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Correlation between B-cell lymphoma 6 with the balance of T helper-1/2 and severity of allergic rhinitis. Allergol Immunopathol (Madr) 2023; 51:1-8. [PMID: 36617815 DOI: 10.15586/aei.v51i1.673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/22/2022] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Allergic rhinitis (AR) is a prevailing immune disorder affecting the nasal mucosa. B-cell lymphoma 6 (BCL6) imposes essential roles in immunity. This study probed into the serum expression of BCL6 and its effect on AR diagnosis and patients' quality of life (QOL). METHODS A total of 113 patients with AR including 38 cases with mild AR (MAR) and 75 cases with moderate-severe AR (MSAR) were enrolled, with 101 healthy people enrolled as control. Serum expression of BCL6 was detected by RT-qPCR and the diagnostic efficacy of BCL6 for AR was analyzed using the receiver operating characteristic curve. The proportion of T helper-1/2 (Th1/Th2) cells in CD4+ T cells in peripheral blood mononuclear cells was detected using flow cytometry. The correlation between BCL6 and Th1/Th2 cells and the effects of BCL6 expression on patients' QOL were assessed by Pearson analysis and Mini-RQLQ questionnaire. RESULTS BCL6 was downregulated in patients with AR, serum BCL6 level < 0.8450 had certain auxiliary diagnostic values for AR, and serum BCL6 level < 0.5400 could assist the diagnosis of AR severity. Th1 cell proportion in CD4+ T cells was decreased, whereas Th2 cell proportion was increased with AR severity. BCL6 was positively-linked with Th1 cells but inversely-correlated with Th2 cells in patients with AR. Patients with AR with low BCL6 expression had a poorer QOL compared with high BCL6 expression. The domains most affected by BCL6 expression were practical problems, nasal symptoms, and lacrimation. CONCLUSION Serum BCL6 is downregulated and low BCL6 expression greatly deteriorates QOL in patients with AR.
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Xia Y, Sandor K, Pai JA, Daniel B, Raju S, Wu R, Hsiung S, Qi Y, Yangdon T, Okamoto M, Chou C, Hiam-Galvez KJ, Schreiber RD, Murphy KM, Satpathy AT, Egawa T. BCL6-dependent TCF-1 + progenitor cells maintain effector and helper CD4 + T cell responses to persistent antigen. Immunity 2022; 55:1200-1215.e6. [PMID: 35637103 PMCID: PMC10034764 DOI: 10.1016/j.immuni.2022.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/04/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022]
Abstract
Soon after activation, CD4+ T cells are segregated into BCL6+ follicular helper (Tfh) and BCL6- effector (Teff) T cells. Here, we explored how these subsets are maintained during chronic antigen stimulation using the mouse chronic LCMV infection model. Using single cell-transcriptomic and epigenomic analyses, we identified a population of PD-1+ TCF-1+ CD4+ T cells with memory-like features. TCR clonal tracing and adoptive transfer experiments demonstrated that these cells have self-renewal capacity and continue to give rise to both Teff and Tfh cells, thus functioning as progenitor cells. Conditional deletion experiments showed Bcl6-dependent development of these progenitors, which were essential for sustaining antigen-specific CD4+ T cell responses to chronic infection. An analogous CD4+ T cell population developed in draining lymph nodes in response to tumors. Our study reveals the heterogeneity and plasticity of CD4+ T cells during persistent antigen exposure and highlights their population dynamics through a stable, bipotent intermediate state.
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Affiliation(s)
- Yu Xia
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Joy A Pai
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Saravanan Raju
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sunnie Hsiung
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yanyan Qi
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Tenzin Yangdon
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Mariko Okamoto
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chun Chou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Ruterbusch M, Pruner KB, Shehata L, Pepper M. In Vivo CD4 + T Cell Differentiation and Function: Revisiting the Th1/Th2 Paradigm. Annu Rev Immunol 2021; 38:705-725. [PMID: 32340571 DOI: 10.1146/annurev-immunol-103019-085803] [Citation(s) in RCA: 262] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of CD4+ T cell subset-defining master transcription factors and framing of the Th1/Th2 paradigm ignited the CD4+ T cell field. Advances in in vivo experimental systems, however, have revealed that more complex lineage-defining transcriptional networks direct CD4+ T cell differentiation in the lymphoid organs and tissues. This review focuses on the layers of fate decisions that inform CD4+ T cell differentiation in vivo. Cytokine production by antigen-presenting cells and other innate cells influences the CD4+ T cell effector program [e.g., T helper type 1 (Th1), Th2, Th17]. Signals downstream of the T cell receptor influence whether individual clones bearing hallmarks of this effector program become T follicular helper cells, supporting development of B cells expressing specific antibody isotypes, or T effector cells, which activate microbicidal innate cells in tissues. These bifurcated, parallel axes allow CD4+ T cells to augment their particular effector program and prevent disease.
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Affiliation(s)
- Mikel Ruterbusch
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Kurt B Pruner
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Laila Shehata
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
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4
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Bruton K, Spill P, Vohra S, Baribeau O, Manzoor S, Gadkar S, Davidson M, Walker TD, Koenig JFE, Ellenbogen Y, Florescu A, Wen J, Chu DK, Waserman S, Jiménez-Saiz R, Epelman S, Robbins C, Jordana M. Interrupting reactivation of immunologic memory diverts the allergic response and prevents anaphylaxis. J Allergy Clin Immunol 2021; 147:1381-1392. [PMID: 33338539 DOI: 10.1016/j.jaci.2020.11.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/02/2020] [Accepted: 11/06/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND IgE production against innocuous food antigens can result in anaphylaxis, a severe life-threatening consequence of allergic reactions. The maintenance of IgE immunity is primarily facilitated by IgG+ memory B cells, as IgE+ memory B cells and IgE+ plasma cells are extremely scarce and short-lived, respectively. OBJECTIVE Our aim was to investigate the critical requirements for an IgE recall response in peanut allergy. METHODS We used a novel human PBMC culture platform, a mouse model of peanut allergy, and various experimental readouts to assess the IgE recall response in the presence and absence of IL-4Rα blockade. RESULTS In human PBMCs, we have demonstrated that blockade of IL-4/IL-13 signaling aborted IgE production after activation of a recall response and skewed the cytokine response away from a dominant type 2 signature. TH2A cells, identified by single-cell RNA sequencing, expanded with peanut stimulation and maintained their pathogenic phenotype in spite of IL-4Rα blockade. In mice with allergy, anti-IL-4Rα provided long-lasting suppression of the IgE recall response beyond antibody treatment and fully protected against anaphylaxis. CONCLUSION The findings reported here advance our understanding of events mediating the regeneration of IgE in food allergy.
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Affiliation(s)
- Kelly Bruton
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Paul Spill
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Owen Baribeau
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Saba Manzoor
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Siyon Gadkar
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Malcolm Davidson
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Tina D Walker
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Joshua F E Koenig
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Yosef Ellenbogen
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Alexandra Florescu
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jianping Wen
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Derek K Chu
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada; Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Susan Waserman
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Rodrigo Jiménez-Saiz
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada; Centro Nacional de Biotecnología-CSIC, Department of Immunology and Oncology, Madrid, Spain
| | | | | | - Manel Jordana
- McMaster Immunology Research Centre, Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
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Agonistic CD40 Antibodies in Cancer Treatment. Cancers (Basel) 2021; 13:cancers13061302. [PMID: 33804039 PMCID: PMC8000216 DOI: 10.3390/cancers13061302] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/16/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary CD40 is a costimulatory molecule that is key for the activation of antigen-presenting cells and other innate immune cells. It plays an important role in anti-tumor immunity, and agonists of CD40 have been shown to eliminate tumors in both pre-clinical and clinical settings, alone and in combination with other treatment modalities. Here we assess the expression of CD40 and associations with other mediators of immunity in a variety of tumor types and review the potential of CD40 agonists for cancer treatment, given the promise of enhancing the interplay between innate and adaptive immunity. Abstract CD40 is expressed on a variety of antigen-presenting cells. Stimulation of CD40 results in inflammation by upregulation of other costimulatory molecules, increased antigen presentation, maturation (licensing) of dendritic cells, and activation of CD8+ T cells. Here we analyzed gene expression data from The Cancer Genome Atlas in melanoma, renal cell carcinoma, and pancreatic adenocarcinoma and found correlations between CD40 and several genes involved in antigen presentation and T cell function, supporting further exploration of CD40 agonists to treat cancer. Agonist CD40 antibodies have induced anti-tumor effects in several tumor models and the effect has been more pronounced when used in combination with other treatments (immune checkpoint inhibition, chemotherapy, and colony-stimulating factor 1 receptor inhibition). The reduction in tumor growth and ability to reprogram the tumor microenvironment in preclinical models lays the foundation for clinical development of agonistic CD40 antibodies (APX005M, ChiLob7/4, ADC-1013, SEA-CD40, selicrelumab, and CDX-1140) that are currently being evaluated in early phase clinical trials. In this article, we focus on CD40 expression and immunity in cancer, agonistic human CD40 antibodies, and their pre-clinical and clinical development. With the broad pro-inflammatory effects of CD40 and its ligand on dendritic cells and macrophages, and downstream B and T cell activation, agonists of this pathway may enhance the anti-tumor activity of other systemic therapies.
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Yang R, Mele F, Worley L, Langlais D, Rosain J, Benhsaien I, Elarabi H, Croft CA, Doisne JM, Zhang P, Weisshaar M, Jarrossay D, Latorre D, Shen Y, Han J, Ogishi M, Gruber C, Markle J, Al Ali F, Rahman M, Khan T, Seeleuthner Y, Kerner G, Husquin LT, Maclsaac JL, Jeljeli M, Errami A, Ailal F, Kobor MS, Oleaga-Quintas C, Roynard M, Bourgey M, El Baghdadi J, Boisson-Dupuis S, Puel A, Batteux F, Rozenberg F, Marr N, Pan-Hammarström Q, Bogunovic D, Quintana-Murci L, Carroll T, Ma CS, Abel L, Bousfiha A, Di Santo JP, Glimcher LH, Gros P, Tangye SG, Sallusto F, Bustamante J, Casanova JL. Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria. Cell 2020; 183:1826-1847.e31. [PMID: 33296702 PMCID: PMC7770098 DOI: 10.1016/j.cell.2020.10.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Inborn errors of human interferon gamma (IFN-γ) immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. The patient has extremely low counts of circulating Mycobacterium-reactive natural killer (NK), invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of Mycobacterium-non reactive classic TH1 lymphocytes, with the residual populations of these cells also producing abnormally small amounts of IFN-γ. Other lymphocyte subsets develop normally but produce low levels of IFN-γ, with the exception of CD8+ αβ T and non-classic CD4+ αβ TH1∗ lymphocytes, which produce IFN-γ normally in response to mycobacterial antigens. Human T-bet deficiency thus underlies mycobacterial disease by preventing the development of innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells) and IFN-γ production by them, with mycobacterium-specific, IFN-γ-producing, purely adaptive CD8+ αβ T, and CD4+ αβ TH1∗ cells unable to compensate for this deficit.
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Affiliation(s)
- Rui Yang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA.
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Lisa Worley
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - David Langlais
- Department of Human Genetics, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada; McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Ibithal Benhsaien
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Houda Elarabi
- Pediatrics Department, Hassan II Hospital, 80030 Dakhla, Morocco
| | - Carys A Croft
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France; University of Paris, 75006 Paris, France
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Peng Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Marc Weisshaar
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - David Jarrossay
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Daniela Latorre
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yichao Shen
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Jing Han
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Masato Ogishi
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Janet Markle
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | | | - Taushif Khan
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Lucas T Husquin
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France
| | - Julia L Maclsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mohamed Jeljeli
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Abderrahmane Errami
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Manon Roynard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Mathieu Bourgey
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics, Montreal, QC H3A 0G1, Canada
| | | | - Stéphanie Boisson-Dupuis
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Fréderic Batteux
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Flore Rozenberg
- University of Paris, 75006 Paris, France; Virology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, PO 34110, Qatar
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, 75005 Paris, France
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Gros
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Federica Sallusto
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland; Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jacinta Bustamante
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Study Center for Primary Immunodeficiencies, Necker Children Hospital, AP-HP, 75015 Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
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7
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Opejin A, Surnov A, Misulovin Z, Pherson M, Gross C, Iberg CA, Fallahee I, Bourque J, Dorsett D, Hawiger D. A Two-Step Process of Effector Programming Governs CD4 + T Cell Fate Determination Induced by Antigenic Activation in the Steady State. Cell Rep 2020; 33:108424. [PMID: 33238127 PMCID: PMC7714042 DOI: 10.1016/j.celrep.2020.108424] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/01/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
Various processes induce and maintain immune tolerance, but effector T cells still arise under minimal perturbations of homeostasis through unclear mechanisms. We report that, contrary to the model postulating primarily tolerogenic mechanisms initiated under homeostatic conditions, effector programming is an integral part of T cell fate determination induced by antigenic activation in the steady state. This effector programming depends on a two-step process starting with induction of effector precursors that express Hopx and are imprinted with multiple instructions for their subsequent terminal effector differentiation. Such molecular circuits advancing specific terminal effector differentiation upon re-stimulation include programmed expression of interferon-γ, whose production then promotes expression of T-bet in the precursors. We further show that effector programming coincides with regulatory conversion among T cells sharing the same antigen specificity. However, conventional type 2 dendritic cells (cDC2) and T cell functions of mammalian target of rapamycin complex 1 (mTORC1) increase effector precursor induction while decreasing the proportion of T cells that can become peripheral Foxp3+ regulatory T (pTreg) cells. The mechanisms in the steady state that govern the formation of effector T cells with potentially autoimmune functions remain unclear. Opejin et al. reveal a two-step process starting with induction of effector precursors that express Hopx and are imprinted with multiple instructions for their subsequent terminal effector differentiation.
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Affiliation(s)
- Adeleye Opejin
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alexey Surnov
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Michelle Pherson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Cindy Gross
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Courtney A Iberg
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Ian Fallahee
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Jessica Bourque
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA.
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8
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Gioulbasani M, Galaras A, Grammenoudi S, Moulos P, Dent AL, Sigvardsson M, Hatzis P, Kee BL, Verykokakis M. The transcription factor BCL-6 controls early development of innate-like T cells. Nat Immunol 2020; 21:1058-1069. [PMID: 32719520 PMCID: PMC7442690 DOI: 10.1038/s41590-020-0737-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 06/15/2020] [Indexed: 12/21/2022]
Abstract
Innate T cells, including invariant natural killer T (iNKT) and mucosal-associated innate T (MAIT) cells, are a heterogeneous T lymphocyte population with effector properties pre-programmed during their thymic differentiation. How this program is initiated is currently unclear. Here, we show that the transcription factor BCL-6 was transiently expressed in iNKT cells upon exit from positive selection and was required for their proper development beyond stage 0. Notably, development of MAIT cells was also impaired in the absence of Bcl6. BCL-6–deficient iNKT cells had reduced expression of genes that were associated with the innate T cell lineage, including Zbtb16, which encodes PLZF, and PLZF-targeted genes. BCL-6 contributed to a chromatin accessibility landscape that was permissive for the expression of development-related genes and inhibitory for genes associated with naïve T cell programs. Our results revealed novel functions for BCL-6 and illuminated how this transcription factor controls early iNKT cell development.
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Affiliation(s)
| | - Alexandros Galaras
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari, Greece.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Greece
| | - Sofia Grammenoudi
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari, Greece
| | - Alexander L Dent
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mikael Sigvardsson
- Department of Clinical and Experimental Medicine, Experimental Hematopoiesis Unit, Faculty for Health Sciences, Linköping University, Linköping, Sweden
| | - Pantelis Hatzis
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari, Greece
| | - Barbara L Kee
- Department of Pathology and Committee on Immunology, University of Chicago, Chicago, IL, USA.
| | - Mihalis Verykokakis
- Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, Vari, Greece.
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9
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Patta I, Madhok A, Khare S, Gottimukkala KP, Verma A, Giri S, Dandewad V, Seshadri V, Lal G, Misra-Sen J, Galande S. Dynamic regulation of chromatin organizer SATB1 via TCR-induced alternative promoter switch during T-cell development. Nucleic Acids Res 2020; 48:5873-5890. [PMID: 32392347 PMCID: PMC7293019 DOI: 10.1093/nar/gkaa321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023] Open
Abstract
The chromatin organizer SATB1 is highly enriched in thymocytes and is essential for T-cell development. Although SATB1 regulates a large number of genes important for T-cell development, the mechanism(s) regulating expression of SATB1 during this process remain elusive. Using chromatin immune precipitation-seq-based occupancy profiles of H3K4me3 and H3Kme1 at Satb1 gene locus, we predicted four different alternative promoters of Satb1 in mouse thymocytes and characterized them. The expression of Satb1 transcript variants with distinct 5′ UTRs occurs in a stage-specific manner during T-cell development and is dependent on TCR signaling. The observed discrepancy between the expression levels of SATB1 mRNA and protein in developing thymocytes can be explained by the differential translatability of Satb1 transcript variants as confirmed by polysome profiling and in vitro translation assay. We show that Satb1 alternative promoters exhibit lineage-specific chromatin accessibility during T-cell development from progenitors. Furthermore, TCF1 regulates the Satb1 P2 promoter switch during CD4SP development, via direct binding to the Satb1 P2 promoter. CD4SP T cells from TCF1 KO mice exhibit downregulation of P2 transcript variant expression as well as low levels of SATB1 protein. Collectively, these results provide unequivocal evidence toward alternative promoter switch-mediated developmental stage-specific regulation of SATB1 in thymocytes.
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Affiliation(s)
- Indumathi Patta
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Ayush Madhok
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Satyajeet Khare
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India.,Symbiosis School of Biological Sciences, Pune, Maharashtra 412115, India
| | - Kamalvishnu P Gottimukkala
- National Institute on Aging, NIH and School of Medicine Immunology Graduate Program, Johns Hopkins University, Baltimore, MD 21224, USA
| | - Anjali Verma
- National Institute on Aging, NIH and School of Medicine Immunology Graduate Program, Johns Hopkins University, Baltimore, MD 21224, USA
| | - Shilpi Giri
- National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Vishal Dandewad
- National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Vasudevan Seshadri
- National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Girdhari Lal
- National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Jyoti Misra-Sen
- National Institute on Aging, NIH and School of Medicine Immunology Graduate Program, Johns Hopkins University, Baltimore, MD 21224, USA
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
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10
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Wang Z, Ji N, Chen Z, Sun Z, Wu C, Yu W, Hu F, Huang M, Zhang M. MiR-1165-3p Suppresses Th2 Differentiation via Targeting IL-13 and PPM1A in a Mouse Model of Allergic Airway Inflammation. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:859-876. [PMID: 32638565 PMCID: PMC7346992 DOI: 10.4168/aair.2020.12.5.859] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE CD4⁺T cells are essential in the pathogenesis of allergic asthma. We have previously demonstrated that microRNA-1165-3p (miR-1165-3p) was significantly reduced in T-helper type (Th) 2 cells and that miR-1165-3p was a surrogate marker for atopic asthma. Little is known about the mechanisms of miR-1165-3p in the regulation of Th2-dominated allergic inflammation. We aimed to investigate the associations between Th2 differentiation and miR-1165b-3p in asthma as well as the possible mechanisms. METHODS CD4⁺ naïve T cells were differentiated into Th1 or Th2 cells in vitro. MiR-1165-3p was up-regulated or down-regulated using lentiviral systems during Th1/Th2 differentiation. In vivo, the lentiviral particles with the miR-1165-3p enhancer were administered by tail vein injection on the first day of a house dust mite -induced allergic airway inflammation model. Allergic inflammation and Th1/Th2 differentiation were routinely monitored. To investigate the potential targets of miR-1165-3p, biotin-microRNA pull-down products were sequenced, and the candidates were further verified with a dual-luciferase reporter assay. The roles of a target protein phosphatase, Mg2+/Mn2+-dependent 1A (PPM1A), in Th2 cell differentiation and allergic asthma were further explored. Plasma PPM1A was determined by ELISA in 18 subjects with asthma and 20 controls. RESULTS The lentivirus encoding miR-1165-3p suppressed Th2-cell differentiation in vitro. In contrast, miR-1165-3p silencing promoted Th2-cell development. In the HDM-induced model of allergic airway inflammation, miR-1165-3p up-regulation was accompanied by reduced airway hyper-responsiveness, serum immunoglobulin E, airway inflammation and Th2-cell polarization. IL-13 and PPM1A were the direct targets of miR-1165-3p. The expression of IL-13 or PPM1A was inversely correlated with that of miR-1165-3p. PPM1A regulated the signal transducer and activator of transcription and AKT signaling pathways during Th2 differentiation. Moreover, plasma PPM1A was significantly increased in asthmatic patients. CONCLUSIONS MiR-1165-3p negatively may regulate Th2-cell differentiation by targeting IL-13 and PPM1A in allergic airway inflammation.
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Affiliation(s)
- Zhengxia Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhongqi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhixiao Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chaojie Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenqing Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Infectious Disease, Taizhou People's Hospital, Taizhou, China
| | - Fan Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
| | - Mingshun Zhang
- NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Immunology, Nanjing Medical University, Nanjing, China.
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11
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Poglio S, Merlio JP. SATB1 Is a Pivotal Epigenetic Biomarker in Cutaneous T-Cell Lymphomas. J Invest Dermatol 2019; 138:1694-1696. [PMID: 30032787 DOI: 10.1016/j.jid.2018.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 12/17/2022]
Abstract
The SATB1 protein has been the focus of two recent studies of cutaneous T-cell lymphomas. Fredholm et al. observed a stage-related decrease of SATB1 expression in epidermotropic cutaneous T-cell lymphomas. SATB1 was negatively regulated by STAT5 through microRNA-155, which in turn triggered enhanced expression of T helper type 2 cytokines such as IL-5 and IL-9. In parallel, Sun et al. found that SATB1 expression was up-regulated by promoter demethylation in a subset of cutaneous anaplastic lymphoma and was associated with T helper type 17 polarization in patients with better therapeutic responses.
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Affiliation(s)
- Sandrine Poglio
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France
| | - Jean-Philippe Merlio
- INSERM U1053, Bordeaux Research in Translational Oncology University Bordeaux, Bordeaux, France; Tumor Bank and Tumor Biology Laboratory, Centre Hospitalier Universitaire de Bordeaux, Pessac, France.
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12
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MyD88 Signaling in T Cells Is Critical for Effector CD4 T Cell Differentiation following a Transitional T Follicular Helper Cell Stage. Infect Immun 2018; 86:IAI.00791-17. [PMID: 29507085 DOI: 10.1128/iai.00791-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/28/2018] [Indexed: 12/24/2022] Open
Abstract
Activation of CD4 T cells by dendritic cells leads to their differentiation into various effector lineages. The nature of the effector lineage is determined by the innate cues provided by dendritic cells to newly primed T cells. Although the cytokines necessary for several effector lineages have been identified, the innate cues that drive T follicular helper (Tfh) lineage cell development remain unclear. Here we found that following priming, CD4 T cells undergoing clonal expansion acquire a transient Tfh-like phenotype before differentiating into other effector lineages. In addition, we found that T cell-intrinsic myeloid differentiation antigen 88 (MyD88) signaling, which occurs downstream of interleukin-1 (IL-1) and IL-18 receptors, is critical for the primed CD4 T cells to transition out of the temporary Tfh lineage. Mice with T cell-specific deletion of MyD88 have a higher proportion of Tfh cells and germinal center (GC) B cells. These exaggerated Tfh cell and GC B cell responses, however, do not lead to protective immunity against infections. We demonstrate that T cell-intrinsic MyD88 is critical for effector lineage differentiation as well as production of the cytokines that are necessary for class switching. Overall, our study establishes that following priming and clonal expansion, CD4 T cells undergo a transitional Tfh-like phase and that further differentiation into effector lineages is dictated by T cell-intrinsic MyD88-dependent cues.
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13
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Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases. Nat Commun 2015; 5:3045. [PMID: 24413636 DOI: 10.1038/ncomms4045] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 12/02/2013] [Indexed: 02/06/2023] Open
Abstract
Generation of mouse models by introducing transgenes using homologous recombination is critical for understanding fundamental biology and pathology of human diseases. Here we investigate whether artificial transcription activator-like effector nucleases (TALENs)-powerful tools that induce DNA double-strand breaks at specific genomic locations-can be combined with a targeting vector to induce homologous recombination for the introduction of a transgene in embryonic stem cells and fertilized murine oocytes. We describe the generation of a conditional mouse model using TALENs, which introduce double-strand breaks at the genomic locus of the special AT-rich sequence-binding protein-1 in combination with a large 14.4 kb targeting template vector. We report successful germline transmission of this allele and demonstrate its recombination in primary cells in the presence of Cre-recombinase. These results suggest that TALEN-assisted induction of DNA double-strand breaks can facilitate homologous recombination of complex targeting constructs directly in oocytes.
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14
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Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. Identification of global regulators of T-helper cell lineage specification. Genome Med 2015; 7:122. [PMID: 26589177 PMCID: PMC4654807 DOI: 10.1186/s13073-015-0237-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 11/15/2022] Open
Abstract
Background Activation and differentiation of T-helper (Th) cells into Th1 and Th2 types is a complex process orchestrated by distinct gene activation programs engaging a number of genes. This process is crucial for a robust immune response and an imbalance might lead to disease states such as autoimmune diseases or allergy. Therefore, identification of genes involved in this process is paramount to further understand the pathogenesis of, and design interventions for, immune-mediated diseases. Methods We aimed at identifying protein-coding genes and long non-coding RNAs (lncRNAs) involved in early differentiation of T-helper cells by transcriptome analysis of cord blood-derived naïve precursor, primary and polarized cells. Results Here, we identified lineage-specific genes involved in early differentiation of Th1 and Th2 subsets by integrating transcriptional profiling data from multiple platforms. We have obtained a high confidence list of genes as well as a list of novel genes by employing more than one profiling platform. We show that the density of lineage-specific epigenetic marks is higher around lineage-specific genes than anywhere else in the genome. Based on next-generation sequencing data we identified lineage-specific lncRNAs involved in early Th1 and Th2 differentiation and predicted their expected functions through Gene Ontology analysis. We show that there is a positive trend in the expression of the closest lineage-specific lncRNA and gene pairs. We also found out that there is an enrichment of disease SNPs around a number of lncRNAs identified, suggesting that these lncRNAs might play a role in the etiology of autoimmune diseases. Conclusion The results presented here show the involvement of several new actors in the early differentiation of T-helper cells and will be a valuable resource for better understanding of autoimmune processes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0237-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kartiek Kanduri
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland. .,Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Subhash Tripathi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Antti Larjo
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Henrik Mannerström
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Riikka Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - R David Hawkins
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland. .,Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA. .,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
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15
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EZH2 is crucial for both differentiation of regulatory T cells and T effector cell expansion. Sci Rep 2015; 5:10643. [PMID: 26090605 PMCID: PMC4473539 DOI: 10.1038/srep10643] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/27/2015] [Indexed: 12/24/2022] Open
Abstract
The roles of EZH2 in various subsets of CD4+ T cells are controversial and its mechanisms of action are incompletely understood. FOXP3-positive Treg cells are a critical helper T cell subset, and dysregulation of Treg generation or function results in systemic autoimmunity. FOXP3 associates with EZH2 to mediate gene repression and suppressive function. Herein, we demonstrate that deletion of Ezh2 in CD4 T cells resulted in reduced numbers of Treg cells in vivo and differentiation in vitro and an increased proportion of memory CD4 T cells in part due to exaggerated production of effector cytokines. Furthermore, we found that both Ezh2-deficient Treg cells and T effector cells were functionally impaired in vivo: Tregs failed to constrain autoimmune colitis and T effector cells neither provided a protective response to T. gondii infection nor mediated autoimmune colitis. The dichotomous function of EZH2 in regulating differentiation and senescence in effector and regulatory T cells helps to explain the apparent existing contradictions in literature.
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16
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Hao B, Naik AK, Watanabe A, Tanaka H, Chen L, Richards HW, Kondo M, Taniuchi I, Kohwi Y, Kohwi-Shigematsu T, Krangel MS. An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development. ACTA ACUST UNITED AC 2015; 212:809-24. [PMID: 25847946 PMCID: PMC4419350 DOI: 10.1084/jem.20142207] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/12/2015] [Indexed: 12/12/2022]
Abstract
Rag1 and Rag2 gene expression in CD4(+)CD8(+) double-positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here, we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes.
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Affiliation(s)
- Bingtao Hao
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Abani Kanta Naik
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Akiko Watanabe
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Hirokazu Tanaka
- RIKEN Centre for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Liang Chen
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Hunter W Richards
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720
| | - Motonari Kondo
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
| | - Ichiro Taniuchi
- RIKEN Centre for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshinori Kohwi
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720
| | - Terumi Kohwi-Shigematsu
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA 94720
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710
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17
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Maliniemi P, Hahtola S, Ovaska K, Jeskanen L, Väkevä L, Jäntti K, Stadler R, Michonneau D, Fraitag S, Hautaniemi S, Ranki A. Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes. Orphanet J Rare Dis 2014; 9:160. [PMID: 25928531 PMCID: PMC4320460 DOI: 10.1186/s13023-014-0160-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/09/2014] [Indexed: 12/21/2022] Open
Abstract
Background Subcutaneous panniculitis-like T cell lymphomas represent a rare and difficult to diagnose entity of cutaneous T cell lymphomas. SPTL affects predominantly young adults and presents with multifocal subcutaneous nodules and frequently associated autoimmune features. The pathogenesis of SPTL is not completely understood. Methods The aim of this study was to unravel molecular pathways critical to the SPTL pathogenesis. Therefore, we analyzed 23 skin samples from 20 newly diagnosed SPTL patients and relevant control samples of adipose and non-malignant panniculitis tissue by using gene expression microarray, quantitative PCR, and two-colour immunohistochemistry. Results Interestingly, indoleamine 2,3-dioxygenase (IDO-1), an immunotolerance-inducing enzyme, was among the most highly overexpressed genes in all comparisons. The expression of Th1-specific cytokines, known to be associated with autoimmune inflammation (i.e. IFNG, CXCR3, CXCL9, CXCL10, CXCL11, and CCL5), were also significantly increased. Confirmed using immunohistochemistry, the morphologically malignant lymphocytes expressed CXCR3 and CXCL9. IDO-1 expression was found both in some morphologically malignant lymphocytes rimming the adipocytes and in surrounding CD11c− CD68− cells but not in CD11c+ dendritic cells in the microenvironment. The proportion of FoxP3+ cells in SPTL exceeded that in the benign panniculitis samples. Conclusions Our results indicate that the up regulation of the tolerogenic IDO-1 together with the up regulation of IFNG, CXCR3 ligands, and CCL5 are features of SPTL lesions. We anticipate that the IFNG-inducible IDO-1 expression contributes to the formation of an immunosuppressive microenvironment, favorable for the malignant T cells. This study provides a relevant molecular basis for further studies exploring novel therapeutic means for subcutaneous T cell lymphoma. Electronic supplementary material The online version of this article (doi:10.1186/s13023-014-0160-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pilvi Maliniemi
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Sonja Hahtola
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Kristian Ovaska
- Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland.
| | - Leila Jeskanen
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Liisa Väkevä
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Kirsi Jäntti
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Rudolf Stadler
- Johannes-Wesling-Klinikum Minden, Akademisches Lehrkrankenhaus der Medizinischen Hochschule Hannover, Minden, Germany.
| | - David Michonneau
- Institut Pasteur, Département d'immunologie, Equipe Dynamique des réponses immunes, 25 rue du Docteur Roux, 75015, Paris, France.
| | - Sylvie Fraitag
- Service d'anatomie et de cytologie pathologiques, Hôpital Necker-Enfants-Malades, AP-HP, 149, rue de Sèvres, 75743, Paris Cedex 15, France.
| | - Sampsa Hautaniemi
- Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland.
| | - Annamari Ranki
- Department of Dermatology and Allergology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
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18
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Abstract
Combined with TCR stimuli, extracellular cytokine signals initiate the differentiation of naive CD4(+) T cells into specialized effector T-helper (Th) and regulatory T (Treg) cell subsets. The lineage specification and commitment process occurs through the combinatorial action of multiple transcription factors (TFs) and epigenetic mechanisms that drive lineage-specific gene expression programs. In this article, we review recent studies on the transcriptional and epigenetic regulation of distinct Th cell lineages. Moreover, we review current study linking immune disease-associated single-nucleotide polymorphisms with distal regulatory elements and their potential role in the disease etiology.
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Affiliation(s)
- Subhash K Tripathi
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
- National Doctoral Programme in Informational and
Structural BiologyTurku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM),
University of TurkuTurku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
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19
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Abstract
Molecular mechanisms guiding naïve T helper cell differentiation into functionally specified effector cells are intensively studied. The rapidly growing knowledge is mainly achieved by using mouse cells or disease models. Comparatively exiguous data is gathered from human primary cells although they provide the "ultimate model" for immunology in man, have been exploited in many original studies paving the way for the field, and can be analyzed more easily than ever with the help of modern technology and methods. As usage of mouse models is unavoidable in translational research, parallel human and mouse studies should be performed to assure the relevancy of the hypothesis created during the basic research. In this review, we give an overview on the status of the studies conducted with human primary cells aiming at elucidating the mechanisms instructing the priming of T helper cell subtypes. The special emphasis is given to the recent high-throughput studies. In addition, by comparing the human and mouse studies we intend to point out the regulatory mechanisms and questions which are lacking examination with human primary cells.
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Affiliation(s)
- Soile Tuomela
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
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20
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Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity 2013; 38:1271-84. [PMID: 23791644 DOI: 10.1016/j.immuni.2013.05.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 03/14/2013] [Indexed: 12/22/2022]
Abstract
Naive CD4⁺ T cells can differentiate into specific helper and regulatory T cell lineages in order to combat infection and disease. The correct response to cytokines and a controlled balance of these populations is critical for the immune system and the avoidance of autoimmune disorders. To investigate how early cell-fate commitment is regulated, we generated the first human genome-wide maps of histone modifications that reveal enhancer elements after 72 hr of in vitro polarization toward T helper 1 (Th1) and T helper 2 (Th2) cell lineages. Our analysis indicated that even at this very early time point, cell-specific gene regulation and enhancers were at work directing lineage commitment. Further examination of lineage-specific enhancers identified transcription factors (TFs) with known and unknown T cell roles as putative drivers of lineage-specific gene expression. Lastly, an integrative analysis of immunopathogenic-associated SNPs suggests a role for distal regulatory elements in disease etiology.
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21
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Human T follicular helper cells: development and subsets. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 785:87-94. [PMID: 23456841 DOI: 10.1007/978-1-4614-6217-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Antibody response constitutes one of the key immune protection mechanisms. T follicular helper (Tfh) cells represent the major CD4⁺ T cell subset that provides help to B cells to induce antibody response. How Tfh cells develop and how Tfh cells or their associated subsets regulate antibody response in humans remains largely unknown. In this review, we will summarize the recent discoveries on the biology of Tfh cells, with a particular focus on human Tfh cells.
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22
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Abstract
Various molecules participate in different phases of allergic reactions. This means that many genes are encoding molecules related to allergic reactions, such as cytokines, chemokines, and their receptors as effect or molecules. The transcriptional repressor BCL6 has emerged as a multifunctional regulator of lymphocyte differentiation and immune responses. BCL6-deficient (BCL6) mice display T helper type 2 (Th2)-type inflammation, which is caused by abnormality of both lymphoid cells and nonlymphoid cells. Thus, BCL6 apparently contributes to negative regulation of various central molecules such as cytokines, in particular Th2 cytokines, CC chemokines, and immunoglobulin E in allergic diseases. Therefore, BCL6 may be a molecular target for Th2-type allergic diseases.
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Aijö T, Edelman SM, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H. An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. BMC Genomics 2012; 13:572. [PMID: 23110343 PMCID: PMC3526425 DOI: 10.1186/1471-2164-13-572] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 10/02/2012] [Indexed: 01/19/2023] Open
Abstract
Background A proper balance between different T helper (Th) cell subsets is necessary for normal functioning of the adaptive immune system. Revealing key genes and pathways driving the differentiation to distinct Th cell lineages provides important insight into underlying molecular mechanisms and new opportunities for modulating the immune response. Previous computational methods to quantify and visualize kinetic differential expression data of three or more lineages to identify reciprocally regulated genes have relied on clustering approaches and regression methods which have time as a factor, but have lacked methods which explicitly model temporal behavior. Results We studied transcriptional dynamics of human umbilical cord blood T helper cells cultured in absence and presence of cytokines promoting Th1 or Th2 differentiation. To identify genes that exhibit distinct lineage commitment dynamics and are specific for initiating differentiation to different Th cell subsets, we developed a novel computational methodology (LIGAP) allowing integrative analysis and visualization of multiple lineages over whole time-course profiles. Applying LIGAP to time-course data from multiple Th cell lineages, we identified and experimentally validated several differentially regulated Th cell subset specific genes as well as reciprocally regulated genes. Combining differentially regulated transcriptional profiles with transcription factor binding site and pathway information, we identified previously known and new putative transcriptional mechanisms involved in Th cell subset differentiation. All differentially regulated genes among the lineages together with an implementation of LIGAP are provided as an open-source resource. Conclusions The LIGAP method is widely applicable to quantify differential time-course dynamics of many types of datasets and generalizes to any number of conditions. It summarizes all the time-course measurements together with the associated uncertainty for visualization and manual assessment purposes. Here we identified novel human Th subset specific transcripts as well as regulatory mechanisms important for the initiation of the Th cell subset differentiation.
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Affiliation(s)
- Tarmo Aijö
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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24
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Chromatin organizer SATB1 is an important determinant of T-cell differentiation. Immunol Cell Biol 2012; 90:852-9. [PMID: 22710879 DOI: 10.1038/icb.2012.28] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
T-cell development and differentiation is coordinated by a multitude of signaling molecules and transcription factors that impart distinct functional properties to progenitors. In this review, we focus on the role of the T lineage-enriched chromatin organizer and regulator SATB1 in T-cell differentiation. SATB1 mediates Wnt signaling by recruiting β-catenin to its genomic targets and coordinates T helper type 2 (T(H)2) differentiation by positively regulating GATA-3. In contrast, maintenance of regulatory T cell (Treg) functions are dependent on inhibition of SATB1-mediated modulation of global chromatin organization. We discuss how regulation of the activity of SATB1 has a critical role in driving these two important differentiation pathways in T cells.
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25
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Eifan AO, Furukido K, Dumitru A, Jacobson MR, Schmidt-Weber C, Banfield G, Durham SR, Nouri-Aria KT. Reduced T-bet in addition to enhanced STAT6 and GATA3 expressing T cells contribute to human allergen-induced late responses. Clin Exp Allergy 2012; 42:891-900. [DOI: 10.1111/j.1365-2222.2012.04003.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- A. O. Eifan
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - K. Furukido
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - A. Dumitru
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - M. R. Jacobson
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - C. Schmidt-Weber
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - G. Banfield
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - S. R. Durham
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
| | - K. T. Nouri-Aria
- Allergy and Clinical Immunology; National Heart and Lung Institute; Imperial College; London UK
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26
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Nakayamada S, Kanno Y, Takahashi H, Jankovic D, Lu KT, Johnson TA, Sun HW, Vahedi G, Hakim O, Handon R, Schwartzberg PL, Hager GL, O'Shea JJ. Early Th1 cell differentiation is marked by a Tfh cell-like transition. Immunity 2011; 35:919-31. [PMID: 22195747 PMCID: PMC3244883 DOI: 10.1016/j.immuni.2011.11.012] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 10/12/2011] [Accepted: 11/04/2011] [Indexed: 12/23/2022]
Abstract
Follicular helper T (Tfh) cells comprise an important subset of helper T cells; however, their relationship with other helper lineages is incompletely understood. Herein, we showed interleukin-12 acting via the transcription factor STAT4 induced both Il21 and Bcl6 genes, generating cells with features of both Tfh and Th1 cells. However, STAT4 also induced the transcription factor T-bet. With ChIP-seq, we defined the genome-wide targets of T-bet and found that it repressed Bcl6 and other markers of Tfh cells, thereby attenuating the nascent Tfh cell-like phenotype in the late phase of Th1 cell specification. Tfh-like cells were rapidly generated after Toxoplasma gondii infection in mice, but T-bet constrained Tfh cell expansion and consequent germinal center formation and antibody production. Our data argue that Tfh and Th1 cells share a transitional stage through the signal mediated by STAT4, which promotes both phenotypes. However, T-bet represses Tfh cell functionalities, promoting full Th1 cell differentiation.
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Affiliation(s)
- Shingo Nakayamada
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Vanherberghen M, Bureau F, Peters IR, Day MJ, Clercx C, Peeters D. Analysis of gene expression in canine sino-nasal aspergillosis and idiopathic lymphoplasmacytic rhinitis: a transcriptomic analysis. Vet Microbiol 2011; 157:143-51. [PMID: 22221380 DOI: 10.1016/j.vetmic.2011.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 12/06/2011] [Accepted: 12/08/2011] [Indexed: 10/14/2022]
Abstract
Sino-nasal aspergillosis (SNA) and lymphoplasmacytic rhinitis (LPR) are two common causes of nasal discharge in dog. SNA is typically due to an invasion of Aspergillus fumigatus in the surface of nasal mucosa. The etiology of LPR is poorly understood and a possible implication of fungi is suspected. The purpose of the present study was to explore the immunopathogenesis of these diseases by comparing gene expression in the nasal mucosa from dogs affected by SNA or LPR with healthy dogs, using a canine-specific microarray and quantitative real-time reverse transcriptase polymerase chain reaction for confirmation of the findings of the microarray study. Total RNA was isolated from biopsies of nasal mucosa and gene expression was analyzed via hybridation to the Affymetrix GeneChip(®) Canine Genome 2.0 Array. Selected Affimetrix probes sets identifiers were downloaded into the Database for Annotation, Visualization and Integrated Discovery. Genes of interest were chosen after their fold change and their possible implication in immunopathogenesis of SNA or LPR. The results presented here were in concordance with previous studies on SNA and LPR and highlighted new molecules potentially involved in the pathogenesis of SNA. The over-expression of interleukin (IL)-16, natural killer cell group 7 and chemokine ligand 10 might be related to a potential protective Th1 immunity counterbalanced by other molecules such as DNA-binding protein Ikaros.
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Affiliation(s)
- Morgane Vanherberghen
- Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Belgium.
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28
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Hirahara K, Vahedi G, Ghoreschi K, Yang XP, Nakayamada S, Kanno Y, O'Shea JJ, Laurence A. Helper T-cell differentiation and plasticity: insights from epigenetics. Immunology 2011; 134:235-45. [PMID: 21977994 DOI: 10.1111/j.1365-2567.2011.03483.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
CD4(+) T cells have critical roles in orchestrating immune responses to diverse microbial pathogens. This is accomplished through the differentiation of CD4(+) T helper cells to specialized subsets in response to microbial pathogens, which evoke a distinct cytokine milieu. Signal transducer and activator of transcription family transcription factors sense these cytokines and they in turn regulate expression of lineage-defining master regulators that programme selective gene expression, resulting in distinctive phenotypes. However, phenotype and restricted gene expression are determined not only by the action of transcription factors; chromatin accessibility is required for these factors to exert their effect. Technical advances have greatly expanded our understanding of transcription factor action and dynamic changes in the epigenome that accompany cellular differentiation. In this review, we will discuss recent progress in the understanding of how cytokines influence gene expression and epigenetic modifications, and the impact of these findings on our views of helper cell lineage commitment and plasticity.
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Affiliation(s)
- Kiyoshi Hirahara
- Department of Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-1930, USA.
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29
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Huarcaya E, Best I, Rodriguez-Tafur J, Maguiña C, Solórzano N, Menacho J, Lopez De Guimaraes D, Chauca J, Ventosilla P. Cytokines and T-Lymphocute count in patients in the acute and chronic phases of Bartonella bacilliformis infection in an endemic area in peru: a pilot study. Rev Inst Med Trop Sao Paulo 2011; 53:149-54. [PMID: 21755237 DOI: 10.1590/s0036-46652011000300006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 03/11/2011] [Indexed: 11/22/2022] Open
Abstract
Human Bartonellosis has an acute phase characterized by fever and hemolytic anemia, and a chronic phase with bacillary angiomatosis-like lesions. This cross-sectional pilot study evaluated the immunology patterns using pre- and post-treatment samples in patients with Human Bartonellosis. Patients between five and 60 years of age, from endemic areas in Peru, in the acute or chronic phases were included. In patients in the acute phase of Bartonellosis a state of immune peripheral tolerance should be established for persistence of the infection. Our findings were that elevation of the anti-inflammatory cytokine IL-10 and numeric abnormalities of CD4(+) and CD8(+) T-Lymphocyte counts correlated significantly with an unfavorable immune state. During the chronic phase, the elevated levels of IFN-γ and IL-4 observed in our series correlated with previous findings of endothelial invasion of B. henselae in animal models.
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Affiliation(s)
- Erick Huarcaya
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
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Beyer M, Thabet Y, Müller RU, Sadlon T, Classen S, Lahl K, Basu S, Zhou X, Bailey-Bucktrout SL, Krebs W, Schönfeld EA, Böttcher J, Golovina T, Mayer CT, Hofmann A, Sommer D, Debey-Pascher S, Endl E, Limmer A, Hippen KL, Blazar BR, Balderas R, Quast T, Waha A, Mayer G, Famulok M, Knolle PA, Wickenhauser C, Kolanus W, Schermer B, Bluestone JA, Barry SC, Sparwasser T, Riley JL, Schultze JL. Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation. Nat Immunol 2011; 12:898-907. [PMID: 21841785 PMCID: PMC3669688 DOI: 10.1038/ni.2084] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/07/2011] [Indexed: 12/12/2022]
Abstract
Regulatory T cells (T(reg) cells) are essential for self-tolerance and immune homeostasis. Lack of effector T cell (T(eff) cell) function and gain of suppressive activity by T(reg) cells are dependent on the transcriptional program induced by Foxp3. Here we report that repression of SATB1, a genome organizer that regulates chromatin structure and gene expression, was crucial for the phenotype and function of T(reg) cells. Foxp3, acting as a transcriptional repressor, directly suppressed the SATB1 locus and indirectly suppressed it through the induction of microRNAs that bound the SATB1 3' untranslated region. Release of SATB1 from the control of Foxp3 in T(reg) cells caused loss of suppressive function, establishment of transcriptional T(eff) cell programs and induction of T(eff) cell cytokines. Our data support the proposal that inhibition of SATB1-mediated modulation of global chromatin remodeling is pivotal for maintaining T(reg) cell functionality.
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MESH Headings
- 3' Untranslated Regions/genetics
- 3' Untranslated Regions/immunology
- Animals
- Cell Differentiation/drug effects
- Chromatin Assembly and Disassembly/drug effects
- Chromatin Assembly and Disassembly/immunology
- Flow Cytometry
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/immunology
- Forkhead Transcription Factors/metabolism
- Gene Expression Profiling
- Gene Expression Regulation
- Genome, Human
- Genome-Wide Association Study
- Humans
- Lentivirus
- Lymphocyte Activation/drug effects
- Matrix Attachment Region Binding Proteins/genetics
- Matrix Attachment Region Binding Proteins/immunology
- Matrix Attachment Region Binding Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- MicroRNAs/immunology
- MicroRNAs/metabolism
- MicroRNAs/pharmacology
- RNA Interference
- RNA, Small Interfering/immunology
- RNA, Small Interfering/metabolism
- RNA, Small Interfering/pharmacology
- Reverse Transcriptase Polymerase Chain Reaction
- Self Tolerance/drug effects
- Self Tolerance/genetics
- Self Tolerance/immunology
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Transduction, Genetic
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Affiliation(s)
- Marc Beyer
- Life and Medical Sciences Institute, Laboratory for Genomics and Immunoregulation, University of Bonn, Bonn, Germany
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31
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Human tonsil B-cell lymphoma 6 (BCL6)-expressing CD4+ T-cell subset specialized for B-cell help outside germinal centers. Proc Natl Acad Sci U S A 2011; 108:E488-97. [PMID: 21808017 DOI: 10.1073/pnas.1100898108] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T follicular helper (Tfh) cells represent a Th subset engaged in the help of B-cell responses in germinal centers (GCs). Tfh cells abundantly express the transcription repressor B-cell lymphoma 6 (Bcl6), a factor that is necessary and sufficient for their development in vivo. Whether Tfh or Tfh-committed cells are involved in the help of B cells outside GCs remains unclear, particularly in humans. In this study, we identified a previously undefined BCL6-expressing CD4(+) T-cell subset in human tonsils. This subset expressed IL-7 receptor and chemokine receptor 5 (CXCR5) and inducible costimulator (ICOS) at low levels (CXCR5(lo)ICOS(lo)), and it was found exclusively outside GCs. CXCR5(lo)ICOS(lo) CD4(+) T cells secreted larger amounts of IL-21 and IL-10 than CXCR5(hi)ICOS(hi) GC-Tfh cells upon activation, and they induced proliferation and differentiation of naïve B cells into Ig-producing cells more efficiently than GC-Tfh cells. However, this subset lacked the capacity to help GC-B cells because of the induction of apoptosis of GC-B cells through the FAS/FAS-ligand interaction. CXCR5(lo)ICOS(lo) CD4(+) T cells expressed equivalent amounts of BCL6 transcript with CXCR5(hi)ICOS(hi) GC-Tfh cells, but they expressed less Bcl6 protein. Collectively, our study indicates that CXCR5(lo)ICOS(lo) CD4(+) T cells in human tonsils represent Tfh lineage-committed cells that provide help to naïve and memory B cells outside GCs.
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Kashiwada M, Cassel SL, Colgan JD, Rothman PB. NFIL3/E4BP4 controls type 2 T helper cell cytokine expression. EMBO J 2011; 30:2071-82. [PMID: 21499227 DOI: 10.1038/emboj.2011.111] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 03/17/2011] [Indexed: 12/21/2022] Open
Abstract
Type 2 T helper (T(H)2) cells are critical for the development of allergic immune responses; however, the molecular mechanism controlling their effector function is still largely unclear. Here, we report that the transcription factor NFIL3/E4BP4 regulates cytokine production and effector function by T(H)2 cells. NFIL3 is highly expressed in T(H)2 cells but much less in T(H)1 cells. Production of interleukin (IL)-13 and IL-5 is significantly increased in Nfil3(-/-) T(H)2 cells and is decreased by expression of NFIL3 in wild-type T(H)2 cells. NFIL3 directly binds to and negatively regulates the Il13 gene. In contrast, IL-4 production is decreased in Nfil3(-/-) T(H)2 cells. Increased IL-13 and IL-5 together with decreased IL-4 production by antigen-stimulated splenocytes from the immunized Nfil3(-/-) mice was also observed. The ability of NFIL3 to alter T(H)2 cytokine production is a T-cell intrinsic effect. Taken together, these data indicate that NFIL3 is a key regulator of T(H)2 responses.
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Affiliation(s)
- Masaki Kashiwada
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
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Lei L, Lu L, Xiang L, Xue-song W, De-pei L, Chih-chuan L. Epigenetic repression of SATB1 by polycomb group protein EZH2 in epithelial cells. ACTA ACUST UNITED AC 2011; 25:199-205. [PMID: 21232178 DOI: 10.1016/s1001-9294(11)60002-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To study the regulatory mechanism of SATB1 repression in cells other than T cells or erythroid cells, which have high expression level of SATB1. METHODS HeLa epithelial cells were treated with either histone deacetylase inhibitor (HDACi) trichostatin A (TSA) or DNA methylation inhibitor 5-Aza-C before detecting SATB1 expression. Luciferase reporter system was applied to measure effects of EZH2 on SATB1 promoter activity. Over-expression or knockdown of EZH2 and subsequent quantitative reverse transcription-polymerase chain reaction were performed to determine the effect of this Polycomb group protein on SATB1 transcription. Chromatin immunoprecipitation (ChIP) assay was applied to measure enrichment of EZH2 and trimethylated H3K27 (H3K27me3) at SATB1 promoter in HeLa cells. K562 cells and Jurkat cells, both having high-level expression of SATB1, were used in the ChIP experiment as controls. RESULTS Both TSA and 5-Aza-C increased SATB1 expression in HeLa cells. Over-expression of EZH2 reduced promoter activity as well as the mRNA level of SATB1, while knockdown of EZH2 apparently enhanced SATB1 expression in HeLa cells but not in K562 cells and Jurkat cells. ChIP assay Results suggested that epigenetic silencing of SATB1 by EZH2 in HeLa cells was mediated by trimethylation modification of H3K27. In contrast, enrichment of EZH2 and H3K27me3 was not detected within proximal promoter region of SATB1 in either K562 or Jurkat cells. CONCLUSION SATB1 is a bona fide EZH2 target gene in HeLa cells and the repression of SATB1 by EZH2 may be mediated by trimethylation modification on H3K27.
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Affiliation(s)
- Li Lei
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
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34
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Motomura Y, Kitamura H, Hijikata A, Matsunaga Y, Matsumoto K, Inoue H, Atarashi K, Hori S, Watarai H, Zhu J, Taniguchi M, Kubo M. The transcription factor E4BP4 regulates the production of IL-10 and IL-13 in CD4+ T cells. Nat Immunol 2011; 12:450-9. [PMID: 21460847 DOI: 10.1038/ni.2020] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 03/10/2011] [Indexed: 12/14/2022]
Abstract
The immunoregulatory cytokine interleukin 10 (IL-10) is expressed mainly by T helper type 2 (T(H)2) cells but also by T(H)1 cells during chronic infection. Here we observed plasticity in the expression of IL-10 and IL-13 after chronic T(H)1 stimulation; furthermore, the expression of Il10 and Il13 was regulated by the transcription factor E4BP4. Chronically stimulated E4BP4-deficient (Nfil3(-/-); called 'E4bp4(-/-)' here) T(H)1 cells, regulatory T cells (T(reg) cells) and natural killer T cells (NKT cells) had attenuated expression of IL-10 and IL-13. Enforced expression of E4bp4 initiated the production of IL-10 and IL-13 by conventional T(H)1 cells. E4bp4(-/-) T(H)2 cells showed impairment of IL-10 production with no effect on IL-13. Our results indicate that E4BP4 has multiple functions in controlling the plasticity of IL-13 in T(H)1 cells and IL-10 in T(H)1 cells, T(H)2 cells, T(reg) cells and NKT cells.
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Affiliation(s)
- Yasutaka Motomura
- Laboratory for Signal Network, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Yokohama, Japan
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Abstract
The immune system faces the arduous task of defending the mucosal surfaces from invading pathogens, but must simultaneously repress responses against commensal organisms and other inert antigens that are abundant in the external environment, as inappropriate immune activation might expose the host to increased risk of autoimmunity. The behavior of individual immune cells is governed by the expression of transcription factors that are responsible for switching immune response genes on and off. T-bet (T-box expressed in T cells) has emerged as one of the key transcription factors responsible for controlling the fate of both innate and adaptive immune cells, and its expression in different immune cells found at mucosal surfaces is capable of dictating the critical balance between permitting robust host immunity and limiting susceptibility to autoimmunity and allergy.
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36
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The elusive identity of T follicular helper cells. Trends Immunol 2010; 31:377-83. [DOI: 10.1016/j.it.2010.07.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 06/29/2010] [Accepted: 07/19/2010] [Indexed: 12/12/2022]
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37
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van den Ham H, de Waal L, Andeweg A, de Boer R. Identification of helper T cell master regulator candidates using the polar score method. J Immunol Methods 2010; 361:98-109. [DOI: 10.1016/j.jim.2010.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 07/15/2010] [Accepted: 07/23/2010] [Indexed: 11/26/2022]
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38
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SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation. Blood 2010; 116:1443-53. [PMID: 20522714 DOI: 10.1182/blood-2009-11-252205] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor regulated by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. Here we show that SATB1 controls multiple IL-4 target genes involved in human Th cell polarization or function. Among the genes regulated by SATB1 is that encoding the cytokine IL-5, which is predominantly produced by Th2 cells and plays a key role in the development of eosinophilia in asthma. We demonstrate that, during the early Th2 cell differentiation, IL-5 expression is repressed through direct binding of SATB1 to the IL-5 promoter. Furthermore, SATB1 knockdown-induced up-regulation of IL-5 is partly counteracted by down-regulating GATA3 expression using RNAi in polarizing Th2 cells. Our results suggest that a competitive mechanism involving SATB1 and GATA3 regulates IL-5 transcription, and provide new mechanistic insights into the stringent regulation of IL-5 expression during human Th2 cell differentiation.
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Moulder R, Lönnberg T, Elo LL, Filén JJ, Rainio E, Corthals G, Oresic M, Nyman TA, Aittokallio T, Lahesmaa R. Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation. Mol Cell Proteomics 2010; 9:1937-53. [PMID: 20467038 PMCID: PMC2938108 DOI: 10.1074/mcp.m900483-mcp200] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We used stable isotope labeling with 4-plex iTRAQ (isobaric tags for relative and absolute quantification) reagents and LC-MS/MS to investigate proteomic changes in the nucleus of activated human CD4+ cells during the early stages of Th2 cell differentiation. The effects of IL-4 stimulation upon activated naïve CD4+ cells were measured in the nuclear fractions from 6 and 24 h in three biological replicates, each using pooled cord blood samples derived from seven or more individuals. In these analyses, in the order of 800 proteins were detected with two or more peptides and quantified in three biological replicates. In addition to consistent differences observed with the nuclear localization/expression of established human Th2 and Th1 markers, there were changes that suggested the involvement of several proteins either only recently reported or otherwise not known in this context. These included SATB1 and among the novel changes detected and validated an IL-4-induced increase in the level of YB1. This unique data set from human cord blood CD4+ T cells details an extensive list of protein determinations that compares with and complements previous data determined from the Jurkat cell nucleus.
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Abstract
Dendritic cells (DCs) orchestrate the innate and adaptive immune systems to induce tolerance and immunity. DC plasticity and subsets are prominent determinants in the regulation of immune responses. Our recent studies suggest that humoral and cellular immunity is regulated by different myeloid DC subsets with distinct intrinsic properties in humans. Although antibody response is preferentially mediated by CD14(+) dermal DCs, cytotoxic T-cell response is preferentially mediated by Langerhans cells (LCs). Thus, mechanisms whereby DCs induce humoral and cellular immunity seem to be fundamentally distinct. In this review, we will focus on the role of DCs in the development of humoral immunity. We will also discuss the mechanisms whereby DCs induce CD4(+) T cells associated with aiding B-cell response, including T follicular helper (Tfh) cells, and why human LCs lack this ability.
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Filén S, Ylikoski E, Tripathi S, West A, Björkman M, Nyström J, Ahlfors H, Coffey E, Rao KVS, Rasool O, Lahesmaa R. Activating transcription factor 3 is a positive regulator of human IFNG gene expression. THE JOURNAL OF IMMUNOLOGY 2010; 184:4990-9. [PMID: 20304822 DOI: 10.4049/jimmunol.0903106] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IL-12 and IL-18 are essential for Th1 differentiation, whereas the role of IFN-alpha in Th1 development is less understood. In this microarray-based study, we searched for genes that are regulated by IFN-alpha, IL-12, or the combination of IL-12 plus IL-18 during the early differentiation of human umbilical cord blood CD4(+) Th cells. Twenty-six genes were similarly regulated in response to treatment with IL-12, IFN-alpha, or the combination of IL-12 plus IL-18. These genes could therefore play a role in Th1 lineage decision. Transcription factor activating transcription factor (ATF) 3 was upregulated by these cytokines and selected for further study. Ectopic expression of ATF3 in CD4(+) T cells enhanced the production of IFN-gamma, the hallmark cytokine of Th1 cells, whereas small interfering RNA knockdown of ATF3 reduced IFN-gamma production. Furthermore, ATF3 formed an endogenous complex with JUN in CD4(+) T cells induced to Th1. Chromatin immunoprecipitation and luciferase reporter assays showed that both ATF3 and JUN are recruited to and transactivate the IFNG promoter during early Th1 differentiation. Collectively, these data indicate that ATF3 promotes human Th1 differentiation.
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Affiliation(s)
- Sanna Filén
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, P.O. Box 123, FI-20521 Turku, Finland
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42
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Notani D, Gottimukkala KP, Jayani RS, Limaye AS, Damle MV, Mehta S, Purbey PK, Joseph J, Galande S. Global regulator SATB1 recruits beta-catenin and regulates T(H)2 differentiation in Wnt-dependent manner. PLoS Biol 2010; 8:e1000296. [PMID: 20126258 PMCID: PMC2811152 DOI: 10.1371/journal.pbio.1000296] [Citation(s) in RCA: 164] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 12/16/2009] [Indexed: 12/24/2022] Open
Abstract
Chromatin organizer SATB1 and Wnt transducer β-catenin form a complex and regulate expression of GATA3 and TH2 cytokines in Wnt-dependent manner and orchestrate TH2 lineage commitment. In vertebrates, the conserved Wnt signalling cascade promotes the stabilization and nuclear accumulation of β-catenin, which then associates with the lymphoid enhancer factor/T cell factor proteins (LEF/TCFs) to activate target genes. Wnt/β -catenin signalling is essential for T cell development and differentiation. Here we show that special AT-rich binding protein 1 (SATB1), the T lineage-enriched chromatin organizer and global regulator, interacts with β-catenin and recruits it to SATB1's genomic binding sites. Gene expression profiling revealed that the genes repressed by SATB1 are upregulated upon Wnt signalling. Competition between SATB1 and TCF affects the transcription of TCF-regulated genes upon β-catenin signalling. GATA-3 is a T helper type 2 (TH2) specific transcription factor that regulates production of TH2 cytokines and functions as TH2 lineage determinant. SATB1 positively regulated GATA-3 and siRNA-mediated knockdown of SATB1 downregulated GATA-3 expression in differentiating human CD4+ T cells, suggesting that SATB1 influences TH2 lineage commitment by reprogramming gene expression. In the presence of Dickkopf 1 (Dkk1), an inhibitor of Wnt signalling, GATA-3 is downregulated and the expression of signature TH2 cytokines such as IL-4, IL-10, and IL-13 is reduced, indicating that Wnt signalling is essential for TH2 differentiation. Knockdown of β-catenin also produced similar results, confirming the role of Wnt/β-catenin signalling in TH2 differentiation. Furthermore, chromatin immunoprecipitation analysis revealed that SATB1 recruits β-catenin and p300 acetyltransferase on GATA-3 promoter in differentiating TH2 cells in a Wnt-dependent manner. SATB1 coordinates TH2 lineage commitment by reprogramming gene expression. The SATB1:β-catenin complex activates a number of SATB1 regulated genes, and hence this study has potential to find novel Wnt responsive genes. These results demonstrate that SATB1 orchestrates TH2 lineage commitment by mediating Wnt/β-catenin signalling. This report identifies a new global transcription factor involved in β-catenin signalling that may play a major role in dictating the functional outcomes of this signalling pathway during development, differentiation, and tumorigenesis. In vertebrates the canonical Wnt signalling culminates in β-catenin moving into the nucleus where it activates transcription of target genes. Wnt/β-catenin signalling is essential for the thymic maturation and differentiation of naïve T cells. Here we show that SATB1, a T cell lineage-enriched chromatin organizer and global regulator, binds to β-catenin and recruits it to SATB1's genomic binding sites so that genes formerly repressed by SATB1 are upregulated by Wnt signalling. Some of the genes known to be regulated by SATB1 (such as genes encoding cytokines and the transcription factor GATA3) are required for differentiation of Th2 cells, an important subset of helper T cells. Specifically we show that siRNA-mediated knockdown of SATB1 downregulated GATA-3 expression in differentiating human CD4+ T cells. Inhibiting Wnt signalling led to downregulation of GATA-3 and of signature TH2 cytokines such as IL-4, IL-10, and IL-13. Knockdown of β-catenin also produced similar results, thus together these data confirm the role of Wnt/β-catenin signalling in TH2 differentiation. Our data demonstrate that SATB1 orchestrates TH2 lineage commitment by modulating Wnt/β-catenin signalling.
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Affiliation(s)
- Dimple Notani
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | | | | | | | | | - Sameet Mehta
- National Centre for Cell Science, Ganeshkhind, Pune, India
- Centre for Modelling and Simulation, University of Pune, Ganeshkhind, Pune, India
| | | | - Jomon Joseph
- National Centre for Cell Science, Ganeshkhind, Pune, India
| | - Sanjeev Galande
- National Centre for Cell Science, Ganeshkhind, Pune, India
- * E-mail:
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43
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Teng SL, Huang H. A Statistical Framework to Infer Functional Gene Relationships From Biologically Interrelated Microarray Experiments. J Am Stat Assoc 2009. [DOI: 10.1198/jasa.2009.0037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Srivastava D, Arora N, Singh BP. Current immunological approaches for management of allergic rhinitis and bronchial asthma. Inflamm Res 2009; 58:523-36. [PMID: 19333724 DOI: 10.1007/s00011-009-0033-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 02/18/2009] [Accepted: 03/12/2009] [Indexed: 01/15/2023] Open
Abstract
A large population world over is affected with allergic diseases and asthma. Pharmacotherapy for allergic diseases and asthma is effective in controlling symptoms but on discontinuation of medication, symptoms reoccur. In contrast, immunotherapy modifies and corrects the underlying pathological immune responses in an antigen-specific manner. Immunotherapy shows an increase in IgG (blocking antibody) that competes with IgE for allergen, inhibiting the release of inflammatory mediators. Recent studies suggest that immunotherapy acts by modifying CD4+ T-cell responses either by immune deviation, T-cell anergy and/or both. Current immunological approaches for management of allergies and asthma involve immunization with native allergen, modified allergen, peptides/cDNA of allergen, anti-IgE, adjuvants coupled allergen, including immunostimulatory DNA sequences, cytokines, and bacterial products. These approaches modulate the immune response and are intended to give long-term benefit.
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Affiliation(s)
- Deepsikha Srivastava
- Allergy and Immunology Section, Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110007, India
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45
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Filén JJ, Filén S, Moulder R, Tuomela S, Ahlfors H, West A, Kouvonen P, Kantola S, Björkman M, Katajamaa M, Rasool O, Nyman TA, Lahesmaa R. Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation. Mol Cell Proteomics 2008; 8:32-44. [PMID: 18701445 DOI: 10.1074/mcp.m800139-mcp200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
T helper (Th) cells differentiate into functionally distinct effector cell subsets of which Th1 and Th2 cells are best characterized. Besides T cell receptor signaling, IL-12-induced STAT4 and T-bet- and IL-4-induced STAT6 and GATA3 signaling pathways are the major players regulating the Th1 and Th2 differentiation process, respectively. However, there are likely to be other yet unknown factors or pathways involved. In this study we used quantitative proteomics exploiting cleavable ICAT labeling and LC-MS/MS to identify IL-4-regulated proteins from the microsomal fractions of CD4(+) cells extracted from umbilical cord blood. We were able to identify 557 proteins of which 304 were also quantified. This study resulted in the identification of the down-regulation of small GTPases GIMAP1 and GIMAP4 by IL-4 during Th2 differentiation. We also showed that both GIMAP1 and GIMAP4 genes are up-regulated by IL-12 and other Th1 differentiation-inducing cytokines in cells induced to differentiate toward Th1 lineage and down-regulated by IL-4 in cells induced to Th2. Our results indicate that the GIMAP (GTPase of the immunity-associated protein) family of proteins is differentially regulated during Th cell differentiation.
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Affiliation(s)
- Jan-Jonas Filén
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Tykistökatu 6B, FI-20520 Turku, Finland
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46
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Rowell E, Merkenschlager M, Wilson CB. Long-range regulation of cytokine gene expression. Curr Opin Immunol 2008; 20:272-80. [PMID: 18485687 DOI: 10.1016/j.coi.2008.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Revised: 03/01/2008] [Accepted: 03/25/2008] [Indexed: 11/30/2022]
Abstract
In metazoans, transcription is regulated by promoters and additional elements, which may be located far from their target gene(s). Moreover, genes (including those encoding cytokines and cytokine receptors) are commonly clustered in the genome, providing the opportunity for the shared, competitive, or sequential use of regulatory elements. New techniques, discussed here, are generating an avalanche of high-resolution genome-wide data through which candidate regulatory elements have been identified in specific cell types (including T cells), their functions inferred, and their physical interactions in three-dimensional space demonstrated. As a result, a nearly comprehensive list of regulatory elements in the Th2 cytokine locus, a growing list of elements in the interferon-gamma gene locus, and maps of their three-dimensional interactions are now available, though much remains to be learned about the molecular mechanisms at play, the dynamics of these interactions, and their functional importance.
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Affiliation(s)
- Emily Rowell
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
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47
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Huarcaya E, Maguina C, Best I, Solorzano N, Leeman L. Immunological response in cases of complicated and uncomplicated bartonellosis during pregnancy. Rev Inst Med Trop Sao Paulo 2008; 49:335-7. [PMID: 18026643 DOI: 10.1590/s0036-46652007000500012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 03/26/2007] [Indexed: 11/21/2022] Open
Abstract
Bartonellosis (Carrion's Disease) during pregnancy is associated with high rates of maternal and perinatal mortality. We report the immunological patterns in two cases of human bartonellosis during pregnancy. One patient had an uncomplicated course while the second patient developed life threatening anasarca and cardiac tamponade. The patient with a complicated course had a Th1 response with a higher elevation of IL-10. This elevation has been associated with poor outcome pregnancies during bacterial infections.
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Affiliation(s)
- Erick Huarcaya
- Department of Family & Community Medicine, University of New Mexico, Albuquerque, NM 87131-0001, USA.
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48
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Histone acetylation and DNA demethylation of B cells result in a Hodgkin-like phenotype. Leukemia 2008; 22:835-41. [PMID: 18256685 DOI: 10.1038/leu.2008.12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A unique feature of the tumor cells (Hodgkin/Reed-Sternberg (HRS)) of classical Hodgkin lymphoma (cHL) is the loss of their B-cell phenotype despite their B-cell origin. Several lines of evidence suggest that epigenomic events, especially promoter DNA methylation, are involved in this silencing of many B-cell-associated genes. Here, we show that DNA demethylation alone or in conjunction with histone acetylation is not able to reconstitute the B-cell-gene expression program in cultured HRS cells. Instead, combined DNA demethylation and histone acetylation of B-cell lines induce an almost complete extinction of their B-cell-expression program and a tremendous upregulation of numerous Hodgkin-characteristic genes, including key players such as Id2 known to be involved in the suppression of the B-cell phenotype. Since the upregulation of Hodgkin-characteristic genes and the extinction of the B-cell-expression program occurred simultaneously, epigenetic changes may also be responsible for the malignant transformation of cHL. The epigenetic upregulation of Hodgkin-characteristic genes thus plays--in addition to promoter DNA hypermethylation of B-cell-associated genes--a pivotal role for the reprogramming of HRS cells and explains why DNA demethylation alone is unable to reconstitute the B-cell-expression program in HRS cells.
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49
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Rautajoki KJ, Kylaniemi MK, Raghav SK, Rao K, Lahesmaa R. An insight into molecular mechanisms of human T helper cell differentiation. Ann Med 2008; 40:322-35. [PMID: 18484344 DOI: 10.1080/07853890802068582] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Selective activation of T helper (Th) cell subsets plays an important role in immune response to pathogens as well as in the pathogenesis of human allergy and inflammatory diseases. Th1 cells along with the recently discovered Th17 cells play a role in the pathogenesis of autoimmune diseases. Th2 cytokines lead to series of inflammatory processes characteristic for asthma and other atopic diseases. To understand the pathogenesis of immune-mediated diseases it is crucial to dissect pathways and regulatory networks leading to the development of distinct Th subsets. Such knowledge may lead to better strategies for developing diagnostics and therapies for these diseases. The differentiation of Th1, Th2, and Th17 effector cells is driven by signals originating from T cell and costimulatory receptors as well as cytokines in the surroundings of activated naive T helper cells. There are several proteins involved in the regulation of this differentiation process. Most of the data on T helper cell differentiation have been acquired using mouse. In this review, we have summarized what is known about human T helper differentiation. In addition, selected differences between human and mouse will be discussed.
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Affiliation(s)
- Kirsi J Rautajoki
- Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland
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50
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Sivertsen EA, Huse K, Hystad ME, Kersten C, Smeland EB, Myklebust JH. Inhibitory effects and target genes of bone morphogenetic protein 6 in Jurkat TAg cells. Eur J Immunol 2007; 37:2937-48. [PMID: 17899540 DOI: 10.1002/eji.200636759] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bone morphogenetic proteins (BMP) are multifunctional cytokines that belong to the TGF-beta superfamily. BMP have been shown to regulate haematopoietic stem cells, B lymphopoiesis and early thymocyte differentiation. In the present study we explored the role of BMP-6 in Jurkat TAg cells. BMP-6 rapidly induced phosphorylation of Smad1/5/8, p38 and ERK1/2, followed by a potent up-regulation of ID1, ID2 and ID3. ID1 and ID3 were also induced at the protein level. Genome-wide expression profiling of cells treated with BMP-6 compared to medium confirmed that ID1-ID3 were target genes of BMP-6 together with Noggin and Smad6. Furthermore, several genes involved in transcriptional regulation were also identified, including NFKBIA, HEY1, DLX2, KLF10 and early growth response 1. Stimulation with BMP-6 exerted an antiproliferative effect that was counteracted by inhibitor of DNA binding (Id)1 siRNA, indicating that Id1 is an important downstream mediator in Jurkat TAg cells. A subset of CD4(+) T cells were found to express the BMP receptors Alk-2 and Alk-3 (type I), in addition to BMPRII (type II). BMP-6 also induced phosphorylation of Smad1/5/8, followed by transcriptional increase in ID1-ID3 mRNA expression. However, we did not observe significant changes in Id protein expression in CD4(+) T cells. Altogether, the data indicate a role for BMP-6 in human T lineage cells.
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Affiliation(s)
- Einar A Sivertsen
- Department of Immunology, Institute of Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
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