951
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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952
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Mahadevaraju S, Fear JM, Akeju M, Galletta BJ, Pinheiro MMLS, Avelino CC, Cabral-de-Mello DC, Conlon K, Dell'Orso S, Demere Z, Mansuria K, Mendonça CA, Palacios-Gimenez OM, Ross E, Savery M, Yu K, Smith HE, Sartorelli V, Yang H, Rusan NM, Vibranovski MD, Matunis E, Oliver B. Dynamic sex chromosome expression in Drosophila male germ cells. Nat Commun 2021; 12:892. [PMID: 33563972 PMCID: PMC7873209 DOI: 10.1038/s41467-021-20897-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
Given their copy number differences and unique modes of inheritance, the evolved gene content and expression of sex chromosomes is unusual. In many organisms the X and Y chromosomes are inactivated in spermatocytes, possibly as a defense mechanism against insertions into unpaired chromatin. In addition to current sex chromosomes, Drosophila has a small gene-poor X-chromosome relic (4th) that re-acquired autosomal status. Here we use single cell RNA-Seq on fly larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, based on measuring all genes or a set of broadly expressed genes in testis we identified. In contrast, genes on the single Y chromosome become maximally active in primary spermatocytes. Reduced X transcript levels are due to failed activation of RNA-Polymerase-II by phosphorylation of Serine 2 and 5.
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Affiliation(s)
- Sharvani Mahadevaraju
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Justin M Fear
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Miriam Akeju
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Brian J Galletta
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mara M L S Pinheiro
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Camila C Avelino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Diogo C Cabral-de-Mello
- Instituto de Biociências/IB, Departamento de Biologia Geral e Aplicada, UNESP-Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Katie Conlon
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Stafania Dell'Orso
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zelalem Demere
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Kush Mansuria
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Carolina A Mendonça
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Octavio M Palacios-Gimenez
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
- Department of Evolutionary Biology and Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Eli Ross
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Max Savery
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kevin Yu
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Harold E Smith
- Genomics Core, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Haiwang Yang
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Nasser M Rusan
- Cell Biology and Physiology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria D Vibranovski
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP 05508-090, São Paulo, Brazil
| | - Erika Matunis
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Brian Oliver
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Kidney and Digestive Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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953
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Srivastava S, Furlan SN, Jaeger-Ruckstuhl CA, Sarvothama M, Berger C, Smythe KS, Garrison SM, Specht JM, Lee SM, Amezquita RA, Voillet V, Muhunthan V, Yechan-Gunja S, Pillai SPS, Rader C, Houghton AM, Pierce RH, Gottardo R, Maloney DG, Riddell SR. Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade. Cancer Cell 2021; 39:193-208.e10. [PMID: 33357452 PMCID: PMC7878409 DOI: 10.1016/j.ccell.2020.11.005] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/18/2020] [Accepted: 11/13/2020] [Indexed: 12/27/2022]
Abstract
Adoptive therapy using chimeric antigen receptor-modified T cells (CAR-T cells) is effective in hematologic but not epithelial malignancies, which cause the greatest mortality. In breast and lung cancer patients, CAR-T cells targeting the tumor-associated antigen receptor tyrosine kinase-like orphan receptor 1 (ROR1) infiltrate tumors poorly and become dysfunctional. To test strategies for enhancing efficacy, we adapted the KrasLSL-G12D/+;p53f/f autochthonous model of lung adenocarcinoma to express the CAR target ROR1. Murine ROR1 CAR-T cells transferred after lymphodepletion with cyclophosphamide (Cy) transiently control tumor growth but infiltrate tumors poorly and lose function, similar to what is seen in patients. Adding oxaliplatin (Ox) to the lymphodepletion regimen activates tumor macrophages to express T-cell-recruiting chemokines, resulting in improved CAR-T cell infiltration, remodeling of the tumor microenvironment, and increased tumor sensitivity to anti-PD-L1. Combination therapy with Ox/Cy and anti-PD-L1 synergistically improves CAR-T cell-mediated tumor control and survival, providing a strategy to improve CAR-T cell efficacy in the clinic.
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Affiliation(s)
- Shivani Srivastava
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Megha Sarvothama
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carolina Berger
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly S Smythe
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sarah M Garrison
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jennifer M Specht
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sylvia M Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Robert A Amezquita
- Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Valentin Voillet
- Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vishaka Muhunthan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sushma Yechan-Gunja
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Smitha P S Pillai
- Department of Comparative Medicine, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, Scripps Research Institute, Jupiter, FL, USA
| | - A McGarry Houghton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert H Pierce
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infections Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David G Maloney
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | - Stanley R Riddell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
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954
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Wanet A, Bassal MA, Patel SB, Marchi F, Mariani SA, Ahmed N, Zhang H, Borchiellini M, Chen S, Zhang J, Di Ruscio A, Miyake K, Tsai M, Paranjape A, Park SY, Karasuyama H, Schroeder T, Dzierzak E, Galli SJ, Tenen DG, Welner RS. E-cadherin is regulated by GATA-2 and marks the early commitment of mouse hematopoietic progenitors to the basophil and mast cell fates. Sci Immunol 2021; 6:6/56/eaba0178. [PMID: 33547048 DOI: 10.1126/sciimmunol.aba0178] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 09/09/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
E-cadherin is a calcium-dependent cell-cell adhesion molecule extensively studied for its involvement in tissue formation, epithelial cell behavior, and suppression of cancer. However, E-cadherin expression in the hematopoietic system has not been fully elucidated. Combining single-cell RNA-sequencing analyses and immunophenotyping, we revealed that progenitors expressing high levels of E-cadherin and contained within the granulocyte-monocyte progenitors (GMPs) fraction have an enriched capacity to differentiate into basophils and mast cells. We detected E-cadherin expression on committed progenitors before the expression of other reported markers of these lineages. We named such progenitors pro-BMPs (pro-basophil and mast cell progenitors). Using RNA sequencing, we observed transcriptional priming of pro-BMPs to the basophil and mast cell lineages. We also showed that GATA-2 directly regulates E-cadherin expression in the basophil and mast cell lineages, thus providing a mechanistic connection between the expression of this cell surface marker and the basophil and mast cell fate specification.
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Affiliation(s)
- Anaïs Wanet
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Mahmoud A Bassal
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sweta B Patel
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Samanta A Mariani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Haoran Zhang
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, Novara 28100, Italy.,Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy
| | - Sisi Chen
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Junyan Zhang
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, Novara 28100, Italy.,Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kensuke Miyake
- Inflammation, Infection, Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Mindy Tsai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anuya Paranjape
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shin-Young Park
- Transfusion Medicine, Boston Children's Hospital and Harvard Medical School, Harvard Medical School, Boston, MA 02115, USA
| | - Hajime Karasuyama
- Inflammation, Infection, Immunity Laboratory, Advanced Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Elaine Dzierzak
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology and Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Robert S Welner
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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955
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Cheng S, Li Z, Gao R, Xing B, Gao Y, Yang Y, Qin S, Zhang L, Ouyang H, Du P, Jiang L, Zhang B, Yang Y, Wang X, Ren X, Bei JX, Hu X, Bu Z, Ji J, Zhang Z. A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. Cell 2021; 184:792-809.e23. [PMID: 33545035 DOI: 10.1016/j.cell.2021.01.010] [Citation(s) in RCA: 585] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/16/2020] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Tumor-infiltrating myeloid cells (TIMs) are key regulators in tumor progression, but the similarity and distinction of their fundamental properties across different tumors remain elusive. Here, by performing a pan-cancer analysis of single myeloid cells from 210 patients across 15 human cancer types, we identified distinct features of TIMs across cancer types. Mast cells in nasopharyngeal cancer were found to be associated with better prognosis and exhibited an anti-tumor phenotype with a high ratio of TNF+/VEGFA+ cells. Systematic comparison between cDC1- and cDC2-derived LAMP3+ cDCs revealed their differences in transcription factors and external stimulus. Additionally, pro-angiogenic tumor-associated macrophages (TAMs) were characterized with diverse markers across different cancer types, and the composition of TIMs appeared to be associated with certain features of somatic mutations and gene expressions. Our results provide a systematic view of the highly heterogeneous TIMs and suggest future avenues for rational, targeted immunotherapies.
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Affiliation(s)
- Sijin Cheng
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ziyi Li
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ranran Gao
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Baocai Xing
- Department of Hepatopancreatobiliary Surgery I, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yunong Gao
- Department of Gynecologic Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yu Yang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Shishang Qin
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hanqiang Ouyang
- Department of Orthopaedics, Peking University Third Hospital, Beijing Key Laboratory of Spinal Disease Research, Beijing 100191, China
| | - Peng Du
- Department of Urology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Liang Jiang
- Department of Orthopaedics, Peking University Third Hospital, Beijing Key Laboratory of Spinal Disease Research, Beijing 100191, China
| | - Bin Zhang
- Department of Head and Neck Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yue Yang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiliang Wang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou 510060, China
| | - Xueda Hu
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhaode Bu
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China.
| | - Jiafu Ji
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China; Department of Biobank, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China.
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, China; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China; Peking University International Cancer Institute, Beijing 100191, China.
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956
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Kearney CJ, Vervoort SJ, Ramsbottom KM, Todorovski I, Lelliott EJ, Zethoven M, Pijpers L, Martin BP, Semple T, Martelotto L, Trapani JA, Parish IA, Scott NE, Oliaro J, Johnstone RW. SUGAR-seq enables simultaneous detection of glycans, epitopes, and the transcriptome in single cells. SCIENCE ADVANCES 2021; 7:7/8/eabe3610. [PMID: 33608275 PMCID: PMC7895430 DOI: 10.1126/sciadv.abe3610] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Multimodal single-cell RNA sequencing enables the precise mapping of transcriptional and phenotypic features of cellular differentiation states but does not allow for simultaneous integration of critical posttranslational modification data. Here, we describe SUrface-protein Glycan And RNA-seq (SUGAR-seq), a method that enables detection and analysis of N-linked glycosylation, extracellular epitopes, and the transcriptome at the single-cell level. Integrated SUGAR-seq and glycoproteome analysis identified tumor-infiltrating T cells with unique surface glycan properties that report their epigenetic and functional state.
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Affiliation(s)
- Conor J Kearney
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Stephin J Vervoort
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
| | - Kelly M Ramsbottom
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Izabela Todorovski
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Emily J Lelliott
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Magnus Zethoven
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Lizzy Pijpers
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ben P Martin
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Timothy Semple
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Luciano Martelotto
- Centre for Cancer Research, University of Melbourne, Melbourne 3000, VIC, Australia
| | - Joseph A Trapani
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ian A Parish
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jane Oliaro
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia.
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Ricky W Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Australia
- Cancer Therapeutics Program, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
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957
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Circuits between infected macrophages and T cells in SARS-CoV-2 pneumonia. Nature 2021; 590:635-641. [PMID: 33429418 PMCID: PMC7987233 DOI: 10.1038/s41586-020-03148-w] [Citation(s) in RCA: 466] [Impact Index Per Article: 155.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/21/2020] [Indexed: 01/29/2023]
Abstract
Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia2. Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.
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958
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Chumduri C, Gurumurthy RK, Berger H, Dietrich O, Kumar N, Koster S, Brinkmann V, Hoffmann K, Drabkina M, Arampatzi P, Son D, Klemm U, Mollenkopf HJ, Herbst H, Mangler M, Vogel J, Saliba AE, Meyer TF. Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia. Nat Cell Biol 2021; 23:184-197. [PMID: 33462395 PMCID: PMC7878191 DOI: 10.1038/s41556-020-00619-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/26/2020] [Indexed: 12/11/2022]
Abstract
The transition zones of the squamous and columnar epithelia constitute hotspots for the emergence of cancer, often preceded by metaplasia, in which one epithelial type is replaced by another. It remains unclear how the epithelial spatial organization is maintained and how the transition zone niche is remodelled during metaplasia. Here we used single-cell RNA sequencing to characterize epithelial subpopulations and the underlying stromal compartment of endo- and ectocervix, encompassing the transition zone. Mouse lineage tracing, organoid culture and single-molecule RNA in situ hybridizations revealed that the two epithelia derive from separate cervix-resident lineage-specific stem cell populations regulated by opposing Wnt signals from the stroma. Using a mouse model of cervical metaplasia, we further show that the endocervical stroma undergoes remodelling and increases expression of the Wnt inhibitor Dickkopf-2 (DKK2), promoting the outgrowth of ectocervical stem cells. Our data indicate that homeostasis at the transition zone results from divergent stromal signals, driving the differential proliferation of resident epithelial lineages.
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Affiliation(s)
- Cindrilla Chumduri
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
- Chair of Microbiology, University of Würzburg, Würzburg, Germany.
| | | | - Hilmar Berger
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Oliver Dietrich
- Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Naveen Kumar
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
- Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Stefanie Koster
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Volker Brinkmann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Kirstin Hoffmann
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Marina Drabkina
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | | | - Dajung Son
- Chair of Microbiology, University of Würzburg, Würzburg, Germany
| | - Uwe Klemm
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hans-Joachim Mollenkopf
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Hermann Herbst
- Institute of Pathology, Vivantes Klinikum Berlin, Berlin, Germany
| | - Mandy Mangler
- Department of Gynecology, Charité University Medicine, Berlin, Germany
- Klinik für Gynäkologie und Geburtsmedizin, Vivantes Auguste-Viktoria-Klinikum, Berlin, Germany
| | - Jörg Vogel
- Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Antoine-Emmanuel Saliba
- Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
| | - Thomas F Meyer
- Department of Molecular Biology, Max Planck Institute for Infection Biology, Berlin, Germany.
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology (IKMB), Christian Albrechts University of Kiel, Kiel, Germany.
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959
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Kim HJ, Lin Y, Geddes TA, Yang JYH, Yang P. CiteFuse enables multi-modal analysis of CITE-seq data. Bioinformatics 2021; 36:4137-4143. [PMID: 32353146 DOI: 10.1093/bioinformatics/btaa282] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/30/2023] Open
Abstract
MOTIVATION Multi-modal profiling of single cells represents one of the latest technological advancements in molecular biology. Among various single-cell multi-modal strategies, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) allows simultaneous quantification of two distinct species: RNA and cell-surface proteins. Here, we introduce CiteFuse, a streamlined package consisting of a suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. RESULTS We demonstrate the capacity of CiteFuse to integrate the two data modalities and its relative advantage against data generated from single-modality profiling using both simulations and real-world CITE-seq data. Furthermore, we illustrate a novel doublet detection method based on a combined index of cell hashing and transcriptome data. Finally, we demonstrate CiteFuse for predicting ligand-receptor interactions by using multi-modal CITE-seq data. Collectively, we demonstrate the utility and effectiveness of CiteFuse for the integrative analysis of transcriptome and epitope profiles from CITE-seq data. AVAILABILITY AND IMPLEMENTATION CiteFuse is freely available at http://shiny.maths.usyd.edu.au/CiteFuse/ as an online web service and at https://github.com/SydneyBioX/CiteFuse/ as an R package. CONTACT pengyi.yang@sydney.edu.au. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hani Jieun Kim
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia
| | - Yingxin Lin
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
| | - Thomas A Geddes
- Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney 2006, Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia
| | - Pengyi Yang
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Sydney 2006, Australia.,Charles Perkins Centre, The University of Sydney, Sydney 2006, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia
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960
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Iqbal F, Lupieri A, Aikawa M, Aikawa E. Harnessing Single-Cell RNA Sequencing to Better Understand How Diseased Cells Behave the Way They Do in Cardiovascular Disease. Arterioscler Thromb Vasc Biol 2021; 41:585-600. [PMID: 33327741 PMCID: PMC8105278 DOI: 10.1161/atvbaha.120.314776] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
The transition of healthy arteries and cardiac valves into dense, cell-rich, calcified, and fibrotic tissues is driven by a complex interplay of both cellular and molecular mechanisms. Specific cell types in these cardiovascular tissues become activated following the exposure to systemic stimuli including circulating lipoproteins or inflammatory mediators. This activation induces multiple cascades of events where changes in cell phenotypes and activation of certain receptors may trigger multiple pathways and specific alterations to the transcriptome. Modifications to the transcriptome and proteome can give rise to pathological cell phenotypes and trigger mechanisms that exacerbate inflammation, proliferation, calcification, and recruitment of resident or distant cells. Accumulating evidence suggests that each cell type involved in vascular and valvular diseases is heterogeneous. Single-cell RNA sequencing is a transforming medical research tool that enables the profiling of the unique fingerprints at single-cell levels. Its applications have allowed the construction of cell atlases including the mammalian heart and tissue vasculature and the discovery of new cell types implicated in cardiovascular disease. Recent advances in single-cell RNA sequencing have facilitated the identification of novel resident cell populations that become activated during disease and has allowed tracing the transition of healthy cells into pathological phenotypes. Furthermore, single-cell RNA sequencing has permitted the characterization of heterogeneous cell subpopulations with unique genetic profiles in healthy and pathological cardiovascular tissues. In this review, we highlight the latest groundbreaking research that has improved our understanding of the pathological mechanisms of atherosclerosis and future directions for calcific aortic valve disease.
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Affiliation(s)
- Farwah Iqbal
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Adrien Lupieri
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Masanori Aikawa
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elena Aikawa
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Pathology, Sechenov First Moscow State Medical University, Moscow, 119992, Russia
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961
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Kalish BT, Kim E, Finander B, Duffy EE, Kim H, Gilman CK, Yim YS, Tong L, Kaufman RJ, Griffith EC, Choi GB, Greenberg ME, Huh JR. Maternal immune activation in mice disrupts proteostasis in the fetal brain. Nat Neurosci 2021; 24:204-213. [PMID: 33361822 PMCID: PMC7854524 DOI: 10.1038/s41593-020-00762-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022]
Abstract
Maternal infection and inflammation during pregnancy are associated with neurodevelopmental disorders in offspring, but little is understood about the molecular mechanisms underlying this epidemiologic phenomenon. Here, we leveraged single-cell RNA sequencing to profile transcriptional changes in the mouse fetal brain in response to maternal immune activation (MIA) and identified perturbations in cellular pathways associated with mRNA translation, ribosome biogenesis and stress signaling. We found that MIA activates the integrated stress response (ISR) in male, but not female, MIA offspring in an interleukin-17a-dependent manner, which reduced global mRNA translation and altered nascent proteome synthesis. Moreover, blockade of ISR activation prevented the behavioral abnormalities as well as increased cortical neural activity in MIA male offspring. Our data suggest that sex-specific activation of the ISR leads to maternal inflammation-associated neurodevelopmental disorders.
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Affiliation(s)
- Brian T Kalish
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
| | - Eunha Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Benjamin Finander
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Erin E Duffy
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hyunju Kim
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Casey K Gilman
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yeong Shin Yim
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lilin Tong
- Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Randal J Kaufman
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Eric C Griffith
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gloria B Choi
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael E Greenberg
- Department of Neurobiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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962
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Kildisiute G, Kholosy WM, Young MD, Roberts K, Elmentaite R, van Hooff SR, Pacyna CN, Khabirova E, Piapi A, Thevanesan C, Bugallo-Blanco E, Burke C, Mamanova L, Keller KM, Langenberg-Ververgaert KPS, Lijnzaad P, Margaritis T, Holstege FCP, Tas ML, Wijnen MHWA, van Noesel MM, Del Valle I, Barone G, van der Linden R, Duncan C, Anderson J, Achermann JC, Haniffa M, Teichmann SA, Rampling D, Sebire NJ, He X, de Krijger RR, Barker RA, Meyer KB, Bayraktar O, Straathof K, Molenaar JJ, Behjati S. Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell. SCIENCE ADVANCES 2021; 7:eabd3311. [PMID: 33547074 PMCID: PMC7864567 DOI: 10.1126/sciadv.abd3311] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/18/2020] [Indexed: 05/22/2023]
Abstract
Neuroblastoma is a childhood cancer that resembles developmental stages of the neural crest. It is not established what developmental processes neuroblastoma cancer cells represent. Here, we sought to reveal the phenotype of neuroblastoma cancer cells by comparing cancer (n = 19,723) with normal fetal adrenal single-cell transcriptomes (n = 57,972). Our principal finding was that the neuroblastoma cancer cell resembled fetal sympathoblasts, but no other fetal adrenal cell type. The sympathoblastic state was a universal feature of neuroblastoma cells, transcending cell cluster diversity, individual patients, and clinical phenotypes. We substantiated our findings in 650 neuroblastoma bulk transcriptomes and by integrating canonical features of the neuroblastoma genome with transcriptional signals. Overall, our observations indicate that a pan-neuroblastoma cancer cell state exists, which may be attractive for novel immunotherapeutic and targeted avenues.
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Affiliation(s)
| | - Waleed M Kholosy
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | | | | | | | - Sander R van Hooff
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | | | | | - Alice Piapi
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
| | | | | | - Christina Burke
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
| | | | - Kaylee M Keller
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | | | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Thanasis Margaritis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Frank C P Holstege
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Michelle L Tas
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Marc H W A Wijnen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
| | - Ignacio Del Valle
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
| | - Giuseppe Barone
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | | | - Catriona Duncan
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | - John C Achermann
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, CB10 1SA Hinxton, UK
- Institute of Cellular Medicine, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals, NHS Foundation Trust, NE2 4LP Newcastle upon Tyne, UK
| | | | - Dyanne Rampling
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | - Neil J Sebire
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | - Xiaoling He
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, CB2 0QQ Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ Cambridge, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands
- Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, Netherlands
| | - Roger A Barker
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, CB2 0QQ Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ Cambridge, UK
| | | | | | - Karin Straathof
- UCL Great Ormond Street Institute of Child Health, WC1N 1EH London, UK.
- Great Ormond Street Hospital for Children (GOSH), NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, WC1N 3JH London, UK
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, Netherlands.
| | - Sam Behjati
- Wellcome Sanger Institute, CB10 1SA Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ Cambridge, UK
- Department of Paediatrics, University of Cambridge, CB2 0QQ Cambridge, UK
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963
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Cheloni S, Hillje R, Luzi L, Pelicci PG, Gatti E. XenoCell: classification of cellular barcodes in single cell experiments from xenograft samples. BMC Med Genomics 2021; 14:34. [PMID: 33514375 PMCID: PMC7847033 DOI: 10.1186/s12920-021-00872-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 01/12/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Single-cell sequencing technologies provide unprecedented opportunities to deconvolve the genomic, transcriptomic or epigenomic heterogeneity of complex biological systems. Its application in samples from xenografts of patient-derived biopsies (PDX), however, is limited by the presence of cells originating from both the host and the graft in the analysed samples; in fact, in the bioinformatics workflows it is still a challenge discriminating between host and graft sequence reads obtained in a single-cell experiment. RESULTS We have developed XenoCell, the first stand-alone pre-processing tool that performs fast and reliable classification of host and graft cellular barcodes from single-cell sequencing experiments. We show its application on a mixed species 50:50 cell line experiment from 10× Genomics platform, and on a publicly available PDX dataset obtained by Drop-Seq. CONCLUSIONS XenoCell accurately dissects sequence reads from any host and graft combination of species as well as from a broad range of single-cell experiments and platforms. It is open source and available at https://gitlab.com/XenoCell/XenoCell .
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Affiliation(s)
- Stefano Cheloni
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Roman Hillje
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Lucilla Luzi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.
- Department of Oncology and Hemato-Oncology, Università Degli Studi Di Milano, Milan, Italy.
| | - Elena Gatti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139, Milan, Italy.
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964
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Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang XN, Sayer B, Park JE, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O'Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science 2021; 371:eaba6500. [PMID: 33479125 PMCID: PMC7611557 DOI: 10.1126/science.aba6500] [Citation(s) in RCA: 254] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/03/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022]
Abstract
The skin confers biophysical and immunological protection through a complex cellular network established early in embryonic development. We profiled the transcriptomes of more than 500,000 single cells from developing human fetal skin, healthy adult skin, and adult skin with atopic dermatitis and psoriasis. We leveraged these datasets to compare cell states across development, homeostasis, and disease. Our analysis revealed an enrichment of innate immune cells in skin during the first trimester and clonal expansion of disease-associated lymphocytes in atopic dermatitis and psoriasis. We uncovered and validated in situ a reemergence of prenatal vascular endothelial cell and macrophage cellular programs in atopic dermatitis and psoriasis lesional skin. These data illustrate the dynamism of cutaneous immunity and provide opportunities for targeting pathological developmental programs in inflammatory skin diseases.
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Affiliation(s)
- Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Peter Vegh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Fletcher
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Elizabeth F M Poyner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology, NHS Lothian, Lauriston Building, Edinburgh EH3 9EN, UK
| | - Anna Dubois
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kile Green
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mirjana Efremova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claire Jones
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas Ness
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Christopher Carey
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dorin-Mirel Popescu
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Xiao-Nong Wang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ben Sayer
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Victor A Negri
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Daria Belokhvostova
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - Magnus D Lynch
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - David McDonald
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Akhtar Husain
- Department of Pathology, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Jonathan Coxhead
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alexandra-Chloé Villani
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA 02129, USA
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Edel A O'Toole
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham S Ogg
- MRC Human Immunology Unit, Oxford Biomedical Research Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Neil Rajan
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Nick J Reynolds
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, Guy's Hospital Campus, London SE1 9RT, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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965
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He J, Yan J, Wang J, Zhao L, Xin Q, Zeng Y, Sun Y, Zhang H, Bai Z, Li Z, Ni Y, Gong Y, Li Y, He H, Bian Z, Lan Y, Ma C, Bian L, Zhu H, Liu B, Yue R. Dissecting human embryonic skeletal stem cell ontogeny by single-cell transcriptomic and functional analyses. Cell Res 2021; 31:742-757. [PMID: 33473154 PMCID: PMC8249634 DOI: 10.1038/s41422-021-00467-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/22/2020] [Indexed: 01/15/2023] Open
Abstract
Human skeletal stem cells (SSCs) have been discovered in fetal and adult long bones. However, the spatiotemporal ontogeny of human embryonic SSCs during early skeletogenesis remains elusive. Here we map the transcriptional landscape of human limb buds and embryonic long bones at single-cell resolution to address this fundamental question. We found remarkable heterogeneity within human limb bud mesenchyme and epithelium, and aligned them along the proximal–distal and anterior–posterior axes using known marker genes. Osteo-chondrogenic progenitors first appeared in the core limb bud mesenchyme, which give rise to multiple populations of stem/progenitor cells in embryonic long bones undergoing endochondral ossification. Importantly, a perichondrial embryonic skeletal stem/progenitor cell (eSSPC) subset was identified, which could self-renew and generate the osteochondral lineage cells, but not adipocytes or hematopoietic stroma. eSSPCs are marked by the adhesion molecule CADM1 and highly enriched with FOXP1/2 transcriptional network. Interestingly, neural crest-derived cells with similar phenotypic markers and transcriptional networks were also found in the sagittal suture of human embryonic calvaria. Taken together, this study revealed the cellular heterogeneity and lineage hierarchy during human embryonic skeletogenesis, and identified distinct skeletal stem/progenitor cells that orchestrate endochondral and intramembranous ossification.
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Affiliation(s)
- Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Jing Yan
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Jianfang Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Liangyu Zhao
- Department of Orthopedics, Changzheng Hospital, Naval Medical University, Shanghai, 200003, China
| | - Qian Xin
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yuxi Sun
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, China
| | - Han Zhang
- Department of Transfusion, Daping Hospital, Army Military Medical University, Chongqing, 400042, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Yunqiao Li
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Han He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China
| | - Zhilei Bian
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, Guangdong, 510530, China
| | - Chunyu Ma
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China
| | - Heng Zhu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100071, China. .,State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100071, China. .,Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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966
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Chen F, Ding K, Priedigkeit N, Elangovan A, Levine KM, Carleton N, Savariau L, Atkinson JM, Oesterreich S, Lee AV. Single-Cell Transcriptomic Heterogeneity in Invasive Ductal and Lobular Breast Cancer Cells. Cancer Res 2021; 81:268-281. [PMID: 33148662 PMCID: PMC7856056 DOI: 10.1158/0008-5472.can-20-0696] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 07/14/2020] [Accepted: 10/29/2020] [Indexed: 11/16/2022]
Abstract
Invasive lobular breast carcinoma (ILC), one of the major breast cancer histologic subtypes, exhibits unique features compared with the well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly caused by inactivating mutations, but the contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single-cell RNA sequencing on a panel of IDC and ILC cell lines, and an IDC cell line (T47D) with CRISPR-Cas9-mediated E-cadherin knockout (KO). Inspection of intracell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of MCF7 cells highly expressing an apoptosis-related signature, positively correlated with a preadaptation signature to estrogen deprivation. Investigation of E-cadherin KO-induced alterations showed transcriptomic membranous systems remodeling, elevated resemblance to ILCs in regulon activation, and increased sensitivity to IFNγ-mediated growth inhibition via activation of IRF1. This study reveals single-cell transcriptional heterogeneity in breast cancer cell lines and provides a resource to identify drivers of cancer progression and drug resistance. SIGNIFICANCE: This study represents a key step towards understanding heterogeneity in cancer cell lines and the role of E-cadherin depletion in contributing to the molecular features of invasive lobular breast carcinoma.
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MESH Headings
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Biomarkers, Tumor/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cadherins/antagonists & inhibitors
- Cadherins/genetics
- Cadherins/metabolism
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Mutation
- Prognosis
- Single-Cell Analysis/methods
- Transcriptome
- Tumor Cells, Cultured
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Affiliation(s)
- Fangyuan Chen
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- School of Medicine, Tsinghua University, Beijing, China
| | - Kai Ding
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nolan Priedigkeit
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ashuvinee Elangovan
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kevin M Levine
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Neil Carleton
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Laura Savariau
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Jennifer M Atkinson
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, Pittsburgh, Pennsylvania.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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967
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Acosta J, Ssozi D, van Galen P. Single-Cell RNA Sequencing to Disentangle the Blood System. Arterioscler Thromb Vasc Biol 2021; 41:1012-1018. [PMID: 33441024 PMCID: PMC7901535 DOI: 10.1161/atvbaha.120.314654] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The blood system is often represented as a tree-like structure with stem cells that give rise to mature blood cell types through a series of demarcated steps. Although this representation has served as a model of hierarchical tissue organization for decades, single-cell technologies are shedding new light on the abundance of cell type intermediates and the molecular mechanisms that ensure balanced replenishment of differentiated cells. In this Brief Review, we exemplify new insights into blood cell differentiation generated by single-cell RNA sequencing, summarize considerations for the application of this technology, and highlight innovations that are leading the way to understand hematopoiesis at the resolution of single cells. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
- Jean Acosta
- Division of Hematology, Brigham and Women's Hospital, Boston, MA. Department of Medicine, Harvard Medical School, Boston, MA. Broad Institute of MIT and Harvard, Cambridge, MA
| | - Daniel Ssozi
- Division of Hematology, Brigham and Women's Hospital, Boston, MA. Department of Medicine, Harvard Medical School, Boston, MA. Broad Institute of MIT and Harvard, Cambridge, MA
| | - Peter van Galen
- Division of Hematology, Brigham and Women's Hospital, Boston, MA. Department of Medicine, Harvard Medical School, Boston, MA. Broad Institute of MIT and Harvard, Cambridge, MA
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968
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Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-Cell Sequencing of Brain Cell Transcriptomes and Epigenomes. Neuron 2021; 109:11-26. [PMID: 33412093 PMCID: PMC7808568 DOI: 10.1016/j.neuron.2020.12.010] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/17/2020] [Accepted: 12/08/2020] [Indexed: 12/21/2022]
Abstract
Single-cell sequencing technologies, including transcriptomic and epigenomic assays, are transforming our understanding of the cellular building blocks of neural circuits. By directly measuring multiple molecular signatures in thousands to millions of individual cells, single-cell sequencing methods can comprehensively characterize the diversity of brain cell types. These measurements uncover gene regulatory mechanisms that shape cellular identity and provide insight into developmental and evolutionary relationships between brain cell populations. Single-cell sequencing data can aid the design of tools for targeted functional studies of brain circuit components, linking molecular signatures with anatomy, connectivity, morphology, and physiology. Here, we discuss the fundamental principles of single-cell transcriptome and epigenome sequencing, integrative computational analysis of the data, and key applications in neuroscience.
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Affiliation(s)
- Ethan J Armand
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Junhao Li
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Fangming Xie
- Department of Physics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eran A Mukamel
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA.
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969
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Wang X, Peticone C, Kotsopoulou E, Göttgens B, Calero-Nieto FJ. Single-cell transcriptome analysis of CAR T-cell products reveals subpopulations, stimulation, and exhaustion signatures. Oncoimmunology 2021; 10:1866287. [PMID: 33489472 PMCID: PMC7801130 DOI: 10.1080/2162402x.2020.1866287] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/13/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell adoptive therapy is set to transform the treatment of a rapidly expanding range of malignancies. Although the activation process of normal T cells is well characterized, comparatively little is known about the activation of cells via the CAR. Here we have used flow cytometry together with single-cell transcriptome profiling to characterize the starting material (peripheral blood mononuclear cells) and CAR therapeutic products of 3 healthy donors in the presence and absence of antigen-specific stimulation. Analysis of 53,191 single-cell transcriptomes showed APRIL-based CAR products to contain several subpopulations of cells, with cellular composition reproducible from donor to donor, and all major cellular subsets compatible with CAR expression. Only 50% of CAR-expressing cells displayed transcriptional changes upon CAR-specific antigen exposure. The resulting molecular signature for CAR T-cell activation provides a rich resource for future dissection of underlying mechanisms. Targeted data interrogation also revealed that a small proportion of antigen-responding CAR-expressing cells displayed an exhaustion signature, with both known markers and genes not previously associated with T-cell exhaustion. Comprehensive single-cell transcriptomic analysis thus represents a powerful way to guide the assessment and optimization of clinical-grade CAR-T-cells, and inform future research into the underlying molecular processes.
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Affiliation(s)
- Xiaonan Wang
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- School of Public Health, Shanghai Jiao Tong University, School of Medicine, China
| | | | | | - Berthold Göttgens
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Fernando J Calero-Nieto
- Wellcome and MRC Cambridge Stem Cell Institute and University of Cambridge Department of Haematology, Jeffrey Cheah Biomedical Centre, Cambridge, UK
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970
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Shaw R, Tian X, Xu J. Single-Cell Transcriptome Analysis in Plants: Advances and Challenges. MOLECULAR PLANT 2021; 14:115-126. [PMID: 33152518 DOI: 10.1016/j.molp.2020.10.012] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/08/2020] [Accepted: 10/30/2020] [Indexed: 05/22/2023]
Abstract
The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has demonstrated that this technology is far more than just another way to perform transcriptome analysis. It is not an exaggeration to say that the advent of scRNA-seq is revolutionizing the details of whole-transcriptome snapshots from a tissue to a cell. With this disruptive technology, it is now possible to mine heterogeneity between tissue types and within cells like never before. This enables more rapid identification of rare and novel cell types, simultaneous characterization of multiple different cell types and states, more accurate and integrated understanding of their roles in life processes, and more. However, we are only at the beginning of unlocking the full potential of scRNA-seq applications. This is particularly true for plant sciences, where single-cell transcriptome profiling is in its early stage and has many exciting challenges to overcome. In this review, we compare and evaluate recent pioneering studies using the Arabidopsis root model, which has established new paradigms for scRNA-seq studies in plants. We also explore several new and promising single-cell analysis tools that are available to those wishing to study plant development and physiology at unprecedented resolution and scale. In addition, we propose some future directions on the use of scRNA-seq technology to tackle some of the critical challenges in plant research and breeding.
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Affiliation(s)
- Rahul Shaw
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Xin Tian
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543, Singapore.
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971
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Non-canonical Wnt/PCP signalling regulates intestinal stem cell lineage priming towards enteroendocrine and Paneth cell fates. Nat Cell Biol 2021; 23:23-31. [PMID: 33398177 DOI: 10.1038/s41556-020-00617-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 11/27/2020] [Indexed: 02/07/2023]
Abstract
A detailed understanding of intestinal stem cell (ISC) self-renewal and differentiation is required to treat chronic intestinal diseases. However, the different models of ISC lineage hierarchy1-6 and segregation7-12 are subject to debate. Here, we have discovered non-canonical Wnt/planar cell polarity (PCP)-activated ISCs that are primed towards the enteroendocrine or Paneth cell lineage. Strikingly, integration of time-resolved lineage labelling with single-cell gene expression analysis revealed that both lineages are directly recruited from ISCs via unipotent transition states, challenging the existence of formerly predicted bi- or multipotent secretory progenitors7-12. Transitory cells that mature into Paneth cells are quiescent and express both stem cell and secretory lineage genes, indicating that these cells are the previously described Lgr5+ label-retaining cells7. Finally, Wnt/PCP-activated Lgr5+ ISCs are molecularly indistinguishable from Wnt/β-catenin-activated Lgr5+ ISCs, suggesting that lineage priming and cell-cycle exit is triggered at the post-transcriptional level by polarity cues and a switch from canonical to non-canonical Wnt/PCP signalling. Taken together, we redefine the mechanisms underlying ISC lineage hierarchy and identify the Wnt/PCP pathway as a new niche signal preceding lateral inhibition in ISC lineage priming and segregation.
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972
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Slovin S, Carissimo A, Panariello F, Grimaldi A, Bouché V, Gambardella G, Cacchiarelli D. Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview. Methods Mol Biol 2021; 2284:343-365. [PMID: 33835452 DOI: 10.1007/978-1-0716-1307-8_19] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Thanks to innovative sample-preparation and sequencing technologies, gene expression in individual cells can now be measured for thousands of cells in a single experiment. Since its introduction, single-cell RNA sequencing (scRNA-seq) approaches have revolutionized the genomics field as they created unprecedented opportunities for resolving cell heterogeneity by exploring gene expression profiles at a single-cell resolution. However, the rapidly evolving field of scRNA-seq invoked the emergence of various analytics approaches aimed to maximize the full potential of this novel strategy. Unlike population-based RNA sequencing approaches, scRNA seq necessitates comprehensive computational tools to address high data complexity and keep up with the emerging single-cell associated challenges. Despite the vast number of analytical methods, a universal standardization is lacking. While this reflects the fields' immaturity, it may also encumber a newcomer to blend in.In this review, we aim to bridge over the abovementioned hurdle and propose four ready-to-use pipelines for scRNA-seq analysis easily accessible by a newcomer, that could fit various biological data types. Here we provide an overview of the currently available single-cell technologies for cell isolation and library preparation and a step by step guide that covers the entire canonical analytic workflow to analyse scRNA-seq data including read mapping, quality controls, gene expression quantification, normalization, feature selection, dimensionality reduction, and cell clustering useful for trajectory inference and differential expression. Such workflow guidelines will escort novices as well as expert users in the analysis of complex scRNA-seq datasets, thus further expanding the research potential of single-cell approaches in basic science, and envisaging its future implementation as best practice in the field.
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Affiliation(s)
- Shaked Slovin
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Annamaria Carissimo
- Istituto per le Applicazioni del Calcolo "Mauro Picone", Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Valentina Bouché
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Gennaro Gambardella
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Chemical Materials and Industrial Engineering, University of Naples "Federico II", Naples, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.
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973
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Ferchen K, Song B, Grimes HL. A primer on single-cell genomics in myeloid biology. Curr Opin Hematol 2021; 28:11-17. [PMID: 33186153 PMCID: PMC9205579 DOI: 10.1097/moh.0000000000000623] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Understanding the fast-moving field of single-cell technologies, as applied to myeloid biology, requires an appreciation of basic molecular, informatics, and biological concepts. Here, we highlight both key and recent articles to illustrate basic concepts for those new to molecular single-cell analyses in myeloid hematology. RECENT FINDINGS Recent studies apply single-cell omics to discover novel cell populations, construct relationships between cell populations, reconfigure the organization of hematopoiesis, and study hematopoietic lineage tree and fate choices. Accompanying development of technologies, new informatic tools have emerged, providing exciting new insights. SUMMARY Hematopoietic stem and progenitor cells are regulated by complex intrinsic and extrinsic factors to produce blood cell types. In this review, we discuss recent advances in single-cell omics to profile these cells, methods to infer cell type identify, and trajectories from molecular omics data to ultimately derive new insights into hematopoietic stem and progenitor cell biology. We further discuss future applications of these technologies to understand hematopoietic cell interactions, function, and development. The goal is to offer a comprehensive overview of current single-cell technologies and their impact on our understanding of myeloid cell development for those new to single-cell analyses.
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Affiliation(s)
- Kyle Ferchen
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
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974
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Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, Fernando RC, Gardner L, Woodhams B, Arutyunyan A, Polanski K, Hoo R, Sancho-Serra C, Li T, Kwakwa K, Tuck E, Lorenzi V, Massalha H, Prete M, Kleshchevnikov V, Tarkowska A, Porter T, Mazzeo CI, van Dongen S, Dabrowska M, Vaskivskyi V, Mahbubani KT, Park JE, Jimenez-Linan M, Campos L, Kiselev VY, Lindskog C, Ayuk P, Prigmore E, Stratton MR, Saeb-Parsy K, Moffett A, Moore L, Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet 2021; 53:1698-1711. [PMID: 34857954 PMCID: PMC8648563 DOI: 10.1038/s41588-021-00972-2] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/18/2021] [Indexed: 12/24/2022]
Abstract
The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma.
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Affiliation(s)
- Luz Garcia-Alonso
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kenny Roberts
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Konstantina Nikolakopoulou
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ridma C. Fernando
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lucy Gardner
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Benjamin Woodhams
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Anna Arutyunyan
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Krzysztof Polanski
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Regina Hoo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Tong Li
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Elizabeth Tuck
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Valentina Lorenzi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Hassan Massalha
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Martin Prete
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Tarryn Porter
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Stijn van Dongen
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Monika Dabrowska
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Vasyl Vaskivskyi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Krishnaa T. Mahbubani
- grid.5335.00000000121885934Department of Haematology, University of Cambridge, Cambridge, UK ,grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Jong-eun Park
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Mercedes Jimenez-Linan
- grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lia Campos
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Cecilia Lindskog
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paul Ayuk
- grid.420004.20000 0004 0444 2244Department of Women’s Services, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Elena Prigmore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | | | - Kourosh Saeb-Parsy
- grid.454369.9Cambridge Biorepository for Translational Medicine (CBTM), NIHR Cambridge Biomedical Research Centre, Cambridge, UK ,grid.5335.00000000121885934Department of Surgery, University of Cambridge, Cambridge, UK
| | - Ashley Moffett
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luiza Moore
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.24029.3d0000 0004 0383 8386Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Omer A. Bayraktar
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK
| | - Sarah A. Teichmann
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Margherita Y. Turco
- grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK ,grid.5335.00000000121885934Department of Pathology, University of Cambridge, Cambridge, UK ,grid.482245.d0000 0001 2110 3787Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Roser Vento-Tormo
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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975
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Knudsen ES, Kumarasamy V, Chung S, Ruiz A, Vail P, Tzetzo S, Wu J, Nambiar R, Seshadri M, Abrams SI, Wang J, Witkiewicz AK, Wang J, Witkiewicz AK. Targeting dual signalling pathways in concert with immune checkpoints for the treatment of pancreatic cancer. Gut 2021; 70:127-138. [PMID: 32424005 PMCID: PMC7671951 DOI: 10.1136/gutjnl-2020-321000] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/30/2020] [Accepted: 04/19/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE This study exploits the intersection between molecular-targeted therapies and immune-checkpoint inhibition to define new means to treat pancreatic cancer. DESIGN Patient-derived cell lines and xenograft models were used to define the response to CDK4/6 and MEK inhibition in the tumour compartment. Impacts relative to immunotherapy were performed using subcutaneous and orthotopic syngeneic models. Single-cell RNA sequencing and multispectral imaging were employed to delineate effects on the immunological milieu in the tumour microenvironment. RESULTS We found that combination treatment with MEK and CDK4/6 inhibitors was effective across a broad range of PDX models in delaying tumour progression. These effects were associated with stable cell-cycle arrest, as well as the induction of multiple genes associated with interferon response and antigen presentation in an RB-dependent fashion. Using single-cell sequencing and complementary approaches, we found that the combination of CDK4/6 and MEK inhibition had a significant impact on increasing T-cell infiltration and altering myeloid populations, while potently cooperating with immune checkpoint inhibitors. CONCLUSIONS Together, these data indicate that there are canonical and non-canonical features of CDK4/6 and MEK inhibition that impact on the tumour and immune microenvironment. This combination-targeted treatment can promote robust tumour control in combination with immune checkpoint inhibitor therapy.
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Affiliation(s)
- Erik s Knudsen
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA,Molecular & Cellular Biology, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Vishnu Kumarasamy
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA,Molecular & Cellular Biology, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Sejin Chung
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA,Molecular & Cellular Biology, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Amanda Ruiz
- Cancer Center, University of Arizona, Tucson, Arizona,
USA
| | - Paris Vail
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA,Molecular & Cellular Biology, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Stephanie Tzetzo
- Immunology, Roswell Park Comprehensive Cancer Center,
Buffalo, New York, USA
| | - Jin Wu
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ram Nambiar
- Center for Personalized Medicine, Roswell Park
Comprehensive Cancer Center, Buffalo, New York, USA
| | - Mukund Seshadri
- Oral Oncology, Roswell Park Comprehensive Cancer Center,
Buffalo, New York, USA
| | - Scott I Abrams
- Immunology, Roswell Park Comprehensive Cancer Center,
Buffalo, New York, USA
| | - Jianmin Wang
- Biostatistics and Bioinformatics, Roswell Park
comprehensive Cancer Center, Buffalo, New York, USA
| | - Agnieszka K Witkiewicz
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA .,Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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976
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Santoso CS, Li Z, Rottenberg JT, Liu X, Shen VX, Bass JIF. In vitro Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.29.424728. [PMID: 33398281 PMCID: PMC7781316 DOI: 10.1101/2020.12.29.424728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drug combinations on inflammatory cytokine production in peripheral blood mononuclear cells, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.
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Affiliation(s)
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | | | - Xing Liu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Vivian X. Shen
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Juan I. Fuxman Bass
- Department of Biology, Boston University, Boston, MA 02215, USA
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
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977
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Amadei G, Lau KYC, De Jonghe J, Gantner CW, Sozen B, Chan C, Zhu M, Kyprianou C, Hollfelder F, Zernicka-Goetz M. Inducible Stem-Cell-Derived Embryos Capture Mouse Morphogenetic Events In Vitro. Dev Cell 2020; 56:366-382.e9. [PMID: 33378662 PMCID: PMC7883308 DOI: 10.1016/j.devcel.2020.12.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/26/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
The development of mouse embryos can be partially recapitulated by combining embryonic stem cells (ESCs), trophoblast stem cells (TS), and extra-embryonic endoderm (XEN) stem cells to generate embryo-like structures called ETX embryos. Although ETX embryos transcriptionally capture the mouse gastrula, their ability to recapitulate complex morphogenic events such as gastrulation is limited, possibly due to the limited potential of XEN cells. To address this, we generated ESCs transiently expressing transcription factor Gata4, which drives the extra-embryonic endoderm fate, and combined them with ESCs and TS cells to generate induced ETX embryos (iETX embryos). We show that iETX embryos establish a robust anterior signaling center that migrates unilaterally to break embryo symmetry. Furthermore, iETX embryos gastrulate generating embryonic and extra-embryonic mesoderm and definitive endoderm. Our findings reveal that replacement of XEN cells with ESCs transiently expressing Gata4 endows iETX embryos with greater developmental potential, thus enabling the study of the establishment of anterior-posterior patterning and gastrulation in an in vitro system. Stem cells generate mouse-embryo-like structures with improved potential These structures undertake anterior visceral endoderm formation and gastrulation Single-cell sequencing shows improved resemblance to mouse embryo
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Affiliation(s)
- Gianluca Amadei
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Kasey Y C Lau
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Berna Sozen
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA
| | - Christopher Chan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Meng Zhu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Christos Kyprianou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Division of Biology and Biological Engineering, Caltech, Pasadena, CA 91125, USA.
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978
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Young MD, Behjati S. SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. Gigascience 2020; 9:giaa151. [PMID: 33367645 PMCID: PMC7763177 DOI: 10.1093/gigascience/giaa151] [Citation(s) in RCA: 534] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/13/2020] [Accepted: 11/27/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that confounds the biological interpretation of single-cell transcriptomic data. RESULTS We demonstrate that contamination from this "soup" of cell-free RNAs is ubiquitous, with experiment-specific variations in composition and magnitude. We present a method, SoupX, for quantifying the extent of the contamination and estimating "background-corrected" cell expression profiles that seamlessly integrate with existing downstream analysis tools. Applying this method to several datasets using multiple droplet sequencing technologies, we demonstrate that its application improves biological interpretation of otherwise misleading data, as well as improving quality control metrics. CONCLUSIONS We present SoupX, a tool for removing ambient RNA contamination from droplet-based single-cell RNA sequencing experiments. This tool has broad applicability, and its application can improve the biological utility of existing and future datasets.
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Affiliation(s)
- Matthew D Young
- Wellcome Trust Sanger Institute, Cellular Genetics, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Cellular Genetics, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- University of Cambridge, Department of Paediatrics, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
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979
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Wang H, He J, Xu C, Chen X, Yang H, Shi S, Liu C, Zeng Y, Wu D, Bai Z, Wang M, Wen Y, Su P, Xia M, Huang B, Ma C, Bian L, Lan Y, Cheng T, Shi L, Liu B, Zhou J. Decoding Human Megakaryocyte Development. Cell Stem Cell 2020; 28:535-549.e8. [PMID: 33340451 DOI: 10.1016/j.stem.2020.11.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 09/25/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022]
Abstract
Despite our growing understanding of embryonic immune development, rare early megakaryocytes (MKs) remain relatively understudied. Here we used single-cell RNA sequencing of human MKs from embryonic yolk sac (YS) and fetal liver (FL) to characterize the transcriptome, cellular heterogeneity, and developmental trajectories of early megakaryopoiesis. In the YS and FL, we found heterogeneous MK subpopulations with distinct developmental routes and patterns of gene expression that could reflect early functional specialization. Intriguingly, we identified a subpopulation of CD42b+CD14+ MKs in vivo that exhibit high expression of genes associated with immune responses and can also be derived from human embryonic stem cells (hESCs) in vitro. Furthermore, we identified THBS1 as an early marker for MK-biased embryonic endothelial cells. Overall, we provide important insights and invaluable resources for dissection of the molecular and cellular programs underlying early human megakaryopoiesis.
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Affiliation(s)
- Hongtao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Changlu Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Xiaoyuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Hua Yang
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Shujuan Shi
- Tianjin Central Hospital of Gynecology Obstetrics, Tianjin 300052, China
| | - Cuicui Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yang Zeng
- Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Dan Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Mengge Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Yuqi Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Pei Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Meijuan Xia
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Baiming Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Chunyu Ma
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China.
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; CAMS Center for Stem Cell Medicine, PUMC Department of Stem Cell and Regenerative Medicine, Tianjin 300020, China.
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980
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Guo F, Zhang B, Yang H, Fu Y, Wang Y, Huang J, Cheng M, Li X, Shen Z, Li L, He P, Xiang AP, Wang S, Zhang H. Systemic transcriptome comparison between early- And late-onset pre-eclampsia shows distinct pathology and novel biomarkers. Cell Prolif 2020; 54:e12968. [PMID: 33332660 PMCID: PMC7848957 DOI: 10.1111/cpr.12968] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Objectives Pre‐eclampsia is a leading cause of morbidity and mortality during pregnancy. Although the two forms of this disorder, early‐ (EOPE) and late‐onset of pre‐eclampsia (LOPE) are different, the underlying pathology remains elusive. We aim to unravel the difference and to identify novel biomarkers for EOPE and LOPE. Materials and Methods A complete comparison of both placental and peripheral blood transcriptomes was performed to investigate the pathology of pre‐eclampsia. Single‐cell transcriptomics of the maternal‐fetal interface were integrated to identify novel biomarkers for EOPE and LOPE which were further verified at protein or mRNA level in patients. Results We found that the transcriptomes of placentae from EOPE, but not LOPE, were significantly different from their respective controls. Conversely, the transcriptomes of peripheral blood from LOPE were more different from their controls than EOPE. Importantly, we identified that several classical biomarkers of pre‐eclampsia were expressed specifically in extravillous trophoblast and syncytiotrophoblast and only upregulated in EOPE, suggesting they should not be applied to all pre‐eclampsia patients in general. We further identified novel biomarkers for EOPE and LOPE from differentially expressed genes (DEGs) of placental and peripheral blood, respectively. The new biomarkers EBI3, IGF2, ORMDL3, GATA2 and KIR2DL4 were experimentally verified with patient blood samples. Conclusion Our data demonstrate distinct pathology of EOPE and LOPE, and uncover new biomarkers that can be applied in diagnosis for pre‐eclampsia.
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Affiliation(s)
- Fang Guo
- Department of Obstetrics, First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Bao Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hao Yang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yixi Fu
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yaning Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jianming Huang
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Mi Cheng
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiaobo Li
- Core Facilities for Medical Science, Sun Yat-sen University, Guangzhou, China
| | - Zhuojian Shen
- Department of Thoracic Surgery, Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Li Li
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Department of Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Andy Peng Xiang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Shuaiyu Wang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Hongbo Zhang
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China.,The Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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981
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Bharat A, Querrey M, Markov NS, Kim S, Kurihara C, Garza-Castillon R, Manerikar A, Shilatifard A, Tomic R, Politanska Y, Abdala-Valencia H, Yeldandi AV, Lomasney JW, Misharin AV, Budinger GRS. Lung transplantation for patients with severe COVID-19. Sci Transl Med 2020; 12:eabe4282. [PMID: 33257409 PMCID: PMC8050952 DOI: 10.1126/scitranslmed.abe4282] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022]
Abstract
Lung transplantation can potentially be a life-saving treatment for patients with nonresolving COVID-19-associated respiratory failure. Concerns limiting lung transplantation include recurrence of SARS-CoV-2 infection in the allograft, technical challenges imposed by viral-mediated injury to the native lung, and the potential risk for allograft infection by pathogens causing ventilator-associated pneumonia in the native lung. Additionally, the native lung might recover, resulting in long-term outcomes preferable to those of transplant. Here, we report the results of lung transplantation in three patients with nonresolving COVID-19-associated respiratory failure. We performed single-molecule fluorescence in situ hybridization (smFISH) to detect both positive and negative strands of SARS-CoV-2 RNA in explanted lung tissue from the three patients and in additional control lung tissue samples. We conducted extracellular matrix imaging and single-cell RNA sequencing on explanted lung tissue from the three patients who underwent transplantation and on warm postmortem lung biopsies from two patients who had died from COVID-19-associated pneumonia. Lungs from these five patients with prolonged COVID-19 disease were free of SARS-CoV-2 as detected by smFISH, but pathology showed extensive evidence of injury and fibrosis that resembled end-stage pulmonary fibrosis. Using machine learning, we compared single-cell RNA sequencing data from the lungs of patients with late-stage COVID-19 to that from the lungs of patients with pulmonary fibrosis and identified similarities in gene expression across cell lineages. Our findings suggest that some patients with severe COVID-19 develop fibrotic lung disease for which lung transplantation is their only option for survival.
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Affiliation(s)
- Ankit Bharat
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Melissa Querrey
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nikolay S Markov
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Samuel Kim
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chitaru Kurihara
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rafael Garza-Castillon
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Adwaiy Manerikar
- Division of Thoracic Surgery, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rade Tomic
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yuliya Politanska
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Anjana V Yeldandi
- Department of Pathology, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jon W Lomasney
- Department of Pathology, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern Memorial Hospital, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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982
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Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R, Zhang F, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J. A human cell atlas of fetal gene expression. Science 2020; 370:370/6518/eaba7721. [PMID: 33184181 DOI: 10.1126/science.aba7721] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focused on organ-specific specializations of broadly distributed cell types (such as blood, endothelial, and epithelial), sites of fetal erythropoiesis (which notably included the adrenal gland), and integration with mouse developmental atlases (such as conserved specification of blood cells). These data represent a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
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Affiliation(s)
- Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Paul D Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Malte Spielmann
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
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983
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Elmentaite R, Ross ADB, Roberts K, James KR, Ortmann D, Gomes T, Nayak K, Tuck L, Pritchard S, Bayraktar OA, Heuschkel R, Vallier L, Teichmann SA, Zilbauer M. Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease. Dev Cell 2020; 55:771-783.e5. [PMID: 33290721 PMCID: PMC7762816 DOI: 10.1016/j.devcel.2020.11.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/04/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Human gut development requires the orchestrated interaction of differentiating cell types. Here, we generate an in-depth single-cell map of the developing human intestine at 6–10 weeks post-conception. Our analysis reveals the transcriptional profile of cycling epithelial precursor cells; distinct from LGR5-expressing cells. We propose that these cells may contribute to differentiated cell subsets via the generation of LGR5-expressing stem cells and receive signals from surrounding mesenchymal cells. Furthermore, we draw parallels between the transcriptomes of ex vivo tissues and in vitro fetal organoids, revealing the maturation of organoid cultures in a dish. Lastly, we compare scRNA-seq profiles from pediatric Crohn’s disease epithelium alongside matched healthy controls to reveal disease-associated changes in the epithelial composition. Contrasting these with the fetal profiles reveals the re-activation of fetal transcription factors in Crohn’s disease. Our study provides a resource available at www.gutcellatlas.org, and underscores the importance of unraveling fetal development in understanding disease. Single-cell RNA-seq map of the developing and pediatric human intestine Cycling BEX5+ epithelial precursors are distinct from adult LGR5+ stem cells Human fetal intestinal organoids mature in culture Fetal transcription factors are reactivated in the Crohn’s disease epithelium
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alexander D B Ross
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Daniel Ortmann
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge CB2 0QQ, UK
| | - Ludovic Vallier
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK.
| | - Matthias Zilbauer
- Wellcome Trust, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge CB2 0QQ, UK.
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984
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Andrews TS, Kiselev VY, McCarthy D, Hemberg M. Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nat Protoc 2020; 16:1-9. [PMID: 33288955 DOI: 10.1038/s41596-020-00409-w] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/08/2020] [Indexed: 01/01/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( https://scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.
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Affiliation(s)
| | | | - Davis McCarthy
- Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia.,Melbourne Integrative Genomics, Faculty of Science, University of Melbourne, Melbourne, Victoria, Australia
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985
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Aging-Associated Alterations in Mammary Epithelia and Stroma Revealed by Single-Cell RNA Sequencing. Cell Rep 2020; 33:108566. [PMID: 33378681 PMCID: PMC7898263 DOI: 10.1016/j.celrep.2020.108566] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/13/2020] [Accepted: 12/07/2020] [Indexed: 12/11/2022] Open
Abstract
Aging is closely associated with increased susceptibility to breast cancer, yet there have been limited systematic studies of aging-induced alterations in the mammary gland. Here, we leverage high-throughput single-cell RNA sequencing to generate a detailed transcriptomic atlas of young and aged murine mammary tissues. By analyzing epithelial, stromal, and immune cells, we identify age-dependent alterations in cell proportions and gene expression, providing evidence that suggests alveolar maturation and physiological decline. The analysis also uncovers potential pro-tumorigenic mechanisms coupled to the age-associated loss of tumor suppressor function and change in microenvironment. In addition, we identify a rare, age-dependent luminal population co-expressing hormone-sensing and secretory-alveolar lineage markers, as well as two macrophage populations expressing distinct gene signatures, underscoring the complex heterogeneity of the mammary epithelia and stroma. Collectively, this rich single-cell atlas reveals the effects of aging on mammary physiology and can serve as a useful resource for understanding aging-associated cancer risk. Using single-cell RNA-sequencing, Li et al. compare mammary epithelia and stroma in young and aged mice. Age-dependent changes at cell and gene levels provide evidence suggesting alveolar maturation, functional deterioration, and potential pro-tumorigenic and inflammatory alterations. Additionally, identification of heterogeneous luminal and macrophage subpopulations underscores the complexity of mammary lineages.
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986
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Kotliar D, Lin AE, Logue J, Hughes TK, Khoury NM, Raju SS, Wadsworth MH, Chen H, Kurtz JR, Dighero-Kemp B, Bjornson ZB, Mukherjee N, Sellers BA, Tran N, Bauer MR, Adams GC, Adams R, Rinn JL, Melé M, Schaffner SF, Nolan GP, Barnes KG, Hensley LE, McIlwain DR, Shalek AK, Sabeti PC, Bennett RS. Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics. Cell 2020; 183:1383-1401.e19. [PMID: 33159858 PMCID: PMC7707107 DOI: 10.1016/j.cell.2020.10.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/10/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.
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Affiliation(s)
- Dylan Kotliar
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA.
| | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Travis K Hughes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Nadine M Khoury
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Siddharth S Raju
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Marc H Wadsworth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Jonathan R Kurtz
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Bonnie Dighero-Kemp
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Zach B Bjornson
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA
| | - Nancy Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Matthew R Bauer
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ricky Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - John L Rinn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Marta Melé
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain
| | - Stephen F Schaffner
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
| | - David R McIlwain
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
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987
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Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, O'Brien SA, He Y, Wang L, Zhang Q, Kim A, Gao R, Orf J, Wang T, Sawant D, Kang J, Bhatt D, Lu D, Li CM, Rapaport AS, Perez K, Ye Y, Wang S, Hu X, Ren X, Ouyang W, Shen Z, Egen JG, Zhang Z, Yu X. Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer. Cell 2020; 181:442-459.e29. [PMID: 32302573 DOI: 10.1016/j.cell.2020.03.048] [Citation(s) in RCA: 709] [Impact Index Per Article: 177.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/02/2020] [Accepted: 03/20/2020] [Indexed: 12/15/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for defining cellular diversity in tumors, but its application toward dissecting mechanisms underlying immune-modulating therapies is scarce. We performed scRNA-seq analyses on immune and stromal populations from colorectal cancer patients, identifying specific macrophage and conventional dendritic cell (cDC) subsets as key mediators of cellular cross-talk in the tumor microenvironment. Defining comparable myeloid populations in mouse tumors enabled characterization of their response to myeloid-targeted immunotherapy. Treatment with anti-CSF1R preferentially depleted macrophages with an inflammatory signature but spared macrophage populations that in mouse and human expresses pro-angiogenic/tumorigenic genes. Treatment with a CD40 agonist antibody preferentially activated a cDC population and increased Bhlhe40+ Th1-like cells and CD8+ memory T cells. Our comprehensive analysis of key myeloid subsets in human and mouse identifies critical cellular interactions regulating tumor immunity and defines mechanisms underlying myeloid-targeted immunotherapies currently undergoing clinical testing.
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Affiliation(s)
- Lei Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ziyi Li
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Katarzyna M Skrzypczynska
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Qiao Fang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Sarah A O'Brien
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Yao He
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lynn Wang
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Qiming Zhang
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Aeryon Kim
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Ranran Gao
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jessica Orf
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Tao Wang
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Deepali Sawant
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Jiajinlong Kang
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dev Bhatt
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Daniel Lu
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Chi-Ming Li
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Aaron S Rapaport
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Kristy Perez
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Xueda Hu
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China; Analytical Biosciences Limited, Beijing 100084, China
| | - Xianwen Ren
- BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjun Ouyang
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Jackson G Egen
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA.
| | - Zemin Zhang
- Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; BIOPIC and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Xin Yu
- Department of Inflammation and Oncology and Genome Analysis Unit, Amgen Research, Amgen Inc., South San Francisco, CA 94080, USA.
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988
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Domcke S, Hill AJ, Daza RM, Cao J, O'Day DR, Pliner HA, Aldinger KA, Pokholok D, Zhang F, Milbank JH, Zager MA, Glass IA, Steemers FJ, Doherty D, Trapnell C, Cusanovich DA, Shendure J. A human cell atlas of fetal chromatin accessibility. Science 2020; 370:eaba7612. [PMID: 33184180 PMCID: PMC7785298 DOI: 10.1126/science.aba7612] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 09/10/2020] [Indexed: 12/12/2022]
Abstract
The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility and gene expression in fetal tissues. For chromatin accessibility, we devised a three-level combinatorial indexing assay and applied it to 53 samples representing 15 organs, profiling ~800,000 single cells. We leveraged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands of candidate regulatory elements that exhibit cell type-specific chromatin accessibility. We investigated the properties of lineage-specific transcription factors (such as POU2F1 in neurons), organ-specific specializations of broadly distributed cell types (such as blood and endothelial), and cell type-specific enrichments of complex trait heritability. These data represent a rich resource for the exploration of in vivo human gene regulation in diverse tissues and cell types.
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Affiliation(s)
- Silvia Domcke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew J Hill
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Junyue Cao
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Hannah A Pliner
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Kimberly A Aldinger
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Jennifer H Milbank
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Michael A Zager
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ian A Glass
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Darren A Cusanovich
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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989
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Dong R, Yang R, Zhan Y, Lai HD, Ye CJ, Yao XY, Luo WQ, Cheng XM, Miao JJ, Wang JF, Liu BH, Liu XQ, Xie LL, Li Y, Zhang M, Chen L, Song WC, Qian W, Gao WQ, Tang YH, Shen CY, Jiang W, Chen G, Yao W, Dong KR, Xiao XM, Zheng S, Li K, Wang J. Single-Cell Characterization of Malignant Phenotypes and Developmental Trajectories of Adrenal Neuroblastoma. Cancer Cell 2020; 38:716-733.e6. [PMID: 32946775 DOI: 10.1016/j.ccell.2020.08.014] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/08/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023]
Abstract
Neuroblastoma (NB), which is a subtype of neural-crest-derived malignancy, is the most common extracranial solid tumor occurring in childhood. Despite extensive research, the underlying developmental origin of NB remains unclear. Using single-cell RNA sequencing, we generate transcriptomes of adrenal NB from 160,910 cells of 16 patients and transcriptomes of putative developmental cells of origin of NB from 12,103 cells of early human embryos and fetal adrenal glands at relatively late development stages. We find that most adrenal NB tumor cells transcriptionally mirror noradrenergic chromaffin cells. Malignant states also recapitulate the proliferation/differentiation status of chromaffin cells in the process of normal development. Our findings provide insight into developmental trajectories and cellular states underlying human initiation and progression of NB.
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Affiliation(s)
- Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China.
| | - Ran Yang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Yong Zhan
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Hua-Dong Lai
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chun-Jing Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Xiao-Ying Yao
- Family Planning Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Wen-Qin Luo
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao-Mu Cheng
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ju-Ju Miao
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jun-Feng Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Bai-Hui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Xiang-Qi Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Lu-Lu Xie
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Yi Li
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Man Zhang
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Lian Chen
- Department of Pathology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wei-Chen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Wei Qian
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Wei-Qiang Gao
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China; State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yun-Hui Tang
- Family Planning Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Chun-Yan Shen
- Family Planning Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, China
| | - Wei Jiang
- Genergy Bio-technology (Shanghai) Co., Ltd, Shanghai 200235, China
| | - Gong Chen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Wei Yao
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Kui-Ran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Xian-Min Xiao
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China
| | - Kai Li
- Department of Pediatric Surgery, Children's Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defects, Shanghai 201102, China.
| | - Jia Wang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.
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990
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Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM, Inaba A, Bergamaschi L, Smith S, Tran MGB, Petsalaki E, Lyons PA, Espeli M, Huntly BJP, Smith KGC, Cornall RJ, Clatworthy MR, Maxwell PH. Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development. Nat Immunol 2020; 21:1408-1420. [PMID: 32868930 PMCID: PMC7613233 DOI: 10.1038/s41590-020-0772-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/29/2020] [Indexed: 02/02/2023]
Abstract
B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF activity is high in human and murine bone marrow pro-B and pre-B cells and decreases at the immature B cell stage. This stage-specific HIF suppression is required for normal B cell development because genetic activation of HIF-1α in murine B cells led to reduced repertoire diversity, decreased BCR editing and developmental arrest of immature B cells, resulting in reduced peripheral B cell numbers. HIF-1α activation lowered surface BCR, CD19 and B cell-activating factor receptor and increased expression of proapoptotic BIM. BIM deletion rescued the developmental block. Administration of a HIF activator in clinical use markedly reduced bone marrow and transitional B cells, which has therapeutic implications. Together, our work demonstrates that dynamic regulation of HIF-1α is essential for normal B cell development.
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Affiliation(s)
- Natalie Burrows
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
| | - Rachael J M Bashford-Rogers
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford, UK
| | - Vijesh J Bhute
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Ana Peñalver
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Joscelin E G Smith
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mukta Deobagkar-Lele
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Thomas M Connor
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Akimichi Inaba
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Laura Bergamaschi
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sam Smith
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul A Lyons
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Marion Espeli
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris, France
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Richard J Cornall
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford, UK
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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991
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Su Y, Chen D, Yuan D, Lausted C, Choi J, Dai CL, Voillet V, Duvvuri VR, Scherler K, Troisch P, Baloni P, Qin G, Smith B, Kornilov SA, Rostomily C, Xu A, Li J, Dong S, Rothchild A, Zhou J, Murray K, Edmark R, Hong S, Heath JE, Earls J, Zhang R, Xie J, Li S, Roper R, Jones L, Zhou Y, Rowen L, Liu R, Mackay S, O'Mahony DS, Dale CR, Wallick JA, Algren HA, Zager MA, Wei W, Price ND, Huang S, Subramanian N, Wang K, Magis AT, Hadlock JJ, Hood L, Aderem A, Bluestone JA, Lanier LL, Greenberg PD, Gottardo R, Davis MM, Goldman JD, Heath JR. Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19. Cell 2020; 183:1479-1495.e20. [PMID: 33171100 PMCID: PMC7598382 DOI: 10.1016/j.cell.2020.10.037] [Citation(s) in RCA: 388] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 09/16/2020] [Accepted: 10/22/2020] [Indexed: 12/29/2022]
Abstract
We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.
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Affiliation(s)
- Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | | | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Valentin Voillet
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, NPC (HCRISA), Cape Town 8001, South Africa; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | | | | | - Guangrong Qin
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Brett Smith
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | - Alex Xu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jing Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shen Dong
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alissa Rothchild
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jing Zhou
- Isoplexis Corporation, Branford, CT 06405, USA
| | - Kim Murray
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rick Edmark
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - John Earls
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sarah Li
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Ryan Roper
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Lesley Jones
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yong Zhou
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Lee Rowen
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rachel Liu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sean Mackay
- Isoplexis Corporation, Branford, CT 06405, USA
| | - D Shane O'Mahony
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Christopher R Dale
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Julie A Wallick
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Heather A Algren
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Michael A Zager
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Wei Wei
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Naeha Subramanian
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Global Heath, and Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Alan Aderem
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, and Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Philip D Greenberg
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Departments of Immunology and Medicine, University of Washington, Seattle, WA 98109, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Goldman
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA; Division of Allergy & Infectious Diseases, University of Washington, Seattle, WA 98109, USA.
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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992
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snRNA-seq reveals a subpopulation of adipocytes that regulates thermogenesis. Nature 2020; 587:98-102. [PMID: 33116305 DOI: 10.1038/s41586-020-2856-x] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
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993
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Oba T, Long MD, Keler T, Marsh HC, Minderman H, Abrams SI, Liu S, Ito F. Overcoming primary and acquired resistance to anti-PD-L1 therapy by induction and activation of tumor-residing cDC1s. Nat Commun 2020; 11:5415. [PMID: 33110069 PMCID: PMC7592056 DOI: 10.1038/s41467-020-19192-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/02/2020] [Indexed: 01/01/2023] Open
Abstract
The ability of cancer cells to ensure T-cell exclusion from the tumor microenvironment is a significant mechanism of resistance to anti-PD-1/PD-L1 therapy. Evidence indicates crucial roles of Batf3-dependent conventional type-1 dendritic cells (cDC1s) for inducing antitumor T-cell immunity; however, strategies to maximize cDC1 engagement remain elusive. Here, using multiple orthotopic tumor mouse models resistant to anti-PD-L1-therapy, we are testing the hypothesis that in situ induction and activation of tumor-residing cDC1s overcomes poor T-cell infiltration. In situ immunomodulation with Flt3L, radiotherapy, and TLR3/CD40 stimulation induces an influx of stem-like Tcf1+ Slamf6+ CD8+ T cells, triggers regression not only of primary, but also untreated distant tumors, and renders tumors responsive to anti-PD-L1 therapy. Furthermore, serial in situ immunomodulation (ISIM) reshapes repertoires of intratumoral T cells, overcomes acquired resistance to anti-PD-L1 therapy, and establishes tumor-specific immunological memory. These findings provide new insights into cDC1 biology as a critical determinant to overcome mechanisms of intratumoral T-cell exclusion.
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Affiliation(s)
- Takaaki Oba
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mark D Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tibor Keler
- Celldex Therapeutics, Inc., Hampton, NJ, USA
| | | | - Hans Minderman
- Flow & Image Cytometry Shared Resource, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Fumito Ito
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. .,Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. .,Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA. .,Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA.
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994
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Yamamoto R, Ohnishi H, Omori K, Yamamoto N. In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data. Dev Biol 2020; 469:160-171. [PMID: 33131705 DOI: 10.1016/j.ydbio.2020.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
The inner ear comprises four epithelial domains: the cochlea, vestibule, semicircular canals, and endolymphatic duct/sac. These structures are segregated at embryonic day 13.5 (E13.5). However, these four anatomical structures remain undefined at E10.5. Here, we aimed to identify lineage-specific genes in the early developing inner ear using published data obtained from single-cell RNA-sequencing (scRNA-seq) of embryonic mice. We downloaded 5000 single-cell transcriptome data, named 'auditory epithelial trajectory', from the Mouse Organogenesis Cell Atlas. The dataset was supposed to include otic epithelial cells at E9.5-13.5. We projected the 5000 cells onto a two-dimensional space encoding the transcriptional state and visualised the pattern of otic epithelial cell differentiation. We identified 15 clusters, which were annotated as one of the four components of the inner ear epithelium using known genes that characterise the four different tissues. Additionally, we classified 15 clusters into sub-regions of the four inner ear components. By comparing transcriptomes between these 15 clusters, we identified several candidates of lineage-specific genes. Characterising these new candidate genes will help future studies about inner ear development.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Hiroe Ohnishi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
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995
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Gu S, Olszewski R, Taukulis I, Wei Z, Martin D, Morell RJ, Hoa M. Characterization of rare spindle and root cell transcriptional profiles in the stria vascularis of the adult mouse cochlea. Sci Rep 2020; 10:18100. [PMID: 33093630 PMCID: PMC7581811 DOI: 10.1038/s41598-020-75238-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
The stria vascularis (SV) in the cochlea generates and maintains the endocochlear potential, thereby playing a pivotal role in normal hearing. Knowing transcriptional profiles and gene regulatory networks of SV cell types establishes a basis for studying the mechanism underlying SV-related hearing loss. While we have previously characterized the expression profiles of major SV cell types in the adult mouse, transcriptional profiles of rare SV cell types remained elusive due to the limitation of cell capture in single-cell RNA-Seq. The role of these rare cell types in the homeostatic function of the adult SV remain largely undefined. In this study, we performed single-nucleus RNA-Seq on the adult mouse SV in conjunction with sample preservation treatments during the isolation steps. We distinguish rare SV cell types, including spindle cells and root cells, from other cell types, and characterize their transcriptional profiles. Furthermore, we also identify and validate novel specific markers for these rare SV cell types. Finally, we identify homeostatic gene regulatory networks within spindle and root cells, establishing a basis for understanding the functional roles of these cells in hearing. These novel findings will provide new insights for future work in SV-related hearing loss and hearing fluctuation.
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Affiliation(s)
- Shoujun Gu
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Ian Taukulis
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Zheng Wei
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Daniel Martin
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Robert J Morell
- Computational Biology and Genomics Core, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA.
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996
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Luo G, Gao Q, Zhang S, Yan B. Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives. Comput Struct Biotechnol J 2020; 18:2962-2971. [PMID: 33106757 PMCID: PMC7577221 DOI: 10.1016/j.csbj.2020.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.
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Key Words
- 3C, Chromosome Conformation Capture
- ACE2, Angiotensin-Converting Enzyme 2
- ARDS, acute respiratory distress syndrome
- ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing
- BCR, B cell receptor
- CEL-seq, Cell Expression by Linear amplification and Sequencing
- CLU, clusterin
- COVID-19, corona virus disease 2019
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CytoSeq, gene expression cytometry
- DENV, dengue virus
- FACS, fluorescence-activated cell sorting
- GNLY, granulysin
- GO analysis, Gene Ontology analysis
- HIV, Human Immunodeficiency Virus
- IAV, Influenza A virus
- IGHV/HD/HJ/HC, Immune globulin heavy V/D/J/C/ region
- IGLV/LJ/LC, Immune globulin light V/J/C/ region
- ILC, Innate Lymphoid Cell
- Infectious diseases
- LIGER, Linked Inference of Genomics Experimental Relationships
- MAGIC, Markov Affinity-based Graph Imputation of Cells
- MARS-seq, Massively parallel single-cell RNA sequencing
- MATCHER, Manifold Alignment To CHaracterize Experimental Relationships
- MCMV, mouse cytomegalovirus
- MERFISH, Multiplexed, Error Robust Fluorescent In Situ Hybridization
- MLV, Moloney Murine Leukemia Virus
- MOFA, Multi-Omics Factor Analysis
- MOI, multiplicity of infection
- PBMCs, peripheral blood mononuclear cells
- PLAC8, placenta-associated 8
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SAVER, Single-cell Analysis Via Expression Recovery
- SPLit-seq, split pool ligation-based tranome sequencing
- STARTRAC, Single T-cell Analysis by RNA sequencing and TCR TRACking
- STRT-seq, Single-cell Tagged Reverse Transcription sequencing
- Single-cell RNA sequencing
- TCR, T cell receptor
- TSLP, thymic stromal lymphopoietin
- UMAP, Uniform Manifold Approximation and Projection
- UMI, Unique Molecular Identifier
- mcSCRB-seq, molecular crowding single-cell RNA barcoding and sequencing
- pDCs, plasmacytoid dendritic cells
- scRNA-seq, single cell RNA sequencing technology
- sci-RNA-seq, single-cell combinatorial indexing RNA sequencing
- seqFISH, sequential Fluorescent In Situ Hybridization
- smart-seq, switching mechanism at 5′ end of the RNA transcript sequencing
- t-SNE, t-Distributed stochastic neighbor embedding
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Affiliation(s)
- Geyang Luo
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Gao
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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997
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Pfisterer U, Petukhov V, Demharter S, Meichsner J, Thompson JJ, Batiuk MY, Asenjo-Martinez A, Vasistha NA, Thakur A, Mikkelsen J, Adorjan I, Pinborg LH, Pers TH, von Engelhardt J, Kharchenko PV, Khodosevich K. Identification of epilepsy-associated neuronal subtypes and gene expression underlying epileptogenesis. Nat Commun 2020; 11:5038. [PMID: 33028830 PMCID: PMC7541486 DOI: 10.1038/s41467-020-18752-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/08/2020] [Indexed: 11/20/2022] Open
Abstract
Epilepsy is one of the most common neurological disorders, yet its pathophysiology is poorly understood due to the high complexity of affected neuronal circuits. To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects. We found that the largest transcriptomic changes occur in distinct neuronal subtypes from several families of principal neurons (L5-6_Fezf2 and L2-3_Cux2) and GABAergic interneurons (Sst and Pvalb), whereas other subtypes in the same families were less affected. Furthermore, the subtypes with the largest epilepsy-related transcriptomic changes may belong to the same circuit, since we observed coordinated transcriptomic shifts across these subtypes. Glutamate signaling exhibited one of the strongest dysregulations in epilepsy, highlighted by layer-wise transcriptional changes in multiple glutamate receptor genes and strong upregulation of genes coding for AMPA receptor auxiliary subunits. Overall, our data reveal a neuronal subtype-specific molecular phenotype of epilepsy. The pathophysiology of epilepsy is unclear. Here, the authors present single-nuclei transcriptomic profiling of human temporal lobe epilepsy from patients. They identified epilepsy-associated neuronal subtypes, and a panel of dysregulated genes, predicting neuronal circuits contributing to epilepsy.
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Affiliation(s)
- Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Viktor Petukhov
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Samuel Demharter
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Johanna Meichsner
- Institute of Pathophysiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jonatan J Thompson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Mykhailo Y Batiuk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Andrea Asenjo-Martinez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Navneet A Vasistha
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ashish Thakur
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jens Mikkelsen
- Department of Neurology and Neurobiology Research Unit, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Istvan Adorjan
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Lars H Pinborg
- Neurobiology Research Unit, Copenhagen University Hospital, Rigshospitalet, 2200, Copenhagen, Denmark.,Epilepsy Clinic, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2200, Copenhagen, Denmark
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jakob von Engelhardt
- Institute of Pathophysiology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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998
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Wong R, Belk JA, Govero J, Uhrlaub JL, Reinartz D, Zhao H, Errico JM, D'Souza L, Ripperger TJ, Nikolich-Zugich J, Shlomchik MJ, Satpathy AT, Fremont DH, Diamond MS, Bhattacharya D. Affinity-Restricted Memory B Cells Dominate Recall Responses to Heterologous Flaviviruses. Immunity 2020; 53:1078-1094.e7. [PMID: 33010224 DOI: 10.1016/j.immuni.2020.09.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
Memory B cells (MBCs) can respond to heterologous antigens either by molding new specificities through secondary germinal centers (GCs) or by selecting preexisting clones without further affinity maturation. To distinguish these mechanisms in flavivirus infections and immunizations, we studied recall responses to envelope protein domain III (DIII). Conditional deletion of activation-induced cytidine deaminase (AID) between heterologous challenges of West Nile, Japanese encephalitis, Zika, and dengue viruses did not affect recall responses. DIII-specific MBCs were contained mostly within the plasma-cell-biased CD80+ subset, and few GCs arose following heterologous boosters, demonstrating that recall responses are confined by preexisting clonal diversity. Measurement of monoclonal antibody (mAb) binding affinity to DIII proteins, timed AID deletion, single-cell RNA sequencing, and lineage tracing experiments point to selection of relatively low-affinity MBCs as a mechanism to promote diversity. Engineering immunogens to avoid this MBC diversity may facilitate flavivirus-type-specific vaccines with minimized potential for infection enhancement.
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Affiliation(s)
- Rachel Wong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer Govero
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Dakota Reinartz
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - John M Errico
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Lucas D'Souza
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Tyler J Ripperger
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | | | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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999
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Parker KR, Migliorini D, Perkey E, Yost KE, Bhaduri A, Bagga P, Haris M, Wilson NE, Liu F, Gabunia K, Scholler J, Montine TJ, Bhoj VG, Reddy R, Mohan S, Maillard I, Kriegstein AR, June CH, Chang HY, Posey AD, Satpathy AT. Single-Cell Analyses Identify Brain Mural Cells Expressing CD19 as Potential Off-Tumor Targets for CAR-T Immunotherapies. Cell 2020; 183:126-142.e17. [PMID: 32961131 PMCID: PMC7640763 DOI: 10.1016/j.cell.2020.08.022] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/26/2020] [Accepted: 08/12/2020] [Indexed: 12/18/2022]
Abstract
CD19-directed immunotherapies are clinically effective for treating B cell malignancies but also cause a high incidence of neurotoxicity. A subset of patients treated with chimeric antigen receptor (CAR) T cells or bispecific T cell engager (BiTE) antibodies display severe neurotoxicity, including fatal cerebral edema associated with T cell infiltration into the brain. Here, we report that mural cells, which surround the endothelium and are critical for blood-brain-barrier integrity, express CD19. We identify CD19 expression in brain mural cells using single-cell RNA sequencing data and confirm perivascular staining at the protein level. CD19 expression in the brain begins early in development alongside the emergence of mural cell lineages and persists throughout adulthood across brain regions. Mouse mural cells demonstrate lower levels of Cd19 expression, suggesting limitations in preclinical animal models of neurotoxicity. These data suggest an on-target mechanism for neurotoxicity in CD19-directed therapies and highlight the utility of human single-cell atlases for designing immunotherapies.
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MESH Headings
- Animals
- Antibodies, Bispecific/immunology
- Antigens, CD19/immunology
- B-Lymphocytes/immunology
- Blood-Brain Barrier/immunology
- Blood-Brain Barrier/metabolism
- Brain/immunology
- Brain/metabolism
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Epithelial Cells/metabolism
- Humans
- Immunotherapy/adverse effects
- Immunotherapy/methods
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Muscle, Smooth, Vascular/metabolism
- Neoplasms
- Receptors, Antigen, T-Cell/immunology
- Receptors, Chimeric Antigen/immunology
- Single-Cell Analysis/methods
- T-Lymphocytes/immunology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Kevin R Parker
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Denis Migliorini
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Translational Research in Onco-Hematology and Department of Oncology, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.
| | - Eric Perkey
- Graduate Program in Cellular and Molecular Biology and Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA; Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Puneet Bagga
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohammad Haris
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Functional and Molecular Imaging Laboratory, Research Branch, Sidra Medicine, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Neil E Wilson
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Fang Liu
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Khatuna Gabunia
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John Scholler
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijay G Bhoj
- Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ravinder Reddy
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Suyash Mohan
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Carl H June
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Avery D Posey
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Ansuman T Satpathy
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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1000
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Wolock SL, Krishnan I, Tenen DE, Matkins V, Camacho V, Patel S, Agarwal P, Bhatia R, Tenen DG, Klein AM, Welner RS. Mapping Distinct Bone Marrow Niche Populations and Their Differentiation Paths. Cell Rep 2020; 28:302-311.e5. [PMID: 31291568 DOI: 10.1016/j.celrep.2019.06.031] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/05/2019] [Accepted: 06/07/2019] [Indexed: 12/21/2022] Open
Abstract
The bone marrow microenvironment is composed of heterogeneous cell populations of non-hematopoietic cells with complex phenotypes and undefined trajectories of maturation. Among them, mesenchymal cells maintain the production of stromal, bone, fat, and cartilage cells. Resolving these unique cellular subsets within the bone marrow remains challenging. Here, we used single-cell RNA sequencing of non-hematopoietic bone marrow cells to define specific subpopulations. Furthermore, by combining computational prediction of the cell state hierarchy with the known expression of key transcription factors, we mapped differentiation paths to the osteocyte, chondrocyte, and adipocyte lineages. Finally, we validated our findings using lineage-specific reporter strains and targeted knockdowns. Our analysis reveals differentiation hierarchies for maturing stromal cells, determines key transcription factors along these trajectories, and provides an understanding of the complexity of the bone marrow microenvironment.
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Affiliation(s)
- Samuel L Wolock
- Department of System Biology, Harvard Medical School, Boston, MA, USA
| | - Indira Krishnan
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Danielle E Tenen
- Division of Endocrinology, Diabetes, and Metabolism, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Victoria Matkins
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Virginia Camacho
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sweta Patel
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Puneet Agarwal
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ravi Bhatia
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA; Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Allon M Klein
- Department of System Biology, Harvard Medical School, Boston, MA, USA
| | - Robert S Welner
- Division of Hematology/Oncology, University of Alabama at Birmingham, Birmingham, AL, USA.
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