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Cossarini F, Shang J, Krek A, Al-Taie Z, Hou R, Canales-Herrerias P, Tokuyama M, Tankelevich M, Tillowiz A, Jha D, Livanos AE, Leyre L, Uzzan M, Martinez-Delgado G, Tylor M, Sharma K, Bourgonje AR, Cruz M, Ioannou G, Dawson T, D'Souza D, Kim-Schulze S, Akm A, Aberg JA, Chen BK, Gnjatic S, Polydorides AD, Cerutti A, Argmann C, Vujkovic-Cvijin I, Suarez-Farinas M, Petralia F, Faith JJ, Mehandru S. HIV-1 infection is associated with depletion of germinal center B cells and a decrease in IgA + plasma cells in the GI tract. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.590425. [PMID: 38826293 PMCID: PMC11142040 DOI: 10.1101/2024.05.17.590425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Gastrointestinal (GI) B cells and plasma cells (PCs), critical to mucosal homeostasis, play an important role in the host response to HIV-1 infection. Here, high resolution mapping of human B cells and PCs from colon and ileum during both viremic and suppressed HIV-1 infection identified a significant reduction in germinal center (GC) B cells and Follicular Dendritic Cells (FDCs) during HIV-1 viremia. Further, IgA + PCs, the major cellular output of intestinal GCs were significantly reduced during viremic HIV-1 infection. PC-associated transcriptional perturbations, including type I interferon signaling persisted in antiretroviral therapy (ART) treated individuals, suggesting ongoing disruption of the intestinal immune milieu during ART. GI humoral immune perturbations associated with changes in intestinal microbiome composition and systemic inflammation. Herein, we highlight a key immune defect in the GI mucosa due to HIV-1 viremia, with major implications. One Sentence Summary Major perturbations in intestinal GC dynamics in viremic HIV-1 infection relate to reduced IgA + plasma cells, systemic inflammation and microbiota changes.
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2
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Massoni-Badosa R, Aguilar-Fernández S, Nieto JC, Soler-Vila P, Elosua-Bayes M, Marchese D, Kulis M, Vilas-Zornoza A, Bühler MM, Rashmi S, Alsinet C, Caratù G, Moutinho C, Ruiz S, Lorden P, Lunazzi G, Colomer D, Frigola G, Blevins W, Romero-Rivero L, Jiménez-Martínez V, Vidal A, Mateos-Jaimez J, Maiques-Diaz A, Ovejero S, Moreaux J, Palomino S, Gomez-Cabrero D, Agirre X, Weniger MA, King HW, Garner LC, Marini F, Cervera-Paz FJ, Baptista PM, Vilaseca I, Rosales C, Ruiz-Gaspà S, Talks B, Sidhpura K, Pascual-Reguant A, Hauser AE, Haniffa M, Prosper F, Küppers R, Gut IG, Campo E, Martin-Subero JI, Heyn H. An atlas of cells in the human tonsil. Immunity 2024; 57:379-399.e18. [PMID: 38301653 PMCID: PMC10869140 DOI: 10.1016/j.immuni.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/07/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas of the human tonsil composed of >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well as spatial transcriptomics. This census identified 121 cell types and states, defined developmental trajectories, and enabled an understanding of the functional units of the tonsil. Exemplarily, we stratified myeloid slan-like subtypes, established a BCL6 enhancer as locally active in follicle-associated T and B cells, and identified SIX5 as putative transcriptional regulator of plasma cell maturation. Analyses of a validation cohort confirmed the presence, annotation, and markers of tonsillar cell types and provided evidence of age-related compositional shifts. We demonstrate the value of this resource by annotating cells from B cell-derived mantle cell lymphomas, linking transcriptional heterogeneity to normal B cell differentiation states of the human tonsil.
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Affiliation(s)
| | | | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Amaia Vilas-Zornoza
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marco Matteo Bühler
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Sonal Rashmi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Clara Alsinet
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Catia Moutinho
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Sara Ruiz
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Patricia Lorden
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Giulia Lunazzi
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Gerard Frigola
- Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain
| | - Will Blevins
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Lucia Romero-Rivero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Anna Vidal
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Judith Mateos-Jaimez
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alba Maiques-Diaz
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sara Ovejero
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France
| | - Jérôme Moreaux
- Department of Biological Hematology, CHU Montpellier, Montpellier, France; Institute of Human Genetics, UMR 9002 CNRS-UM, Montpellier, France; Department of Clinical Hematology, CHU Montpellier, Montpellier, France
| | - Sara Palomino
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - David Gomez-Cabrero
- Translational Bioinformatics Unit (TransBio), Navarrabiomed, Navarra Health Department (CHN), Public University of Navarra (UPNA), Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Bioscience Program, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Xabier Agirre
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Marc A Weniger
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Hamish W King
- Epigenetics and Development Division, Walter and Eliza Hall Institute, Parkville, Australia
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Peter M Baptista
- Department of Otorhinolaryngology, University of Navarra, Pamplona, Spain
| | - Isabel Vilaseca
- Otorhinolaryngology Head-Neck Surgery Department, Hospital Clínic, IDIBAPS Universitat de Barcelona, Barcelona, Spain
| | - Cecilia Rosales
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Benjamin Talks
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Otolaryngology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Keval Sidhpura
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna Pascual-Reguant
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), Berlin, Germany
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Felipe Prosper
- Hemato-Oncology Program, Center for Applied Medical Research (CIMA), University of Navarra, IDISNA, Universidad de Navarra, Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Departamento de Hematología, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Hematopathology Section, Pathology Department, Hospital Clinic, Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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3
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Suma S, Suehara Y, Fujisawa M, Abe Y, Hattori K, Makishima K, Sakamoto T, Sawa A, Bando H, Kaji D, Sugio T, Kato K, Akashi K, Matsue K, Carreras J, Nakamura N, Suzuki A, Suzuki Y, Ito K, Shiiba H, Chiba S, Sakata-Yanagimoto M. Tumor heterogeneity and immune-evasive T follicular cell lymphoma phenotypes at single-cell resolution. Leukemia 2024; 38:340-350. [PMID: 38012392 PMCID: PMC10844096 DOI: 10.1038/s41375-023-02093-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
T follicular helper (TFH) cell lymphomas (TFHLs) are characterized by TFH-like properties and accompanied by substantial immune-cell infiltration into tumor tissues. Nevertheless, the comprehensive understanding of tumor-cell heterogeneity and immune profiles of TFHL remains elusive. To address this, we conducted single-cell transcriptomic analysis on 9 lymph node (LN) and 16 peripheral blood (PB) samples from TFHL patients. Tumor cells were divided into 5 distinct subclusters, with significant heterogeneity observed in the expression levels of TFH markers. Copy number variation (CNV) and trajectory analyses indicated that the accumulation of CNVs, together with gene mutations, may drive the clonal evolution of tumor cells towards TFH-like and cell proliferation phenotypes. Additionally, we identified a novel tumor-cell-specific marker, PLS3. Notably, we found a significant increase in exhausted CD8+ T cells with oligoclonal expansion in TFHL LNs and PB, along with distinctive immune evasion characteristics exhibited by infiltrating regulatory T, myeloid, B, and natural killer cells. Finally, in-silico and spatial cell-cell interaction analyses revealed complex networking between tumor and immune cells, driving the formation of an immunosuppressive microenvironment. These findings highlight the remarkable tumor-cell heterogeneity and immunoevasion in TFHL beyond previous expectations, suggesting potential roles in treatment resistance.
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Affiliation(s)
- Sakurako Suma
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Yasuhito Suehara
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Manabu Fujisawa
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Yoshiaki Abe
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Keiichiro Hattori
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kenichi Makishima
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
| | - Tatsuhiro Sakamoto
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Aya Sawa
- Department of Breast-Thyroid-Endocrine Surgery, University of Tsukuba Hospital, Tsukuba, Japan
| | - Hiroko Bando
- Department of Breast-Thyroid-Endocrine Surgery, University of Tsukuba Hospital, Tsukuba, Japan
| | - Daisuke Kaji
- Department of Hematology, Toranomon Hospital, Tokyo, Japan
| | - Takeshi Sugio
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA, USA
| | - Koji Kato
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Kosei Matsue
- Division of Hematology/Oncology, Department of Internal Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Joaquim Carreras
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Naoya Nakamura
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, Kashiwa, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, the University of Tokyo, Kashiwa, Japan
| | - Ken Ito
- Oncology Business Unit, Eisai Co., Ltd., Tsukuba, Japan
| | - Hiroyuki Shiiba
- Oncology Department, Medical Head Quarters, Eisai Co., Ltd., Tokyo, Japan
| | - Shigeru Chiba
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mamiko Sakata-Yanagimoto
- Department of Hematology, University of Tsukuba Hospital, Tsukuba, Japan.
- Department of Hematology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan.
- Division of Advanced Hemato-Oncology, Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.
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4
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Carty SA, Murga-Zamalloa CA, Wilcox RA. SOHO State of the Art Updates and Next Questions | New Pathways and New Targets in PTCL: Staying on Target. CLINICAL LYMPHOMA, MYELOMA & LEUKEMIA 2023; 23:561-574. [PMID: 37142534 PMCID: PMC10565700 DOI: 10.1016/j.clml.2023.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/05/2023] [Accepted: 04/16/2023] [Indexed: 05/06/2023]
Abstract
While the peripheral T-cell lymphomas (PTCL) remain a therapeutic challenge, and increasingly account for a disproportionate number of lymphoma-related deaths, improved understanding of disease pathogenesis and classification, and the development of novel therapeutic agents over the past decade, all provide reasons for a more optimistic outlook in the next. Despite their genetic and molecular heterogeneity, many PTCL are dependent upon signaling input provided by antigen, costimulatory, and cytokine receptors. While gain-of-function alterations effecting these pathways are recurrently observed in many PTCL, more often than not, signaling remains ligand-and tumor microenvironment (TME)-dependent. Consequently, the TME and its constituents are increasingly recognized as "on target". Utilizing a "3 signal" model, we will review new-and old-therapeutic targets that are relevant for the more common nodal PTCL subtypes.
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Affiliation(s)
- Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI
| | | | - Ryan A Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan, Ann Arbor, MI.
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5
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Bélanger S, Haupt S, Faliti CE, Getzler A, Choi J, Diao H, Karunadharma PP, Bild NA, Pipkin ME, Crotty S. The Chromatin Regulator Mll1 Supports T Follicular Helper Cell Differentiation by Controlling Expression of Bcl6, LEF-1, and TCF-1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1752-1760. [PMID: 37074193 PMCID: PMC10334568 DOI: 10.4049/jimmunol.2200927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/17/2023] [Indexed: 04/20/2023]
Abstract
T follicular helper (TFH) cells are essential for developing protective Ab responses following vaccination. Greater understanding of the genetic program leading to TFH differentiation is needed. Chromatin modifications are central in the control of gene expression. However, detailed knowledge of how chromatin regulators (CRs) regulate differentiation of TFH cells is limited. We screened a large short hairpin RNA library targeting all known CRs in mice and identified the histone methyltransferase mixed lineage leukemia 1 (Mll1) as a positive regulator of TFH differentiation. Loss of Mll1 expression reduced formation of TFH cells following acute viral infection or protein immunization. In addition, expression of the TFH lineage-defining transcription factor Bcl6 was reduced in the absence of Mll1. Transcriptomics analysis identified Lef1 and Tcf7 as genes dependent on Mll1 for their expression, which provides one mechanism for the regulation of TFH differentiation by Mll1. Taken together, CRs such as Mll1 substantially influence TFH differentiation.
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Affiliation(s)
- Simon Bélanger
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Sonya Haupt
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Biomedical Sciences (BMS) Graduate Program. School of Medicine, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Caterina E. Faliti
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
| | - Adam Getzler
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Jinyong Choi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 03083, Republic of Korea
| | - Huitian Diao
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | | | - Nicholas A. Bild
- Genomics Core, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Matthew E. Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 9203,7USA
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6
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Kim YJ, Oh J, Jung S, Kim CJ, Choi J, Jeon YK, Kim HJ, Kim JW, Suh CH, Lee Y, Im SH, Crotty S, Choi YS. The transcription factor Mef2d regulates B:T synapse-dependent GC-T FH differentiation and IL-21-mediated humoral immunity. Sci Immunol 2023; 8:eadf2248. [PMID: 36961907 PMCID: PMC10311795 DOI: 10.1126/sciimmunol.adf2248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Communication between CD4 T cells and cognate B cells is key for the former to fully mature into germinal center-T follicular helper (GC-TFH) cells and for the latter to mount a CD4 T cell-dependent humoral immune response. Although this interaction occurs in a B:T synapse-dependent manner, how CD4 T cells transcriptionally regulate B:T synapse formation remains largely unknown. Here, we report that Mef2d, an isoform of the myocyte enhancer factor 2 (Mef2) transcription factor family, is a critical regulator of this process. In CD4 T cells, Mef2d negatively regulates expression of Sh2d1a, which encodes SLAM-associated protein (SAP), a critical regulator of B:T synapses. We found that Mef2d regulates Sh2d1a expression via DNA binding-dependent transcriptional repression, inhibiting SAP-dependent B:T synapse formation and preventing antigen-specific CD4 T cells from differentiating into GC-TFH cells. Mef2d also impeded IL-21 production by CD4 T cells, an important B cell help signaling molecule, via direct repression of the Il21 gene. In contrast, CD4 T cell-specific disruption of Mef2d led to a substantial increase in GC-TFH differentiation in response to protein immunization, concurrent with enhanced SAP expression. MEF2D mRNA expression inversely correlates with human systemic lupus erythematosus (SLE) patient autoimmune parameters, including circulating TFH-like cell frequencies, autoantibodies, and SLEDAI scores. These findings highlight Mef2d as a pivotal rheostat in CD4 T cells for controlling GC formation and antibody production by B cells.
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Affiliation(s)
- Ye-Ji Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jeein Oh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Soohan Jung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Jinyong Choi
- Department of Microbiology, Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Jik Kim
- Department of Otorhinolaryngology, Seoul National University Hospital, Seoul, Korea
| | - Ji-Won Kim
- Department of Rheumatology, Ajou University School of Medicine, Gyeonggi-do, Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University School of Medicine, Gyeonggi-do, Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
- ImmunoBiome Inc., Pohang, Korea
- Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Seoul, Korea
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- University of California San Diego, Department of Medicine, Division of Infectious Diseases and Global Public Health, La Jolla, CA, USA
| | - Youn Soo Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea
- Transplantation Research Institute, Seoul National University Hospital, Seoul, Korea
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7
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Read KA, Jones DM, Pokhrel S, Hales EDS, Varkey A, Tuazon JA, Eisele CD, Abdouni O, Saadey A, Leonard MR, Warren RT, Powell MD, Boss JM, Hemann EA, Yount JS, Xin G, Ghoneim HE, Lio CWJ, Freud AG, Collins PL, Oestreich KJ. Aiolos represses CD4 + T cell cytotoxic programming via reciprocal regulation of T FH transcription factors and IL-2 sensitivity. Nat Commun 2023; 14:1652. [PMID: 36964178 PMCID: PMC10039023 DOI: 10.1038/s41467-023-37420-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 03/16/2023] [Indexed: 03/26/2023] Open
Abstract
During intracellular infection, T follicular helper (TFH) and T helper 1 (TH1) cells promote humoral and cell-mediated responses, respectively. Another subset, CD4-cytotoxic T lymphocytes (CD4-CTLs), eliminate infected cells via functions typically associated with CD8+ T cells. The mechanisms underlying differentiation of these populations are incompletely understood. Here, we identify the transcription factor Aiolos as a reciprocal regulator of TFH and CD4-CTL programming. We find that Aiolos deficiency results in downregulation of key TFH transcription factors, and consequently reduced TFH differentiation and antibody production, during influenza virus infection. Conversely, CD4-CTL programming is elevated, including enhanced Eomes and cytolytic molecule expression. We further demonstrate that Aiolos deficiency allows for enhanced IL-2 sensitivity and increased STAT5 association with CD4-CTL gene targets, including Eomes, effector molecules, and IL2Ra. Thus, our collective findings identify Aiolos as a pivotal regulator of CD4-CTL and TFH programming and highlight its potential as a target for manipulating CD4+ T cell responses.
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Affiliation(s)
- Kaitlin A Read
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Devin M Jones
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Srijana Pokhrel
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Emily D S Hales
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Aditi Varkey
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Jasmine A Tuazon
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
- Medical Scientist Training Program, Columbus, OH, 43210, USA
| | - Caprice D Eisele
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
- Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Omar Abdouni
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Abbey Saadey
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Biomedical Sciences Graduate Program, Columbus, OH, 43210, USA
| | - Melissa R Leonard
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Combined Anatomic Pathology Residency/PhD Program, The Ohio State University College of Veterinary Medicine, Columbus, USA
| | - Robert T Warren
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
| | - Gang Xin
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Chan-Wang J Lio
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Aharon G Freud
- Department of Pathology, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Patrick L Collins
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Kenneth J Oestreich
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA.
- Infectious Diseases Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, The Ohio State Comprehensive Cancer Center, Columbus, OH, 43210, USA.
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8
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Jung SM, Baek IW, Park KS, Kim KJ. De novo molecular subtyping of salivary gland tissue in the context of Sjögren's syndrome heterogeneity. Clin Immunol 2022; 245:109171. [DOI: 10.1016/j.clim.2022.109171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 11/08/2022]
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9
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Lai CY, Marcel N, Yaldiko AW, Delpoux A, Hedrick SM. A Bcl6 Intronic Element Regulates T Follicular Helper Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2022; 209:1118-1127. [DOI: 10.4049/jimmunol.2100777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 07/07/2022] [Indexed: 01/04/2023]
Abstract
Abstract
In response to an intracellular infectious agent, the immune system produces a specific cellular response as well as a T cell–dependent Ab response. Precursor T cells differentiate into effector T cells, including Th1 cells, and T follicular helper (TFH) cells. The latter cooperate with B cells to form germinal centers and induce the formation of Ab-forming plasmacytes. One major focal point for control of T cell differentiation is the transcription factor BCL6. In this study, we demonstrated that the Bcl6 gene is regulated by FOXO1-binding, cis-acting sequences located in a highly conserved region of the first Bcl6 intron. In both mouse and human T cells, deletion of the tandem FOXO1 binding sites increased the expression of BCL6 and enhanced the proportion of TFH cells. These results reveal a fundamental control point for cellular versus humoral immunity.
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Affiliation(s)
- Chen-Yen Lai
- Molecular Biology Section, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Nimi Marcel
- Molecular Biology Section, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Allen W. Yaldiko
- Molecular Biology Section, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Arnaud Delpoux
- Molecular Biology Section, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
| | - Stephen M. Hedrick
- Molecular Biology Section, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA
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10
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Ribeiro F, Perucha E, Graca L. T follicular cells: the regulators of germinal centre homeostasis. Immunol Lett 2022; 244:1-11. [DOI: 10.1016/j.imlet.2022.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 01/05/2023]
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11
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Robles-Valero J, Fernández-Nevado L, Lorenzo-Martín LF, Cuadrado M, Fernández-Pisonero I, Rodríguez-Fdez S, Astorga-Simón EN, Abad A, Caloto R, Bustelo XR. Cancer-associated mutations in VAV1 trigger variegated signaling outputs and T-cell lymphomagenesis. EMBO J 2021; 40:e108125. [PMID: 34617326 PMCID: PMC8591544 DOI: 10.15252/embj.2021108125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Mutations in VAV1, a gene that encodes a multifunctional protein important for lymphocytes, are found at different frequencies in peripheral T‐cell lymphoma (PTCL), non‐small cell lung cancer, and other tumors. However, their pathobiological significance remains unsettled. After cataloguing 51 cancer‐associated VAV1 mutations, we show here that they can be classified in five subtypes according to functional impact on the three main VAV1 signaling branches, GEF‐dependent activation of RAC1, GEF‐independent adaptor‐like, and tumor suppressor functions. These mutations target new and previously established regulatory layers of the protein, leading to quantitative and qualitative changes in VAV1 signaling output. We also demonstrate that the most frequent VAV1 mutant subtype drives PTCL formation in mice. This process requires the concurrent engagement of two downstream signaling branches that promote the chronic activation and transformation of follicular helper T cells. Collectively, these data reveal the genetic constraints associated with the lymphomagenic potential of VAV1 mutant subsets, similarities with other PTCL driver genes, and potential therapeutic vulnerabilities.
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Affiliation(s)
- Javier Robles-Valero
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Lucía Fernández-Nevado
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - L Francisco Lorenzo-Martín
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Myriam Cuadrado
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Isabel Fernández-Pisonero
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Sonia Rodríguez-Fdez
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Elsa N Astorga-Simón
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Antonio Abad
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Rubén Caloto
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
| | - Xosé R Bustelo
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Salamanca, Spain
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12
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Strazza M, Bukhari S, Tocheva AS, Mor A. PD-1-induced proliferating T cells exhibit a distinct transcriptional signature. Immunology 2021; 164:555-568. [PMID: 34164813 PMCID: PMC8517598 DOI: 10.1111/imm.13388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/24/2021] [Accepted: 06/19/2021] [Indexed: 12/12/2022] Open
Abstract
Ligation of the inhibitory receptor PD-1 on T cells results in the inhibition of numerous cellular functions. Despite the overtly inhibitory outcome of PD-1 signalling, there are additionally a collection of functions that are activated. We have observed that CD4+ T cells stimulated through the T-cell receptor and PD-1 primarily do not proliferate; however, there is a population of cells that proliferates more than T-cell receptor stimulation alone. These highly proliferating cells could potentially be associated with PD-1-blockade unresponsiveness in patients. In this study, we have performed RNA sequencing and found that following PD-1 ligation proliferating and non-proliferating T cells have distinct transcriptional signatures. Remarkably, the proliferating cells showed an enrichment of genes associated with an activated state despite PD-1 signalling. Additionally, circulating follicular helper T cells were significantly more prevalent in the non-proliferating population, demonstrated by enrichment of the associated genes CXCR5, CCR7, TCF7, BCL6 and PRDM1 and validated at the protein level. Translationally, we also show that there are more follicular helper T cells in patients that respond favourably to PD-1 blockade. Overall, the presence of transcriptionally and functionally distinct T cell populations responsive to PD-1 ligation may provide insights into the clinical differences observed following therapeutic PD-1 blockade.
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Affiliation(s)
- Marianne Strazza
- Columbia Center for Translational ImmunologyColumbia University Medical CenterNew YorkNYUSA
| | - Shoiab Bukhari
- Columbia Center for Translational ImmunologyColumbia University Medical CenterNew YorkNYUSA
| | - Anna S. Tocheva
- Columbia Center for Translational ImmunologyColumbia University Medical CenterNew YorkNYUSA
| | - Adam Mor
- Columbia Center for Translational ImmunologyColumbia University Medical CenterNew YorkNYUSA
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13
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Chromatin Modifications in 22q11.2 Deletion Syndrome. J Clin Immunol 2021; 41:1853-1864. [PMID: 34435264 DOI: 10.1007/s10875-021-01123-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 08/11/2021] [Indexed: 12/31/2022]
Abstract
PURPOSE Chromosome 22q11.2 deletion syndrome is a common inborn error of immunity. The early consequences of thymic hypoplasia are low T cell numbers. Later in life, atopy, autoimmunity, inflammation, and evolving hypogammaglobulinemia can occur and the causes of these features are not understood. This study utilized an unbiased discovery approach to define alterations in histone modifications. Our goal was to identify durable chromatin changes that could influence cell behavior. METHODS CD4 T cells and CD19 B cells underwent ChIP-seq analysis using antibodies to H3K4me3, H3K27ac, and H4ac. RNA effects were defined in CD4 T cells by RNA-seq. Serum cytokines were examined by Luminex. RESULTS Histone marks of transcriptional activation at CD4 T cell promoters and enhancers were globally increased. The promoter activation signature had elements related to T cell activation and inflammation, concordant with effects seen in the transcriptome. B cells, in contrast, had a minimally altered epigenetic landscape in 22q11.2. Both cell types had an "edge" effect with markedly altered chromatin adjacent to the deletion. CONCLUSIONS People with 22q11.2 deletion have altered CD4 T cell chromatin and a transcriptome concordant with the changes in the epigenome. These effects support a disease model where qualitative changes to T cells occur in addition to quantitative defects that have been well characterized. This study offers unique insight into qualitative differences in the T cells in 22q11.2 deletion, an aspect that has received limited attention.
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14
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Hart AP, Laufer TM. A review of signaling and transcriptional control in T follicular helper cell differentiation. J Leukoc Biol 2021; 111:173-195. [PMID: 33866600 DOI: 10.1002/jlb.1ri0121-066r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
T follicular helper (Tfh) cells are a critical component of adaptive immunity and assist in optimal Ab-mediated defense. Multiple effector functions of Tfh support germinal center B cell survival, Ab class switching, and plasma cell maturation. In the past 2 decades, the phenotype and functional characteristics of GC Tfh have been clarified allowing for robust studies of the Th subset including activation signals and environmental cues controlling Tfh differentiation and migration during an immune response. A unique, 2-step differentiation process of Tfh has been proposed but the mechanisms underlying transition between unstable Tfh precursors and functional mature Tfh remain elusive. Likewise, newly identified transcriptional regulators of Tfh development have not yet been incorporated into our understanding of how these cells might function in disease. Here, we review the signals and downstream transcription factors that shape Tfh differentiation including what is known about the epigenetic processes that maintain Tfh identity. It is proposed that further evaluation of the stepwise differentiation pattern of Tfh will yield greater insights into how these cells become dysregulated in autoimmunity.
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Affiliation(s)
- Andrew P Hart
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Terri M Laufer
- Division of Rheumatology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Rheumatology, Department of Medicine, Corporal Michael C. Crescenz VA Medical Center, Philadelphia, PA, 19104, USA
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15
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Liu C, Martins AJ, Lau WW, Rachmaninoff N, Chen J, Imberti L, Mostaghimi D, Fink DL, Burbelo PD, Dobbs K, Delmonte OM, Bansal N, Failla L, Sottini A, Quiros-Roldan E, Han KL, Sellers BA, Cheung F, Sparks R, Chun TW, Moir S, Lionakis MS, Rossi C, Su HC, Kuhns DB, Cohen JI, Notarangelo LD, Tsang JS. Time-resolved systems immunology reveals a late juncture linked to fatal COVID-19. Cell 2021; 184:1836-1857.e22. [PMID: 33713619 PMCID: PMC7874909 DOI: 10.1016/j.cell.2021.02.018] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/16/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023]
Abstract
COVID-19 exhibits extensive patient-to-patient heterogeneity. To link immune response variation to disease severity and outcome over time, we longitudinally assessed circulating proteins as well as 188 surface protein markers, transcriptome, and T cell receptor sequence simultaneously in single peripheral immune cells from COVID-19 patients. Conditional-independence network analysis revealed primary correlates of disease severity, including gene expression signatures of apoptosis in plasmacytoid dendritic cells and attenuated inflammation but increased fatty acid metabolism in CD56dimCD16hi NK cells linked positively to circulating interleukin (IL)-15. CD8+ T cell activation was apparent without signs of exhaustion. Although cellular inflammation was depressed in severe patients early after hospitalization, it became elevated by days 17-23 post symptom onset, suggestive of a late wave of inflammatory responses. Furthermore, circulating protein trajectories at this time were divergent between and predictive of recovery versus fatal outcomes. Our findings stress the importance of timing in the analysis, clinical monitoring, and therapeutic intervention of COVID-19.
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Affiliation(s)
- Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Graduate Program in Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - William W Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Office of Intramural Research, CIT, NIH, Bethesda, MD 20892, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; Graduate Program in Biological Sciences, University of Maryland, College Park, MD 20742, USA
| | - Jinguo Chen
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luisa Imberti
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Darius Mostaghimi
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Danielle L Fink
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD 20892, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Laura Failla
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alessandra Sottini
- CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Kyu Lee Han
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rachel Sparks
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Camillo Rossi
- ASST Spedali Civili di Brescia, Brescia 25123, Italy
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 20701, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA; NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA.
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16
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Zhao M, Jia S, Gao X, Qiu H, Wu R, Wu H, Lu Q. Comparative Analysis of Global Proteome and Lysine Acetylome Between Naive CD4 + T Cells and CD4 + T Follicular Helper Cells. Front Immunol 2021; 12:643441. [PMID: 33841426 PMCID: PMC8027069 DOI: 10.3389/fimmu.2021.643441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/19/2021] [Indexed: 12/05/2022] Open
Abstract
As a subgroup of CD4+ T helper cells, follicular helper T (Tfh) cells provide help to germinal center B cells and mediate the development of long-lived humoral immunity. Dysregulation of Tfh cells is associated with several major autoimmune diseases. Although recent studies showed that Tfh cell differentiation is controlled by the transcription factor Bcl6, cytokines, and cell-cell signals, limited information is available on the proteome and post-translational modifications (PTMs) of proteins in human Tfh cells. In the present study, we investigated quantitative proteome and acetylome in human naive CD4+ T cells and in vitro induced Tfh (iTfh) cells using the tandem mass tag (TMT) labeling technique, antibody-based affinity enrichment, and high-resolution liquid chromatography-mass spectrometry (LC-MS)/mass spectrometry (MS) analysis. In total, we identified 802 upregulated proteins and 598 downregulated proteins at the threshold of 1.5-fold in iTfh cells compared to naive CD4+ T cells. With the aid of intensive bioinformatics, the biological process, the cellular compartment, the molecular function, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein–protein interaction of these differentially expressed proteins were revealed. Moreover, the acetylome data showed that 22 lysine (K) acetylated proteins are upregulated and 26 K acetylated proteins are downregulated in iTfh cells compared to the naive CD4+ T cells, among which 11 differentially acetylated K residues in core histones were identified, indicating that protein acetylation and epigenetic mechanism are involved in regulating Tfh cell differentiation. The study provides some important clues for investigating T cell activation and Tfh cell differentiation.
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Affiliation(s)
- Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Sujie Jia
- Department of Pharmaceutics, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaofei Gao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Hong Qiu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Ruifang Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-Related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, China
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17
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Ebersole JL, Kirakodu SS, Orraca L, Gonzalez Martinez J, Gonzalez OA. Gingival transcriptomics of follicular T cell footprints in progressing periodontitis. Clin Exp Immunol 2021; 204:373-395. [PMID: 33565609 DOI: 10.1111/cei.13584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/22/2022] Open
Abstract
Follicular helper T cells (Tfh) cells have been identified in the circulation and in tertiary lymphoid structures in chronic inflammation. Gingival tissues with periodontitis reflect chronic inflammation, so genomic footprints of Tfh cells should occur in these tissues and may differ related to aging effects. Macaca mulatta were used in a ligature-induced periodontitis model [adult group (aged 12-23 years); young group (aged 3-7 years)]. Gingival tissue and subgingival microbiome samples were obtained at matched healthy ligature-induced disease and clinical resolution sites. Microarray analysis examined Tfh genes (n = 54) related to microbiome characteristics documented using 16S MiSeq. An increase in the major transcription factor of Tfh cells, BCL6, was found with disease in both adult and young animals, while master transcription markers of other T cell subsets were either decreased or showed minimal change. Multiple Tfh-related genes, including surface receptors and transcription factors, were also significantly increased during disease. Specific microbiome patterns were significantly associated with profiles indicative of an increased presence/function of Tfh cells. Importantly, unique microbial complexes showed distinctive patterns of interaction with Tfh genes differing in health and disease and with the age of the animals. An increase in Tfh cell responsiveness occurred in the progression of periodontitis, affected by age and related to specific microbial complexes in the oral microbiome. The capacity of gingival Tfh cells to contribute to localized B cell activation and active antibody responses, including affinity maturation, may be critical for controlling periodontal lesions and contributing to limiting and/or resolving the lesions.
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Affiliation(s)
- J L Ebersole
- Department of Biomedical Science, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - S S Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - L Orraca
- School of Dental Medicine, University of Puerto Rico, San Juan, PR, USA
| | - J Gonzalez Martinez
- Caribbean Primate Research Center, University of Puerto Rico, Toa Baja, PR, USA
| | - O A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA.,Division of Periodontology, College of Dentistry, University of Kentucky, Lexington, KY, USA
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18
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Choi J, Crotty S. Bcl6-Mediated Transcriptional Regulation of Follicular Helper T cells (T FH). Trends Immunol 2021; 42:336-349. [PMID: 33663954 DOI: 10.1016/j.it.2021.02.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/01/2023]
Abstract
Follicular helper T cells (TFH) are essential B cell-help providers in the formation of germinal centers (GCs), affinity maturation of GC B cells, differentiation of high-affinity antibody-producing plasma cells, and production of memory B cells. The transcription factor (TF) B cell lymphoma 6 (Bcl6) is at the center of gene regulation in TFH biology, including differentiation and function, but how Bcl6 does this, and what additional TFs contribute, remain complex questions. This review focuses on advances in our understanding of Bcl6-mediated gene regulation of TFH functions, and the modulation of TFH by other TFs. These advances may have important implications in deciphering how repressor TFs can regulate many immunological cell types. An improved understanding of TFH biology will likely provide insights into biomedically relevant diseases.
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Affiliation(s)
- Jinyong Choi
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
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19
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Razzaghi R, Agarwal S, Kotlov N, Plotnikova O, Nomie K, Huang DW, Wright GW, Smith GA, Li M, Takata K, Yamadi M, Yao C, O’Shea JJ, Phelan JD, Pittaluga S, Scott DW, Muppidi JR. Compromised counterselection by FAS creates an aggressive subtype of germinal center lymphoma. J Exp Med 2021; 218:e20201173. [PMID: 33237303 PMCID: PMC7694576 DOI: 10.1084/jem.20201173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022] Open
Abstract
Fas is highly expressed on germinal center (GC) B cells, and mutations of FAS have been reported in diffuse large B cell lymphoma (DLBCL). Although GC-derived DLBCL has better overall outcomes than other DLBCL types, some cases are refractory, and the molecular basis for this is often unknown. We show that Fas is a strong cell-intrinsic regulator of GC B cells that promotes cell death in the light zone, likely via T follicular helper (Tfh) cell-derived Fas ligand. In the absence of Fas, GCs were more clonally diverse due to an accumulation of cells that did not demonstrably bind antigen. FAS alterations occurred most commonly in GC-derived DLBCL, were associated with inferior outcomes and an enrichment of Tfh cells, and co-occurred with deficiency in HVEM and PD-L1 that regulate the Tfh-B cell interaction. This work shows that Fas is critically required for GC homeostasis and suggests that loss of Tfh-mediated counterselection in the GC contributes to lethality in GC-derived lymphoma.
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Affiliation(s)
- Raud Razzaghi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Shreya Agarwal
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | | | - Da Wei Huang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - George W. Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Grace A. Smith
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Moyi Li
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Maryam Yamadi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Chen Yao
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - John J. O’Shea
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - James D. Phelan
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David W. Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jagan R. Muppidi
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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20
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Ioannidou K, Ndiaye DR, Noto A, Fenwick C, Fortis SP, Pantaleo G, Petrovas C, de Leval L. In Situ Characterization of Follicular Helper CD4 T Cells Using Multiplexed Imaging. Front Immunol 2021; 11:607626. [PMID: 33633728 PMCID: PMC7901994 DOI: 10.3389/fimmu.2020.607626] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/24/2020] [Indexed: 12/19/2022] Open
Abstract
Follicular helper CD4 T (Tfh) cells play an essential role in the formation of germinal centers (GCs), where mature B cells proliferate, differentiate, and provide long-term protective humoral responses. Despite the extensive phenotypic characterization and identification of human Tfh cell subsets, their spatial positioning at tissue level is not well understood. Here, we describe a quantitative multiplexed immunofluorescence approach allowing for the comprehensive in situ characterization of Tfh cells in human tonsils and lymph nodes (LNs) from individuals with angioimmunoblastic T-cell lymphoma (AITL). We have developed eight multiplexed panels comprising a spectrum of Tfh cell markers, like PD-1, CXCR5, and ICOS, along with transcription factors (Bcl6, Tbet, GATA3), to assess their expression, frequencies, spatial distribution and co-localization in a quantitative manner. Combined analysis of relevant markers revealed the presence of several Tfh cell subsets at tissue level based on the differential expression of surface receptors, nuclear factors as well as their distinct localization within the follicular areas. Interestingly, we found a considerable amount of tonsillar Tfh cells expressing high levels of the Th2 regulator GATA3. The co-expression of GATA3, CXCR5, and BCL6, points to an important role of GATA3 for the generation of effector human Tfh cells. Furthermore, our data revealed significantly different Tfh cell profile signatures between health and disease. Therefore, our imaging platform generates meaningful information for the in situ characterization of human Tfh cells and could provide the base for future studies aiming to a comprehensive understanding of Tfh cell tissue heterogeneity.
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Affiliation(s)
- Kalliopi Ioannidou
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Daba-Rokhya Ndiaye
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Alessandra Noto
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Sotirios P Fortis
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Constantinos Petrovas
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland.,Tissue Analysis Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Laurence de Leval
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
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21
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Chu CS, Hellmuth JC, Singh R, Ying HY, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG. Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage. Mol Cell 2020; 80:845-861.e10. [PMID: 33232656 DOI: 10.1016/j.molcel.2020.10.036] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/09/2020] [Accepted: 10/27/2020] [Indexed: 12/23/2022]
Abstract
Locus control region (LCR) functions define cellular identity and have critical roles in diseases such as cancer, although the hierarchy of structural components and associated factors that drive functionality are incompletely understood. Here we show that OCA-B, a B cell-specific coactivator essential for germinal center (GC) formation, forms a ternary complex with the lymphoid-enriched OCT2 and GC-specific MEF2B transcription factors and that this complex occupies and activates an LCR that regulates the BCL6 proto-oncogene and is uniquely required by normal and malignant GC B cells. Mechanistically, through OCA-B-MED1 interactions, this complex is required for Mediator association with the BCL6 promoter. Densely tiled CRISPRi screening indicates that only LCR segments heavily bound by this ternary complex are essential for its function. Our results demonstrate how an intimately linked complex of lineage- and stage-specific factors converges on specific and highly essential enhancer elements to drive the function of a cell-type-defining LCR.
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Affiliation(s)
- Chi-Shuen Chu
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rajat Singh
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Hsia-Yuan Ying
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lucy Skrabanek
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY 10065, USA
| | - Matthew R Teater
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ashley S Doane
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA; Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ari M Melnick
- Department of Medicine, Division of Hematology & Medical Oncology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA.
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22
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Ren HM, Kolawole EM, Ren M, Jin G, Netherby-Winslow CS, Wade Q, Shwetank, Rahman ZSM, Evavold BD, Lukacher AE. IL-21 from high-affinity CD4 T cells drives differentiation of brain-resident CD8 T cells during persistent viral infection. Sci Immunol 2020; 5:5/51/eabb5590. [PMID: 32948671 DOI: 10.1126/sciimmunol.abb5590] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/25/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
Development of tissue-resident memory (TRM) CD8 T cells depends on CD4 T cells. In polyomavirus central nervous system infection, brain CXCR5hi PD-1hi CD4 T cells produce interleukin-21 (IL-21), and CD8 T cells lacking IL-21 receptors (IL21R-/-) fail to become bTRM IL-21+ CD4 T cells exhibit elevated T cell receptor (TCR) affinity and higher TCR density. IL21R-/- brain CD8 T cells do not express CD103, depend on vascular CD8 T cells for maintenance, are antigen recall defective, and lack TRM core signature genes. CD4 T cell-deficient and IL21R-/- brain CD8 T cells show similar deficiencies in expression of genes for oxidative metabolism, and intrathecal delivery of IL-21 to CD4 T cell-depleted mice restores expression of electron transport genes in CD8 T cells to wild-type levels. Thus, high-affinity CXCR5hi PD-1hi CD4 T cells in the brain produce IL-21, which drives CD8 bTRM differentiation in response to a persistent viral infection.
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Affiliation(s)
- Heather M Ren
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Mingqiang Ren
- Consortium for Health and Military Performance, Department of Military & Emergency Medicine, Uniformed Services University, Bethesda, MD 20814, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20814, USA
| | - Ge Jin
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | | | - Quinn Wade
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Shwetank
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Ziaur S M Rahman
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Aron E Lukacher
- Department of Microbiology and Immunology, Penn State College of Medicine, Hershey, PA 17033, USA.
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23
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Mapping effector genes at lupus GWAS loci using promoter Capture-C in follicular helper T cells. Nat Commun 2020; 11:3294. [PMID: 32620744 PMCID: PMC7335045 DOI: 10.1038/s41467-020-17089-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/02/2020] [Indexed: 01/14/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is mediated by autoreactive antibodies that damage multiple tissues. Genome-wide association studies (GWAS) link >60 loci with SLE risk, but the causal variants and effector genes are largely unknown. We generated high-resolution spatial maps of SLE variant accessibility and gene connectivity in human follicular helper T cells (TFH), a cell type required for anti-nuclear antibodies characteristic of SLE. Of the ~400 potential regulatory variants identified, 90% exhibit spatial proximity to genes distant in the 1D genome sequence, including variants that loop to regulate the canonical TFH genes BCL6 and CXCR5 as confirmed by genome editing. SLE ‘variant-to-gene’ maps also implicate genes with no known role in TFH/SLE disease biology, including the kinases HIPK1 and MINK1. Targeting these kinases in TFH inhibits production of IL-21, a cytokine crucial for class-switched B cell antibodies. These studies offer mechanistic insight into the SLE-associated regulatory architecture of the human genome. T cells are a major cell type involved in systemic lupus erythematosus (SLE). Here, the authors use promoter capture-C and ATAC-seq in human follicular T helper cells to identify SLE genes distant from GWAS loci (via 3D interaction) and validate the function of key regulatory elements and genes in vitro.
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24
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Burkholder A, Akrobetu D, Pandiri AR, Ton K, Kim S, Labow BI, Nuzzi LC, Firriolo JM, Schneider SS, Fenton SE, Shaw ND. Investigation of the adolescent female breast transcriptome and the impact of obesity. Breast Cancer Res 2020; 22:44. [PMID: 32393308 PMCID: PMC7216667 DOI: 10.1186/s13058-020-01279-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/15/2020] [Indexed: 01/07/2023] Open
Abstract
Background Early life environmental exposures affect breast development and breast cancer risk in adulthood. The breast is particularly vulnerable during puberty when mammary epithelial cells proliferate exponentially. In overweight/obese (OB) women, inflammation increases breast aromatase expression and estrogen synthesis and promotes estrogen-receptor (ER)-positive breast cancer. In contrast, recent epidemiological studies suggest that obesity during childhood decreases future breast cancer risk. Studies on environmental exposures and breast cancer risk have thus far been limited to animal models. Here, we present the first interrogation of the human adolescent breast at the molecular level and investigate how obesity affects the immature breast. Methods We performed RNA-seq in 62 breast tissue samples from adolescent girls/young women (ADOL; mean age 17.8 years) who underwent reduction mammoplasty. Thirty-one subjects were non-overweight/obese (NOB; mean BMI 23.4 kg/m2) and 31 were overweight/obese (OB; BMI 32.1 kg/m2). We also compared our data to published mammary transcriptome datasets from women (mean age 39 years) and young adult mice, rats, and macaques. Results The ADOL breast transcriptome showed limited (30%) overlap with other species, but 88% overlap with adult women for the 500 most highly expressed genes in each dataset; only 43 genes were shared by all groups. In ADOL, there were 120 differentially expressed genes (DEG) in OB compared with NOB samples (padj < 0.05). Based on these DEG, Ingenuity Pathway Analysis (IPA) identified the cytokines CSF1 and IL-10 and the chemokine receptor CCR2 as among the most highly activated upstream regulators, suggesting increased inflammation in the OB breast. Classical ER targets (e.g., PR, AREG) were not differentially expressed, yet IPA identified the ER and PR and growth factors/receptors (VEGF, HGF, HER3) and kinases (AKT1) involved in hormone-independent ER activation as activated upstream regulators in OB breast tissue. Conclusions These studies represent the first investigation of the human breast transcriptome during late puberty/young adulthood and demonstrate that obesity is associated with a transcriptional signature of inflammation which may augment estrogen action in the immature breast microenvironment. We anticipate that these studies will prompt more comprehensive cellular and molecular investigations of obesity and its effect on the breast during this critical developmental window.
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Affiliation(s)
- Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA
| | - Dennis Akrobetu
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA
| | - Arun R Pandiri
- Cellular and Molecular Pathology Branch, Division of National Toxicology Program (DNTP), NIEHS, Research Triangle Park, NC, USA
| | - Kiki Ton
- Cellular and Molecular Pathology Branch, Division of National Toxicology Program (DNTP), NIEHS, Research Triangle Park, NC, USA
| | - Sue Kim
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA
| | - Brian I Labow
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura C Nuzzi
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph M Firriolo
- Adolescent Breast Clinic, the Department of Plastic and Oral Surgery, Division of Adolescent/Young Adult Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sallie S Schneider
- Biospecimen Resource and Molecular Analysis Facility, Baystate Medical Center, Springfield, MA, USA
| | - Suzanne E Fenton
- National Toxicology Program Laboratory, DNTP, NIEHS, Research Triangle Park, NC, USA
| | - Natalie D Shaw
- Clinical Research Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Drive, MD A2-03, Research Triangle Park, NC, 27709, USA.
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25
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Li K, Zhang Y, Liu X, Liu Y, Gu Z, Cao H, Dickerson KE, Chen M, Chen W, Shao Z, Ni M, Xu J. Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies. Cancer Discov 2020; 10:724-745. [PMID: 32188707 DOI: 10.1158/2159-8290.cd-19-1128] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 01/27/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022]
Abstract
Mutations in protein-coding genes are well established as the basis for human cancer, yet how alterations within noncoding genome, a substantial fraction of which contain cis-regulatory elements (CRE), contribute to cancer pathophysiology remains elusive. Here, we developed an integrative approach to systematically identify and characterize noncoding regulatory variants with functional consequences in human hematopoietic malignancies. Combining targeted resequencing of hematopoietic lineage-associated CREs and mutation discovery, we uncovered 1,836 recurrently mutated CREs containing leukemia-associated noncoding variants. By enhanced CRISPR/dCas9-based CRE perturbation screening and functional analyses, we identified 218 variant-associated oncogenic or tumor-suppressive CREs in human leukemia. Noncoding variants at KRAS and PER2 enhancers reside in proximity to nuclear receptor (NR) binding regions and modulate transcriptional activities in response to NR signaling in leukemia cells. NR binding sites frequently colocalize with noncoding variants across cancer types. Hence, recurrent noncoding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. SIGNIFICANCE: We describe an integrative approach to identify noncoding variants in human leukemia, and reveal cohorts of variant-associated oncogenic and tumor-suppressive cis-regulatory elements including KRAS and PER2 enhancers. Our findings support a model in which noncoding regulatory variants connect enhancer dysregulation with nuclear receptor signaling to modulate gene programs in hematopoietic malignancies.See related commentary by van Galen, p. 646.This article is highlighted in the In This Issue feature, p. 627.
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Affiliation(s)
- Kailong Li
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xin Liu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yuxuan Liu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhimin Gu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hui Cao
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kathryn E Dickerson
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mingyi Chen
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Weina Chen
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zhen Shao
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Ni
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jian Xu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, Texas. .,Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas
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26
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Yao WQ, Wu F, Zhang W, Chuang SS, Thompson JS, Chen Z, Zhang SW, Clipson A, Wang M, Liu H, Bibawi H, Huang Y, Campos L, Grant JW, Wright P, Ei-Daly H, Rásó-Barnett L, Farkas L, Follows GA, Gao Z, Attygalle AD, Ashton-Key M, Liu W, Du MQ. Angioimmunoblastic T-cell lymphoma contains multiple clonal T-cell populations derived from a common TET2 mutant progenitor cell. J Pathol 2020; 250:346-357. [PMID: 31859368 PMCID: PMC7064999 DOI: 10.1002/path.5376] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/28/2019] [Accepted: 12/12/2019] [Indexed: 02/05/2023]
Abstract
Angioimmunoblastic T‐cell lymphoma (AITL) is a neoplastic proliferation of T follicular helper cells with clinical and histological presentations suggesting a role of antigenic drive in its development. Genetically, it is characterized by a stepwise acquisition of somatic mutations, with early mutations involving epigenetic regulators (TET2, DNMT3A) and occurring in haematopoietic stem cells, with subsequent changes involving signaling molecules (RHOA, VAV1, PLCG1, CD28) critical for T‐cell biology. To search for evidence of potential oncogenic cooperation between genetic changes and intrinsic T cell receptor (TCR) signaling, we investigated somatic mutations and T‐cell receptor β (TRB) rearrangement in 119 AITL, 11 peripheral T‐cell lymphomas with T follicular helper phenotype (PTCL‐TFH), and 25 PTCL‐NOS using Fluidigm polymerase chain reaction (PCR) and Illumina MiSeq sequencing. We confirmed frequent TET2, DNMT3A, and RHOA mutations in AITL (72%, 34%, 61%) and PTCL‐TFH (73%, 36%, 45%) and showed multiple TET2 mutations (2 or 3) in 57% of the involved AITL and PTCL‐TFH. Clonal TRB rearrangement was seen in 76 cases with multiple functional rearrangements (2–4) in 18 cases (24%). In selected cases, we confirmed bi‐clonal T‐cell populations and further demonstrated that these independent T‐cell populations harboured identical TET2 mutations by using BaseScope in situ hybridization, suggesting their derivation from a common TET2 mutant progenitor cell population. Furthermore, both T‐cell populations expressed CD4. Finally, in comparison with tonsillar TFH cells, both AITL and PTCL‐TFH showed a significant overrepresentation of several TRB variable family members, particularly TRBV19*01. Our findings suggest the presence of parallel neoplastic evolutions from a common TET2 mutant haematopoietic progenitor pool in AITL and PTCL‐TFH, albeit to be confirmed in a large series of cases. The biased TRBV usage in these lymphomas suggests that antigenic stimulation may play an important role in predilection of T cells to clonal expansion and malignant transformation. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Wen-Qing Yao
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Fangtian Wu
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Department of Haematology, Jiangsu Province Hospital, Nanjing Medical University, Nanjing, PR China
| | - Wenyan Zhang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | | | - Joe S Thompson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Zi Chen
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Shao-Wei Zhang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Alexandra Clipson
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ming Wang
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Hongxiang Liu
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hani Bibawi
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yuanxue Huang
- Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Luis Campos
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - John W Grant
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Penny Wright
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Hesham Ei-Daly
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lívia Rásó-Barnett
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lorant Farkas
- The Haematopathology and Oncology Diagnostic Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - George A Follows
- Department of Haematology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zifen Gao
- Department of Pathology, Health Science Centre, Peking University, Beijing, PR China
| | | | - Margaret Ashton-Key
- Department of Cellular Pathology, Southampton University Hospitals National Health Service Foundation Trust, Southampton, UK
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, PR China
| | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK.,Molecular Malignancy Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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27
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Xu W, Zhao X, Wang X, Feng H, Gou M, Jin W, Wang X, Liu X, Dong C. The Transcription Factor Tox2 Drives T Follicular Helper Cell Development via Regulating Chromatin Accessibility. Immunity 2019; 51:826-839.e5. [DOI: 10.1016/j.immuni.2019.10.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 07/02/2019] [Accepted: 10/18/2019] [Indexed: 01/08/2023]
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28
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Nakhoul H, Lin Z, Wang X, Roberts C, Dong Y, Flemington E. High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments. mSphere 2019; 4:e00248-19. [PMID: 31292228 PMCID: PMC6620372 DOI: 10.1128/msphere.00248-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Certain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported. Here we utilized published whole-transcriptome RNA sequencing (RNA-seq) data sets from seven different PTCL studies and new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across PTCL subtypes. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma (AITL) and extranodal NK/T-cell lymphoma (ENKTL), two PTCL subtypes with well-established EBV associations, we also detected EBV in several cases of anaplastic large-cell lymphoma (ALCL), and we found evidence of infection by the oncogenic viruses Kaposi's sarcoma-associated herpesvirus and human T-cell leukemia virus type 1 in isolated PTCL cases. In AITLs, EBV gene expression analysis showed expression of immediate early, early, and late lytic genes, suggesting either low-level lytic gene expression or productive infection in a subset of EBV-infected B-lymphocyte stromal cells. Deconvolution of immune cell subpopulations demonstrated a greater B-cell signal in AITLs than in other PTCL subtypes, consistent with a larger role for B-cell support in the pathogenesis of AITL. Reconstructed T-cell receptor (TCR) and B-cell receptor (BCR) repertoires demonstrated increased BCR diversity in AITLs, consistent with a possible EBV-driven polyclonal response. These findings indicate potential alternative roles for EBV in PTCLs, in addition to the canonical oncogenic mechanisms associated with EBV latent infection. Our findings also suggest the involvement of other viruses in PTCL pathogenesis and demonstrate immunological alterations associated with these cancers.IMPORTANCE In this study, we utilized next-generation sequencing data from 7 different studies of peripheral T-cell lymphoma (PTCL) patient samples to globally assess viral associations, provide insights into the contributions of EBV gene expression to the tumor phenotype, and assess the unique roles of EBV in modulating the immune cell tumor microenvironment. These studies revealed potential roles for EBV replication genes in some PTCL subtypes, the possible role of additional human tumor viruses in rare cases of PTCLs, and a role for EBV in providing a unique immune microenvironmental niche in one subtype of PTCLs. Together, these studies provide new insights into the understudied role of tumor viruses in PTCLs.
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Affiliation(s)
- Hani Nakhoul
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Zhen Lin
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Xia Wang
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Claire Roberts
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Erik Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
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29
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Vella LA, Buggert M, Manne S, Herati RS, Sayin I, Kuri-Cervantes L, Bukh Brody I, O'Boyle KC, Kaprielian H, Giles JR, Nguyen S, Muselman A, Antel JP, Bar-Or A, Johnson ME, Canaday DH, Naji A, Ganusov VV, Laufer TM, Wells AD, Dori Y, Itkin MG, Betts MR, Wherry EJ. T follicular helper cells in human efferent lymph retain lymphoid characteristics. J Clin Invest 2019; 129:3185-3200. [PMID: 31264971 DOI: 10.1172/jci125628] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
T follicular helper cells (Tfh), a subset of CD4+ T cells, provide requisite help to B cells in the germinal centers (GC) of lymphoid tissue. GC Tfh are identified by high expression of the chemokine receptor CXCR5 and the inhibitory molecule PD-1. Although more accessible, blood contains lower frequencies of CXCR5+ and PD-1+ cells that have been termed circulating Tfh (cTfh). However, it remains unclear whether GC Tfh exit lymphoid tissues and populate this cTfh pool. To examine exiting cells, we assessed the phenotype of Tfh present within the major conduit of efferent lymph from lymphoid tissues into blood, the human thoracic duct. Unlike what was found in blood, we consistently identified a CXCR5-bright PD-1-bright (CXCR5BrPD-1Br) Tfh population in thoracic duct lymph (TDL). These CXCR5BrPD-1Br TDL Tfh shared phenotypic and transcriptional similarities with GC Tfh. Moreover, components of the epigenetic profile of GC Tfh could be detected in CXCR5BrPD-1Br TDL Tfh and the transcriptional imprint of this epigenetic signature was enriched in an activated cTfh subset known to contain vaccine-responding cells. Together with data showing shared TCR sequences between the CXCR5BrPD-1Br TDL Tfh and cTfh, these studies identify a population in TDL as a circulatory intermediate connecting the biology of Tfh in blood to Tfh in lymphoid tissue.
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Affiliation(s)
- Laura A Vella
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marcus Buggert
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Sasikanth Manne
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramin S Herati
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ismail Sayin
- Department of Medicine, Case Western Reserve University and Cleveland Veterans Affairs, Cleveland, Ohio, USA
| | - Leticia Kuri-Cervantes
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Irene Bukh Brody
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaitlin C O'Boyle
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hagop Kaprielian
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Josephine R Giles
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Son Nguyen
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alexander Muselman
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Amit Bar-Or
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Neuroimmunology Unit, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.,Center for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew E Johnson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - David H Canaday
- Department of Medicine, Case Western Reserve University and Cleveland Veterans Affairs, Cleveland, Ohio, USA
| | - Ali Naji
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Terri M Laufer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Andrew D Wells
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yoav Dori
- Division of Cardiology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Maxim G Itkin
- Center for Lymphatic Disorders, Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael R Betts
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Parker Institute for Cancer Immunotherapy at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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30
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Laguna-Goya R, Suàrez-Fernández P, Paz-Artal E. Follicular helper T cells and humoral response in organ transplantation. Transplant Rev (Orlando) 2019; 33:183-190. [PMID: 31327572 DOI: 10.1016/j.trre.2019.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/17/2019] [Accepted: 06/28/2019] [Indexed: 02/07/2023]
Abstract
Antibody mediated rejection has been recognized as an important contributor to long-term graft loss in most solid organ transplants. Current immunosuppressive regimes are not capable of preventing anti-HLA antibody formation and eventual damage to the graft, and there is a need to develop drugs directed against novel targets to avoid graft allorecognition. In this review we introduce follicular helper T cells (Tfh), a subtype of lymphocyte specialized in helping B cells to differentiate into plasmablasts and produce class-switched antibodies. We focus on the role of Tfh in solid organ transplantation, what is known about Tfh and the production of alloantibodies, how current immunosuppressive therapies affect Tfh and what new molecules could be used to target Tfh in transplantation, with the goal of improving graft survival.
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Affiliation(s)
- R Laguna-Goya
- Immunology Department, Hospital Universitario 12 de Octubre, Madrid, Spain; Instituto de investigación Hospital Universitario 12 de Octubre (Imas12), Madrid, Spain; School of Medicine, Universidad Complutense de Madrid, Spain.
| | - P Suàrez-Fernández
- Instituto de investigación Hospital Universitario 12 de Octubre (Imas12), Madrid, Spain
| | - E Paz-Artal
- Immunology Department, Hospital Universitario 12 de Octubre, Madrid, Spain; Instituto de investigación Hospital Universitario 12 de Octubre (Imas12), Madrid, Spain; School of Medicine, Universidad Complutense de Madrid, Spain
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31
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Genetic drivers of oncogenic pathways in molecular subgroups of peripheral T-cell lymphoma. Blood 2019; 133:1664-1676. [PMID: 30782609 DOI: 10.1182/blood-2018-09-872549] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/10/2019] [Indexed: 02/07/2023] Open
Abstract
Peripheral T-cell lymphoma (PTCL) is a group of complex clinicopathological entities, often associated with an aggressive clinical course. Angioimmunoblastic T-cell lymphoma (AITL) and PTCL-not otherwise specified (PTCL-NOS) are the 2 most frequent categories, accounting for >50% of PTCLs. Gene expression profiling (GEP) defined molecular signatures for AITL and delineated biological and prognostic subgroups within PTCL-NOS (PTCL-GATA3 and PTCL-TBX21). Genomic copy number (CN) analysis and targeted sequencing of these molecular subgroups revealed unique CN abnormalities (CNAs) and oncogenic pathways, indicating distinct oncogenic evolution. PTCL-GATA3 exhibited greater genomic complexity that was characterized by frequent loss or mutation of tumor suppressor genes targeting the CDKN2A /B-TP53 axis and PTEN-PI3K pathways. Co-occurring gains/amplifications of STAT3 and MYC occurred in PTCL-GATA3. Several CNAs, in particular loss of CDKN2A, exhibited prognostic significance in PTCL-NOS as a single entity and in the PTCL-GATA3 subgroup. The PTCL-TBX21 subgroup had fewer CNAs, primarily targeting cytotoxic effector genes, and was enriched in mutations of genes regulating DNA methylation. CNAs affecting metabolic processes regulating RNA/protein degradation and T-cell receptor signaling were common in both subgroups. AITL showed lower genomic complexity compared with other PTCL entities, with frequent co-occurring gains of chromosome 5 (chr5) and chr21 that were significantly associated with IDH2 R172 mutation. CN losses were enriched in genes regulating PI3K-AKT-mTOR signaling in cases without IDH2 mutation. Overall, we demonstrated that novel GEP-defined PTCL subgroups likely evolve by distinct genetic pathways and provided biological rationale for therapies that may be investigated in future clinical trials.
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32
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Michaelovsky E, Carmel M, Frisch A, Salmon-Divon M, Pasmanik-Chor M, Weizman A, Gothelf D. Risk gene-set and pathways in 22q11.2 deletion-related schizophrenia: a genealogical molecular approach. Transl Psychiatry 2019; 9:15. [PMID: 30710087 PMCID: PMC6358611 DOI: 10.1038/s41398-018-0354-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 11/15/2022] Open
Abstract
The 22q11.2 deletion is a strong, but insufficient, "first hit" genetic risk factor for schizophrenia (SZ). We attempted to identify "second hits" from the entire genome in a unique multiplex 22q11.2 deletion syndrome (DS) family. Bioinformatic analysis of whole-exome sequencing and comparative-genomic hybridization array identified de novo and inherited, rare and damaging variants, including copy number variations, outside the 22q11.2 region. A specific 22q11.2-haplotype was associated with psychosis. The interaction of the identified "second hits" with the 22q11.2 haploinsufficiency may affect neurodevelopmental processes, including neuron projection, cytoskeleton activity, and histone modification in 22q11.2DS-ralated psychosis. A larger load of variants, involved in neurodevelopment, in combination with additional molecular events that affect sensory perception, olfactory transduction and G-protein-coupled receptor signaling may account for the development of 22q11.2DS-related SZ. Comprehensive analysis of multiplex families is a promising approach to the elucidation of the molecular pathophysiology of 22q11.2DS-related SZ with potential relevance to treatment.
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Affiliation(s)
- Elena Michaelovsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Felsenstein Medical Research Center, Petah Tikva, Israel.
| | - Miri Carmel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
| | - Amos Frisch
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
| | | | - Metsada Pasmanik-Chor
- Bioinformatics Unit, G.S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Weizman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Petah Tikva, Israel
- Geha Mental Health Center, Petah Tikva, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- The Behavioral Neurogenetics Center, Sheba Medical Center, Tel Hashomer, Israel
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33
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Braud VM, Biton J, Becht E, Knockaert S, Mansuet-Lupo A, Cosson E, Damotte D, Alifano M, Validire P, Anjuère F, Cremer I, Girard N, Gossot D, Seguin-Givelet A, Dieu-Nosjean MC, Germain C. Expression of LLT1 and its receptor CD161 in lung cancer is associated with better clinical outcome. Oncoimmunology 2018; 7:e1423184. [PMID: 29721382 PMCID: PMC5927544 DOI: 10.1080/2162402x.2017.1423184] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/18/2022] Open
Abstract
Co-stimulatory and inhibitory receptors expressed by immune cells in the tumor microenvironment modulate the immune response and cancer progression. Their expression and regulation are still not fully characterized and a better understanding of these mechanisms is needed to improve current immunotherapies. Our previous work has identified a novel ligand/receptor pair, LLT1/CD161, that modulates immune responses. Here, we extensively characterize its expression in non-small cell lung cancer (NSCLC). We show that LLT1 expression is restricted to germinal center (GC) B cells within tertiary lymphoid structures (TLS), representing a new hallmark of the presence of active TLS in the tumor microenvironment. CD161-expressing immune cells are found at the vicinity of these structures, with a global enrichment of NSCLC tumors in CD161+ CD4+ and CD8+ T cells as compared to normal distant lung and peripheral blood. CD161+ CD4+ T cells are more activated and produce Th1-cytokines at a higher frequency than their matched CD161-negative counterparts. Interestingly, CD161+ CD4+ T cells highly express OX40 co-stimulatory receptor, less frequently 4-1BB, and display an activated but not completely exhausted PD-1-positive Tim-3-negative phenotype. Finally, a meta-analysis revealed a positive association of CLEC2D (coding for LLT1) and KLRB1 (coding for CD161) gene expression with favorable outcome in NSCLC, independently of the size of T and B cell infiltrates. These data are consistent with a positive impact of LLT1/CD161 on NSCLC patient survival, and make CD161-expressing CD4+ T cells ideal candidates for efficient anti-tumor recall responses.
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Affiliation(s)
- Véronique M. Braud
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Jérôme Biton
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Etienne Becht
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Samantha Knockaert
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Audrey Mansuet-Lupo
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Department of Pathology, Hôpitaux Universitaires Paris Centre, AP-HP, Paris, France
| | - Estelle Cosson
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Diane Damotte
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Department of Pathology, Hôpitaux Universitaires Paris Centre, AP-HP, Paris, France
| | - Marco Alifano
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
- Department of Thoracic Surgery, Hôpitaux Universitaires Paris Centre, AP-HP, Paris, France
| | - Pierre Validire
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- Department of Pathology, Institut Mutualiste Montsouris, Paris, France
| | - Fabienne Anjuère
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Isabelle Cremer
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Nicolas Girard
- University of Lyon, University Lyon 1, Lyon, France
- Institut du Thorax Curie-Montsouris, Institut Curie, Paris, France
| | - Dominique Gossot
- Thoracic Department, Institut du Thorax Curie-Montsouris, Institut Mutualiste Montsouris, Paris, France
| | - Agathe Seguin-Givelet
- Thoracic Department, Institut du Thorax Curie-Montsouris, Institut Mutualiste Montsouris, Paris, France
- Paris 13 University, Sorbonne Paris Cité, Faculty of Medicine SMBH, Bobigny, France
| | - Marie-Caroline Dieu-Nosjean
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
| | - Claire Germain
- Laboratory “Immune Microenvironment and Tumors”, Department “Cancer, Immunology, Immunotherapy”, INSERM UMRS 1138, Cordeliers Research Center, Paris, France
- University Pierre and Marie Curie/Paris VI, Paris, France
- University Paris Descartes/Paris V, Sorbonne Paris Cité, Paris, France
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Ren C, Liu F, Ouyang Z, An G, Zhao C, Shuai J, Cai S, Bo X, Shu W. Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease. Sci Rep 2017; 7:15518. [PMID: 29138457 PMCID: PMC5686184 DOI: 10.1038/s41598-017-15822-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/03/2017] [Indexed: 12/28/2022] Open
Abstract
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures. Gene Ontology (GO) analysis revealed that eRNAs play key roles in human cell identity. Furthermore, we detected numerous known and novel functional RNA structures within eRNA regions. To better characterize the cis-regulatory effects of non-coding variation in these structural ncRNAs, we performed a comprehensive analysis of the genetic variants of structural ncRNAs in eRNA regions that are associated with inflammatory autoimmune diseases. Disease-associated variants of the structural ncRNAs were disproportionately enriched in immune-specific cell types. We also identified riboSNitches in lymphoid eRNAs and investigated the potential pathogenic mechanisms by which eRNAs might function in autoimmune diseases. Collectively, our findings offer valuable insights into the function of eRNAs and suggest that eRNAs might be effective diagnostic and therapeutic targets for human diseases.
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Affiliation(s)
- Chao Ren
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Feng Liu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.,Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Zhangyi Ouyang
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Gaole An
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Chenghui Zhao
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Jun Shuai
- Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Shuhong Cai
- Department of Information, The 188th Hospital of ChaoZhou, ChaoZhou, China
| | - Xiaochen Bo
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.
| | - Wenjie Shu
- Department of Biotechnology, Beijing Institute of Radiation Medicine, Beijing, China.
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35
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Bolotin DA, Poslavsky S, Davydov AN, Frenkel FE, Fanchi L, Zolotareva OI, Hemmers S, Putintseva EV, Obraztsova AS, Shugay M, Ataullakhanov RI, Rudensky AY, Schumacher TN, Chudakov DM. Antigen receptor repertoire profiling from RNA-seq data. Nat Biotechnol 2017; 35:908-911. [PMID: 29020005 PMCID: PMC6169298 DOI: 10.1038/nbt.3979] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Dmitriy A Bolotin
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Stanislav Poslavsky
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | | | - Lorenzo Fanchi
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Saskia Hemmers
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Ekaterina V Putintseva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Anna S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail Shugay
- MiLaboratory LLC, Skolkovo Innovation Center, Moscow, Russia
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Ravshan I Ataullakhanov
- BostonGene LLC, Lincoln, Massachusetts, USA
- Institute of Immunology FMBA, Moscow, Russia
- Faculties for Physics and Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
- Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ton N Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
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36
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Gong Q, Wang C, Zhang W, Iqbal J, Hu Y, Greiner TC, Cornish A, Kim JH, Rabadan R, Abate F, Wang X, Inghirami GG, McKeithan TW, Chan WC. Assessment of T-cell receptor repertoire and clonal expansion in peripheral T-cell lymphoma using RNA-seq data. Sci Rep 2017; 7:11301. [PMID: 28900149 PMCID: PMC5595876 DOI: 10.1038/s41598-017-11310-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/22/2017] [Indexed: 12/11/2022] Open
Abstract
T-cell clonality of peripheral T-cell lymphoma (PTCL) is routinely evaluated with a PCR-based method using genomic DNA. However, there are limitations with this approach. The purpose of this study was to determine the utility of RNA-seq for assessing T-cell clonality and T-cell antigen receptor (TCR) repertoire of the neoplastic T-cells in 108 PTCL samples. TCR transcripts, including complementarity-determining region 3 (CDR3) sequences, were assessed. In normal T cells, the CDR3 sequences were extremely diverse, without any clonotype representing more than 2% of the overall TCR population. Dominant clones could be identified in 65 out of 76 PTCL cases (86%) with adequate TCR transcript expression. In monoclonal cases, the dominant clone varied between 11% and 99% of TCRβ transcripts. No unique Vα or Vβ usage was observed. Small T-cell clones were often observed in T- and NK-cell tumors in a percentage higher than observed in reactive conditions. γ chain expression was very low in tumors expressing TCRαβ, but its expression level was high and clonality was detected in a TCRγδ expressing tumor. NK cell lymphoma (NKCL) did not express significant levels of TCR Vβ or Vγ genes. RNA-seq is a useful tool for detecting and characterizing clonal TCR rearrangements in PTCL.
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Affiliation(s)
- Qiang Gong
- Department of Pathology, City of Hope National Medical Center, Duarte, 91010, CA, United States
| | - Chao Wang
- Department of Pathology, City of Hope National Medical Center, Duarte, 91010, CA, United States.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.,Department of Hematology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, P.R. China
| | - Weiwei Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Javeed Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Yang Hu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Adam Cornish
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jo-Heon Kim
- Department of Pathology, City of Hope National Medical Center, Duarte, 91010, CA, United States.,Department of Pathology, Chonnam National University Medical School and Research Institute of Medical Sciences, Gwangju, South Korea
| | - Raul Rabadan
- Department of Biomedical Informatics, Columbia University, New York, NY, United States
| | - Francesco Abate
- Department of Biomedical Informatics, Columbia University, New York, NY, United States
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital affiliated to Shandong University, Jinan, P.R. China
| | - Giorgio G Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Timothy W McKeithan
- Department of Pathology, City of Hope National Medical Center, Duarte, 91010, CA, United States
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, 91010, CA, United States.
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37
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Hosokawa J, Suzuki K, Meguro K, Tanaka S, Maezawa Y, Suto A, Fujimura L, Sakamoto A, Clevers H, Ohara O, Nakajima H. IκBNS enhances follicular helper T-cell differentiation and function downstream of ASCl2. J Allergy Clin Immunol 2017; 140:288-291.e8. [DOI: 10.1016/j.jaci.2016.10.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/20/2016] [Accepted: 10/25/2016] [Indexed: 12/20/2022]
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38
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Pattarini L, Trichot C, Bogiatzi S, Grandclaudon M, Meller S, Keuylian Z, Durand M, Volpe E, Madonna S, Cavani A, Chiricozzi A, Romanelli M, Hori T, Hovnanian A, Homey B, Soumelis V. TSLP-activated dendritic cells induce human T follicular helper cell differentiation through OX40-ligand. J Exp Med 2017; 214:1529-1546. [PMID: 28428203 PMCID: PMC5413322 DOI: 10.1084/jem.20150402] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 12/30/2016] [Accepted: 03/02/2017] [Indexed: 12/27/2022] Open
Abstract
T follicular helper cells (Tfh) are implicated in various pathological conditions, but how they differentiate in Th2-skewed environments is unknown. Pattarini et al. delineate a pathway for human Tfh differentiation induced by TSLP through OX40L, relevant to atopic dermatitis. T follicular helper cells (Tfh) are important regulators of humoral responses. Human Tfh polarization pathways have been thus far associated with Th1 and Th17 polarization pathways. How human Tfh cells differentiate in Th2-skewed environments is unknown. We show that thymic stromal lymphopoietin (TSLP)–activated dendritic cells (DCs) promote human Tfh differentiation from naive CD4 T cells. We identified a novel population, distinct from Th2 cells, expressing IL-21 and TNF, suggestive of inflammatory cells. TSLP-induced T cells expressed CXCR5, CXCL13, ICOS, PD1, BCL6, BTLA, and SAP, among other Tfh markers. Functionally, TSLP-DC–polarized T cells induced IgE secretion by memory B cells, and this depended on IL-4Rα. TSLP-activated DCs stimulated circulating memory Tfh cells to produce IL-21 and CXCL13. Mechanistically, TSLP-induced Tfh differentiation depended on OX40-ligand, but not on ICOS-ligand. Our results delineate a pathway of human Tfh differentiation in Th2 environments.
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Affiliation(s)
- Lucia Pattarini
- Institut Curie, PSL Research University, Institut National de la Santé et de la Recherche Médicale (INSERM), U932, F-75005 Paris, France
| | - Coline Trichot
- Institut Curie, PSL Research University, Institut National de la Santé et de la Recherche Médicale (INSERM), U932, F-75005 Paris, France
| | - Sofia Bogiatzi
- Service de dermatologie et venereologie, CHUV University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Maximilien Grandclaudon
- Institut Curie, PSL Research University, Institut National de la Santé et de la Recherche Médicale (INSERM), U932, F-75005 Paris, France
| | - Stephan Meller
- Department of Dermatology, Heinrich-Heine-University Medical Faculty, 40225 Düsseldorf, Germany
| | - Zela Keuylian
- INSERM, UMR 1163, Laboratory of Genetic Skin Diseases, Imagine Institute and Paris Descartes University, F-75015 Paris, France
| | - Melanie Durand
- Institut Curie, PSL Research University, Institut National de la Santé et de la Recherche Médicale (INSERM), U932, F-75005 Paris, France
| | - Elisabetta Volpe
- Laboratory of Neuroimmunology, Fondazione Santa Lucia, 00142 Rome, Italy
| | - Stefania Madonna
- Laboratory of Experimental Immunology, Istituto Dermopatico dell'Immacolata-Istituto di Ricovero e Cura a Carattere Scientifico, Fondazione Luigi Maria Monti, 00167 Rome, Italy
| | - Andrea Cavani
- National Institute of Health, Migration and Poverty, 00153 Rome, Italy
| | | | - Marco Romanelli
- Department of Dermatology, University of Pisa, 56100 Pisa, Italy
| | - Toshiyuki Hori
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Alain Hovnanian
- INSERM, UMR 1163, Laboratory of Genetic Skin Diseases, Imagine Institute and Paris Descartes University, F-75015 Paris, France
| | - Bernhard Homey
- Department of Dermatology, Heinrich-Heine-University Medical Faculty, 40225 Düsseldorf, Germany
| | - Vassili Soumelis
- Institut Curie, PSL Research University, Institut National de la Santé et de la Recherche Médicale (INSERM), U932, F-75005 Paris, France
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39
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Pathologically expanded peripheral T helper cell subset drives B cells in rheumatoid arthritis. Nature 2017; 542:110-114. [PMID: 28150777 DOI: 10.1038/nature20810] [Citation(s) in RCA: 682] [Impact Index Per Article: 97.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 11/18/2016] [Indexed: 12/24/2022]
Abstract
CD4+ T cells are central mediators of autoimmune pathology; however, defining their key effector functions in specific autoimmune diseases remains challenging. Pathogenic CD4+ T cells within affected tissues may be identified by expression of markers of recent activation. Here we use mass cytometry to analyse activated T cells in joint tissue from patients with rheumatoid arthritis, a chronic immune-mediated arthritis that affects up to 1% of the population. This approach revealed a markedly expanded population of PD-1hiCXCR5-CD4+ T cells in synovium of patients with rheumatoid arthritis. However, these cells are not exhausted, despite high PD-1 expression. Rather, using multidimensional cytometry, transcriptomics, and functional assays, we define a population of PD-1hiCXCR5- 'peripheral helper' T (TPH) cells that express factors enabling B-cell help, including IL-21, CXCL13, ICOS, and MAF. Like PD-1hiCXCR5+ T follicular helper cells, TPH cells induce plasma cell differentiation in vitro through IL-21 secretion and SLAMF5 interaction (refs 3, 4). However, global transcriptomics highlight differences between TPH cells and T follicular helper cells, including altered expression of BCL6 and BLIMP1 and unique expression of chemokine receptors that direct migration to inflamed sites, such as CCR2, CX3CR1, and CCR5, in TPH cells. TPH cells appear to be uniquely poised to promote B-cell responses and antibody production within pathologically inflamed non-lymphoid tissues.
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40
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Tough DF, Prinjha RK. Immune disease-associated variants in gene enhancers point to BET epigenetic mechanisms for therapeutic intervention. Epigenomics 2016; 9:573-584. [PMID: 27925476 DOI: 10.2217/epi-2016-0144] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide polymorphisms in the human genome that are statistically associated with particular disease traits. In this Perspective, we review emerging data suggesting that most single nucleotide polymorphisms associated with immune-mediated diseases are found in regulatory regions of the DNA - parts of the genome that control expression of the protein encoding genes - rather than causing mutations in proteins. We discuss how the emerging understanding of particular gene regulatory regions, gene enhancers and the epigenetic mechanisms by which they are regulated is opening up new opportunities for the treatment of immune-mediated diseases, focusing particularly on the BET family of epigenetic reader proteins as potential therapeutic targets.
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Affiliation(s)
- David F Tough
- Epigenetics DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, UK
| | - Rab K Prinjha
- Epigenetics DPU, Immuno-Inflammation Therapy Area Unit, GlaxoSmithKline, Medicines Research Centre, Stevenage SG1 2NY, UK
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41
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Jiang K, Wong L, Sawle AD, Frank MB, Chen Y, Wallace CA, Jarvis JN. Whole blood expression profiling from the TREAT trial: insights for the pathogenesis of polyarticular juvenile idiopathic arthritis. Arthritis Res Ther 2016; 18:157. [PMID: 27388672 PMCID: PMC4936089 DOI: 10.1186/s13075-016-1059-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/22/2016] [Indexed: 12/22/2022] Open
Abstract
Background The Trial of Early Aggressive Therapy in Juvenile Idiopathic Arthritis (TREAT trial) was accompanied by a once-in-a-generation sample collection for translational research. In this paper, we report the results of whole blood gene expression analyses and genomic data-mining designed to cast light on the immunopathogenesis of polyarticular juvenile idiopathic arthritis (JIA). Methods TREAT samples and samples from an independent cohort were analyzed on Affymetrix microarrays and compared to healthy controls. Data from the independent cohort were used to validate the TREAT data. Pathways analysis was used to characterize gene expression profiles. Furthermore, we correlated differential gene expression with new information about functional regulatory elements within the genome to develop models of aberrant gene expression in JIA. Results There was a strong concordance in gene expression between TREAT samples and the independent cohort. In addition, rheumatoid factor (RF)-positive and RF-negative patients showed only small differences on whole blood expression profiles. Analysis of the combined samples showed 158 genes represented by 176 probes that showed differential expression between TREAT subjects at baseline and healthy controls. None of the differentially expressed genes were encoded within linkage disequilibrium blocks containing single nucleotide polymorphisms known to be associated with risk for JIA. Functional analysis of these genes showed functional associations with multiple processes associated with innate and adaptive immunity, and appeared to reflect overall suppression of STAT1–3/interferon response factor-mediated pathways. Conclusions Despite their limitations, whole blood expression profiles clearly distinguish children with polyarticular JIA from healthy controls. Whole blood expression profiles identify several immunologic pathways of biologic relevance that will need to be pursued in homogeneous cell populations in order to clarify mechanisms of pathogenesis. Trial registration ClinicalTrials.gov registry #NCT00443430, originally registered 2 March 2007 and last updated 30 May 2013.
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Affiliation(s)
- Kaiyu Jiang
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Laiping Wong
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Ashley D Sawle
- Irving Cancer institute, Columbia University College of Physicians and Surgeons, 1130 Saint Nicholas Ave., New York, NY, 10032, USA
| | - M Barton Frank
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 800 NE 13th St., Oklahoma City, OK, 73104, USA
| | - Yanmin Chen
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA
| | - Carol A Wallace
- Division of Rheumatology, Seattle Children's Hospital and Research Institute, 4800 Sand Point Way NE, MA.7.110, Seattle, WA, 98105, USA.,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - James N Jarvis
- Department of Pediatrics, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Clinical & Translational Research Center, 875 Ellicott St., Buffalo, NY, USA. .,Genetics, Genomics, and Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA.
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42
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Martinez GJ, Hu JK, Pereira RM, Crampton JS, Togher S, Bild N, Crotty S, Rao A. Cutting Edge: NFAT Transcription Factors Promote the Generation of Follicular Helper T Cells in Response to Acute Viral Infection. THE JOURNAL OF IMMUNOLOGY 2016; 196:2015-9. [PMID: 26851216 DOI: 10.4049/jimmunol.1501841] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/05/2016] [Indexed: 12/25/2022]
Abstract
Follicular CD4(+) Th (Tfh) cells provide B cell help in germinal center reactions that support class switching, somatic hypermutation, and the generation of high-affinity Abs. In this article, we show that deficiency in NFAT1 and NFAT2 in CD4(+) T cells leads to impaired germinal center reactions upon viral infection because of reduced Tfh cell differentiation and defective expression of proteins involved in T/B interactions and B cell help, including ICOS, PD-1, and SLAM family receptors. Genome-wide chromatin immunoprecipitation data suggest that NFAT proteins likely directly participate in regulation of genes important for Tfh cell differentiation and function. NFAT proteins are important TCR and Ca(2+)-dependent regulators of T cell biology, and in this article we demonstrate a major positive role of NFAT family members in Tfh differentiation.
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Affiliation(s)
- Gustavo J Martinez
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037;
| | - Joyce K Hu
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037
| | - Renata M Pereira
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Jordan S Crampton
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037
| | - Susan Togher
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Nicholas Bild
- Genomics Core, The Scripps Research Institute, Jupiter, FL, 33458
| | - Shane Crotty
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037; Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037
| | - Anjana Rao
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093; and Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037
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43
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Rohr J, Guo S, Huo J, Bouska A, Lachel C, Li Y, Simone PD, Zhang W, Gong Q, Wang C, Cannon A, Heavican T, Mottok A, Hung S, Rosenwald A, Gascoyne R, Fu K, Greiner TC, Weisenburger DD, Vose JM, Staudt LM, Xiao W, Borgstahl GEO, Davis S, Steidl C, McKeithan T, Iqbal J, Chan WC. Recurrent activating mutations of CD28 in peripheral T-cell lymphomas. Leukemia 2015; 30:1062-70. [PMID: 26719098 DOI: 10.1038/leu.2015.357] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/30/2015] [Accepted: 12/15/2015] [Indexed: 11/09/2022]
Abstract
Peripheral T-cell lymphomas (PTCLs) comprise a heterogeneous group of mature T-cell neoplasms with a poor prognosis. Recently, mutations in TET2 and other epigenetic modifiers as well as RHOA have been identified in these diseases, particularly in angioimmunoblastic T-cell lymphoma (AITL). CD28 is the major co-stimulatory receptor in T cells which, upon binding ligand, induces sustained T-cell proliferation and cytokine production when combined with T-cell receptor stimulation. We have identified recurrent mutations in CD28 in PTCLs. Two residues-D124 and T195-were recurrently mutated in 11.3% of cases of AITL and in one case of PTCL, not otherwise specified (PTCL-NOS). Surface plasmon resonance analysis of mutations at these residues with predicted differential partner interactions showed increased affinity for ligand CD86 (residue D124) and increased affinity for intracellular adaptor proteins GRB2 and GADS/GRAP2 (residue T195). Molecular modeling studies on each of these mutations suggested how these mutants result in increased affinities. We found increased transcription of the CD28-responsive genes CD226 and TNFA in cells expressing the T195P mutant in response to CD3 and CD86 co-stimulation and increased downstream activation of NF-κB by both D124V and T195P mutants, suggesting a potential therapeutic target in CD28-mutated PTCLs.
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Affiliation(s)
- J Rohr
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - S Guo
- Department of Pathology, Xi Jing Hospital, Fourth Military Medical University, Xi'an, Shaan Xi Province, China
| | - J Huo
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - A Bouska
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - C Lachel
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Y Li
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - P D Simone
- Internal Medicine Residency Program, Florida Atlantic University College of Medicine, Boca Raton, FL, USA
| | - W Zhang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Q Gong
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - C Wang
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA.,School of Medicine, Shandong University, Jinan, China
| | - A Cannon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - T Heavican
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - A Mottok
- Department for Lymphoid Cancer Research, Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - S Hung
- Department for Lymphoid Cancer Research, Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - A Rosenwald
- Institute of Pathology and Comprehensive Cancer Center Mainfranken (CCC MF), University of Wuerzburg, Wuerzburg, Germany
| | - R Gascoyne
- Department for Lymphoid Cancer Research, Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - K Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - T C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - D D Weisenburger
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - J M Vose
- Department of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - L M Staudt
- National Institutes of Health, Bethesda, MD, USA
| | - W Xiao
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, Washington, DC, USA
| | - G E O Borgstahl
- Eppley Institute for Cancer Research and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - S Davis
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - C Steidl
- Department for Lymphoid Cancer Research, Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - T McKeithan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - J Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - W C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
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Bcl6 middle domain repressor function is required for T follicular helper cell differentiation and utilizes the corepressor MTA3. Proc Natl Acad Sci U S A 2015; 112:13324-9. [PMID: 26460037 DOI: 10.1073/pnas.1507312112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T follicular helper (Tfh) cells are essential providers of help to B cells. The transcription factor B-cell CLL/lymphoma 6 (Bcl6) is a lineage-defining regulator of Tfh cells and germinal center B cells. In B cells, Bcl6 has the potential to recruit distinct transcriptional corepressors through its BTB domain or its poorly characterized middle domain (also known as RDII), but in Tfh cells the roles of the Bcl6 middle domain have yet to be clarified. Mimicked acetylation of the Bcl6 middle domain (K379Q) in CD4 T cells results in significant reductions in Tfh differentiation in vivo. Blimp1 (Prdm1) is a potent inhibitor of Tfh cell differentiation. Although Bcl6 K379Q still bound to the Prdm1 cis-regulatory elements in Tfh cells, Prdm1 expression was derepressed. This was a result of the failure of Bcl6 K379Q to recruit metastasis-associated protein 3 (MTA3). The loss of Bcl6 function in Bcl6 K379Q-expressing CD4 T cells could be partially rescued by abrogating Prdm1 expression. In addition to Prdm1, we found that Bcl6 recruits MTA3 to multiple genes involved in Tfh cell biology, including genes important for cell migration, cell survival, and alternative differentiation pathways. Thus, Bcl6 middle domain mediated repression is a major mechanism of action by which Bcl6 controls CD4 T-cell fate and function.
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Awe O, Hufford MM, Wu H, Pham D, Chang HC, Jabeen R, Dent AL, Kaplan MH. PU.1 Expression in T Follicular Helper Cells Limits CD40L-Dependent Germinal Center B Cell Development. THE JOURNAL OF IMMUNOLOGY 2015; 195:3705-15. [PMID: 26363052 DOI: 10.4049/jimmunol.1500780] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/10/2015] [Indexed: 01/31/2023]
Abstract
PU.1 is an ETS family transcription factor that is important for the development of multiple hematopoietic cell lineages. Previous work demonstrated a critical role for PU.1 in promoting Th9 development and in limiting Th2 cytokine production. Whether PU.1 has functions in other Th lineages is not clear. In this study, we examined the effects of ectopic expression of PU.1 in CD4(+) T cells and observed decreased expression of genes involved with the function of T follicular helper (Tfh) cells, including Il21 and Tnfsf5 (encoding CD40L). T cells from conditional mutant mice that lack expression of PU.1 in T cells (Sfpi1(lck-/-)) demonstrated increased production of CD40L and IL-21 in vitro. Following adjuvant-dependent or adjuvant-independent immunization, we observed that Sfpi1(lck-/-) mice had increased numbers of Tfh cells, increased germinal center B cells (GCB cells), and increased Ab production in vivo. This correlated with increased expression of IL-21 and CD40L in Tfh cells from Sfpi1(lck-/-) mice compared with control mice. Finally, although blockade of IL-21 did not affect GCB cells in Sfpi1(lck-/-) mice, anti-CD40L treatment of immunized Sfpi1(lck-/-) mice decreased GCB cell numbers and Ag-specific Ig concentrations. Together, these data indicate an inhibitory role for PU.1 in the function of Tfh cells, germinal centers, and Tfh-dependent humoral immunity.
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Affiliation(s)
- Olufolakemi Awe
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Matthew M Hufford
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Hao Wu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Duy Pham
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Hua-Chen Chang
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202
| | - Rukhsana Jabeen
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Alexander L Dent
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202; and
| | - Mark H Kaplan
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202; and
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IDH2R172 mutations define a unique subgroup of patients with angioimmunoblastic T-cell lymphoma. Blood 2015; 126:1741-52. [PMID: 26268241 DOI: 10.1182/blood-2015-05-644591] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/18/2015] [Indexed: 12/22/2022] Open
Abstract
Angioimmunoblastic T-cell lymphoma (AITL) is a common subtype of peripheral T-cell lymphoma (PTCL) with a poor prognosis. We performed targeted resequencing on 92 cases of PTCL and identified frequent mutations affecting RHOA, TET2, DNMT3A, and isocitrate dehydrogenase 2 (IDH2). Although IDH2 mutations are largely confined to AITL, mutations of the other 3 can be found in other types of PTCL, although at lower frequencies. These findings indicate a key role of epigenetic regulation in the pathogenesis of AITL. However, the epigenetic alterations induced by these mutations and their role in AITL pathogenesis are still largely unknown. We correlated mutational status with gene expression and global DNA methylation changes in AITL. Strikingly, AITL cases with IDH2(R172) mutations demonstrated a distinct gene expression signature characterized by downregulation of genes associated with TH1 differentiation (eg, STAT1 and IFNG) and a striking enrichment of an interleukin 12-induced gene signature. Ectopic expression of IDH2(R172K) in the Jurkat cell line and CD4(+) T cells led to markedly increased levels of 2-hydroxyglutarate, histone-3 lysine methylation, and 5-methylcytosine and a decrease of 5-hydroxymethylcytosine. Correspondingly, clinical samples with IDH2 mutations displayed a prominent increase in H3K27me3 and DNA hypermethylation of gene promoters. Integrative analysis of gene expression and promoter methylation revealed recurrently hypermethylated genes involved in T-cell receptor signaling and T-cell differentiation that likely contribute to lymphomagenesis in AITL.
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Hatzi K, Nance JP, Kroenke MA, Bothwell M, Haddad EK, Melnick A, Crotty S. BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms. ACTA ACUST UNITED AC 2015; 212:539-53. [PMID: 25824819 PMCID: PMC4387288 DOI: 10.1084/jem.20141380] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 03/12/2015] [Indexed: 12/31/2022]
Abstract
Follicular helper T cells (Tfh cells) are required for T cell help to B cells, and BCL6 is the defining transcription factor of Tfh cells. However, the functions of BCL6 in Tfh cells have largely remained unclear. Here we defined the BCL6 cistrome in primary human germinal center Tfh cells to assess mechanisms of BCL6 regulation of CD4 T cells, comparing and contrasting BCL6 function in T and B cells. BCL6 primarily acts as a repressor in Tfh cells, and BCL6 binding was associated with control of Tfh cell migration and repression of alternative cell fates. Interestingly, although some BCL6-bound genes possessed BCL6 DNA-binding motifs, many BCL6-bound loci were instead characterized by the presence of DNA motifs for AP1 or STAT. AP1 complexes are key positive downstream mediators of TCR signaling and external stimuli. We show that BCL6 can directly bind AP1, and BCL6 depends on AP1 for recruitment to BCL6-binding sites with AP1 motifs, suggesting that BCL6 subverts AP1 activity. These findings reveal that BCL6 has broad and multifaceted effects on Tfh biology and provide insight into how this master regulator mediates distinct cell context-dependent phenotypes.
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Affiliation(s)
- Katerina Hatzi
- Division of Hematology and Medical Oncology, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - J Philip Nance
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Mark A Kroenke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Marcella Bothwell
- University of California, San Diego Department of Surgery and Division of Pediatric Otolaryngology, Rady Children's Hospital-San Diego, San Diego, CA 92123 University of California, San Diego Department of Surgery and Division of Pediatric Otolaryngology, Rady Children's Hospital-San Diego, San Diego, CA 92123
| | - Elias K Haddad
- Vaccine and Gene Therapy Institute of Florida, Port St. Lucie, FL 34987
| | - Ari Melnick
- Division of Hematology and Medical Oncology, Weill Cornell Medical College, Cornell University, New York, NY 10065
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
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