity in the human forebrain at post-conception weeks (PCW) 8-10. Using single-cell RNA sequencing, we find evidence of the emergence of a first wave of oligodendrocyte lineage cells as early as PCW 8, which we also confirm at the epigenomic level through the use of single-cell ATAC-seq. Using regulatory network inference, we predict key transcriptional events leading to the specification of oligodendrocyte precursor cells (OPCs). Moreover, by profiling the spatial expression of 50 key genes through the use of in situ sequencing (ISS), we identify regions in the human ventral fetal forebrain where oligodendrogenesis first occurs. Our results indicate evolutionary conservation of the first wave of oligodendrogenesis between mice and humans and describe regulatory mechanisms involved in human OPC specification.
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Affiliation(s)
- David van Bruggen
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Fabio Pohl
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | | | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Hower Lee
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden
| | - Alejandro Mossi Albiach
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Mukund Kabbe
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Mandy Meijer
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden
| | - Markus M Hilscher
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 171 65, Solna, Sweden
| | - Erik Sundström
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, BioClinicum, Solna, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, 17177 Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden.
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