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Chen S, Huan X, Xu C, Luo S, Zhao C, Zhong H, Zheng X, Qiao K, Dong Y, Wang Y, Liu C, Huang H, Chen Y, Zou Z. Eomesodermin expression in CD4 +T-cells associated with disease progression in amyotrophic lateral sclerosis. CNS Neurosci Ther 2024; 30:e14503. [PMID: 37850654 PMCID: PMC11017423 DOI: 10.1111/cns.14503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
AIM To clarify the role of Eomesodermin (EOMES) to serve as a disease-relevant biomarker and the intracellular molecules underlying the immunophenotype shifting of CD4+T subsets in amyotrophic lateral sclerosis (ALS). METHODS The derivation and validation cohorts included a total of 148 ALS patients and 101 healthy controls (HCs). Clinical data and peripheral blood were collected. T-cell subsets and the EOMES expression were quantified using multicolor flow cytometry. Serum neurofilament light chain (NFL) was measured. In 1-year longitudinal follow-ups, the ALSFRS-R scores and primary endpoint events were further recorded in the ALS patients of the validation cohort. RESULTS In the derivation cohort, the CD4+EOMES+T-cell subsets were significantly increased (p < 0.001). EOMES+ subset was positively correlated with increased serum NFL levels in patients with onset longer than 12 months. In the validation cohort, the elevated CD4+EOMES+T-cell proportions and their association with NFL levels were also identified. The longitudinal study revealed that ALS patients with higher EOMES expression were associated with higher progression rates (p = .010) and worse prognosis (p = .003). CONCLUSIONS We demonstrated that increased CD4+EOMES+T-cell subsets in ALS were associated with disease progression and poor prognosis. Identifying these associations may contribute to a better understanding of the immunopathological mechanism of ALS.
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Affiliation(s)
- Sheng Chen
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Institute of Clinical NeurologyFujian Medical UniversityFuzhouChina
| | - Xiao Huan
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Chun‐Zuan Xu
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Institute of Clinical NeurologyFujian Medical UniversityFuzhouChina
| | - Su‐Shan Luo
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Chong‐Bo Zhao
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Hua‐Hua Zhong
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Xue‐Ying Zheng
- Department of Biostatistics, School of Public Health and Key Laboratory of Public Health SafetyFudan UniversityShanghaiChina
| | - Kai Qiao
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Yi Dong
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Ying Wang
- Department of PharmacyFudan University Huashan HospitalShanghaiChina
| | - Chang‐Yun Liu
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Institute of Clinical NeurologyFujian Medical UniversityFuzhouChina
| | - Hua‐Pin Huang
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Institute of Clinical NeurologyFujian Medical UniversityFuzhouChina
| | - Yan Chen
- Huashan Rare Disease Center and Department of NeurologyHuashan Hospital, Shanghai Medical College, National Center for Neurological Disorders, Fudan UniversityShanghaiChina
| | - Zhang‐Yu Zou
- Department of NeurologyFujian Medical University Union HospitalFuzhouChina
- Institute of Clinical NeurologyFujian Medical UniversityFuzhouChina
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Pulvirenti N, Silvetri Y, Clemente F, Bosotti R, Carelli E, Moschetti G, Gruarin P, Vasco C, Crosti MC, Sarnicola ML, Valenti L, Prati D, Abrignani S, Geginat J. Characterization of human CD4 +EOMES +GzmK + T-cell subsets unveils an uncoupling of suppressive functions from IL-10-producing capacities. Eur J Immunol 2024; 54:e2350675. [PMID: 38396108 DOI: 10.1002/eji.202350675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/25/2024]
Abstract
Human CD4+EOMES+ T cells are heterogeneous and contain Th1-cells, Tr1-cells, and CD4+CTL. Tr1- cells and non-classical EOMES+ Th1-cells displayed, respectively, anti- and pro-inflammatory cytokine profiles, but both expressed granzyme-K, produced IFN-γ, and suppressed T-cell proliferation. Diffusion map suggested a progressive CD4+T-cell differentiation from naïve to cytotoxic cells and identified EOMES+Th1-cells as putative Tr1-cell precursors (pre-Tr1).
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Affiliation(s)
- Nadia Pulvirenti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Ylenia Silvetri
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Francesca Clemente
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Roberto Bosotti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Elena Carelli
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Giorgia Moschetti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Pharmaceutical Sciences (DISFARM), Università degli Studi, Milan, Italy
| | - Paola Gruarin
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Chiara Vasco
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Cristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Lucia Sarnicola
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Luca Valenti
- Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Biological Resource Center Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi, Milan, Italy
| | - Jens Geginat
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi, Milan, Italy
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3
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Cepika AM, Amaya L, Waichler C, Narula M, Mantilla MM, Thomas BC, Chen PP, Freeborn RA, Pavel-Dinu M, Nideffer J, Porteus M, Bacchetta R, Müller F, Greenleaf WJ, Chang HY, Roncarolo MG. Epigenetic signature and key transcriptional regulators of human antigen-specific type 1 regulatory T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.582969. [PMID: 38559096 PMCID: PMC10979855 DOI: 10.1101/2024.03.07.582969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Human adaptive immunity is orchestrated by effector and regulatory T (Treg) cells. Natural Tregs arise in the thymus where they are shaped to recognize self-antigens, while type 1 Tregs or Tr1 cells are induced from conventional peripheral CD4 + T cells in response to peripheral antigens, such as alloantigens and allergens. Tr1 cells have been developed as a potential therapy for inducing antigen-specific tolerance, because they can be rapidly differentiated in vitro in response to a target antigen. However, the epigenetic landscape and the identity of transcription factors (TFs) that regulate differentiation, phenotype, and functions of human antigen-specific Tr1 cells is largely unknown, hindering Tr1 research and broader clinical development. Here, we reveal the unique epigenetic signature of antigen-specific Tr1 cells, and TFs that regulate their differentiation, phenotype and function. We showed that in vitro induced antigen-specific Tr1 cells are distinct both clonally and transcriptionally from natural Tregs and other conventional CD4 + T cells on a single-cell level. An integrative analysis of Tr1 cell epigenome and transcriptome identified a TF signature unique to antigen-specific Tr1 cells, and predicted that IRF4, BATF, and MAF act as their transcriptional regulators. Using functional genomics, we showed that each of these TFs play a non-redundant role in regulating Tr1 cell differentiation, suppressive function, and expression of co-inhibitory and cytotoxic proteins. By using the Tr1-specific TF signature as a molecular fingerprint, we tracked Tr1 cells in peripheral blood of recipients of allogeneic hematopoietic stem cell transplantation treated with adoptive Tr1 cell therapy. Furthermore, the same signature identified Tr1 cells in resident CD4 + T cells in solid tumors. Altogether, these results reveal the epigenetic signature and the key transcriptional regulators of human Tr1 cells. These data will guide mechanistic studies of human Tr1 cell biology and the development and optimization of adoptive Tr1 cell therapies.
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4
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Joulia E, Michieletto MF, Agesta A, Peillex C, Girault V, Le Dorze AL, Peroceschi R, Bucciarelli F, Szelechowski M, Chaubet A, Hakim N, Marrocco R, Lhuillier E, Lebeurrier M, Argüello RJ, Saoudi A, El Costa H, Adoue V, Walzer T, Sarry JE, Dejean AS. Eomes-dependent mitochondrial regulation promotes survival of pathogenic CD4+ T cells during inflammation. J Exp Med 2024; 221:e20230449. [PMID: 38189779 PMCID: PMC10772920 DOI: 10.1084/jem.20230449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/02/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
The mechanisms whereby Eomes controls tissue accumulation of T cells and strengthens inflammation remain ill-defined. Here, we show that Eomes deletion in antigen-specific CD4+ T cells is sufficient to protect against central nervous system (CNS) inflammation. While Eomes is dispensable for the initial priming of CD4+ T cells, it is required for long-term maintenance of CNS-infiltrating CD4+ T cells. We reveal that the impact of Eomes on effector CD4+ T cell longevity is associated with sustained expression of multiple genes involved in mitochondrial organization and functions. Accordingly, epigenetic studies demonstrate that Eomes supports mitochondrial function by direct binding to either metabolism-associated genes or mitochondrial transcriptional modulators. Besides, the significance of these findings was confirmed in CD4+ T cells from healthy donors and multiple sclerosis patients. Together, our data reveal a new mechanism by which Eomes promotes severity and chronicity of inflammation via the enhancement of CD4+ T cell mitochondrial functions and resistance to stress-induced cell death.
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Affiliation(s)
- Emeline Joulia
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Michaël F. Michieletto
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arantxa Agesta
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Cindy Peillex
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Virginie Girault
- Suivi Immunologique des Thérapeutiques Innovantes, Pôle de Biologie, Pontchaillou University Hospital, Rennes, France
- UMR1236, University of Rennes, Institut National de la Santé et de la Recherche Médicale, Etablissement Français du Sang Bretagne, Rennes, France
| | - Anne-Louise Le Dorze
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Romain Peroceschi
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Florence Bucciarelli
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Marion Szelechowski
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Adeline Chaubet
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Nawad Hakim
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Rémi Marrocco
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Emeline Lhuillier
- GeT-Santé, Plateforme Génome et Transcriptome, GenoToul, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires, Institut National de la Santé et de la Recherche Médicale, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Manuel Lebeurrier
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Rafael J. Argüello
- Aix Marseille University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Abdelhadi Saoudi
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Hicham El Costa
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Veronique Adoue
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale U1111, Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, UMR5308, Lyon, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, UMR1037, Institut National de la Santé et de la Recherche Médicale, Toulouse, France
| | - Anne S. Dejean
- Institut Toulousain des Maladies Infectieuses et Inflammatoires, Institut National de la Santé et de la Recherche Médicale UMR1291, Centre National de la Recherche Scientifique UMR5051, Université Toulouse III, Toulouse, France
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5
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Sur M, Rasquinha MT, Mone K, Massilamany C, Lasrado N, Gurumurthy C, Sobel RA, Reddy J. Investigation into Cardiac Myhc-α 334-352-Specific TCR Transgenic Mice Reveals a Role for Cytotoxic CD4 T Cells in the Development of Cardiac Autoimmunity. Cells 2024; 13:234. [PMID: 38334626 PMCID: PMC10854502 DOI: 10.3390/cells13030234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Myocarditis is one of the major causes of heart failure in children and young adults and can lead to dilated cardiomyopathy. Lymphocytic myocarditis could result from autoreactive CD4+ and CD8+ T cells, but defining antigen specificity in disease pathogenesis is challenging. To address this issue, we generated T cell receptor (TCR) transgenic (Tg) C57BL/6J mice specific to cardiac myosin heavy chain (Myhc)-α 334-352 and found that Myhc-α-specific TCRs were expressed in both CD4+ and CD8+ T cells. To investigate if the phenotype is more pronounced in a myocarditis-susceptible genetic background, we backcrossed with A/J mice. At the fourth generation of backcrossing, we observed that Tg T cells from naïve mice responded to Myhc-α 334-352, as evaluated by proliferation assay and carboxyfluorescein succinimidyl ester staining. The T cell responses included significant production of mainly pro-inflammatory cytokines, namely interferon (IFN)-γ, interleukin-17, and granulocyte macrophage-colony stimulating factor. While the naïve Tg mice had isolated myocardial lesions, immunization with Myhc-α 334-352 led to mild myocarditis, suggesting that further backcrossing to increase the percentage of A/J genome close to 99.99% might show a more severe disease phenotype. Further investigations led us to note that CD4+ T cells displayed the phenotype of cytotoxic T cells (CTLs) akin to those of conventional CD8+ CTLs, as determined by the expression of CD107a, IFN-γ, granzyme B natural killer cell receptor (NKG)2A, NKG2D, cytotoxic and regulatory T cell molecules, and eomesodermin. Taken together, the transgenic system described in this report may be a helpful tool to distinguish the roles of cytotoxic cardiac antigen-specific CD4+ T cells vs. those of CD8+ T cells in the pathogenesis of myocarditis.
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Affiliation(s)
- Meghna Sur
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
| | - Mahima T. Rasquinha
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
| | - Kiruthiga Mone
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
| | - Chandirasegaran Massilamany
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
- CRISPR Therapeutics, Boston, MA 02127, USA
| | - Ninaad Lasrado
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
- Center for Virology and Vaccine Research, Harvard Medical School, Boston, MA 02115, USA
| | - Channabasavaiah Gurumurthy
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Raymond A. Sobel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA;
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; (M.S.); (M.T.R.); (K.M.); (C.M.); (N.L.)
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Hausmann F, Ergen C, Khatri R, Marouf M, Hänzelmann S, Gagliani N, Huber S, Machart P, Bonn S. DISCERN: deep single-cell expression reconstruction for improved cell clustering and cell subtype and state detection. Genome Biol 2023; 24:212. [PMID: 37730638 PMCID: PMC10510283 DOI: 10.1186/s13059-023-03049-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering and cell type identification. RESULTS Here, we present DISCERN, a novel deep generative network that precisely reconstructs missing single-cell gene expression using a reference dataset. DISCERN outperforms competing algorithms in expression inference resulting in greatly improved cell clustering, cell type and activity detection, and insights into the cellular regulation of disease. We show that DISCERN is robust against differences between batches and is able to keep biological differences between batches, which is a common problem for imputation and batch correction algorithms. We use DISCERN to detect two unseen COVID-19-associated T cell types, cytotoxic CD4+ and CD8+ Tc2 T helper cells, with a potential role in adverse disease outcome. We utilize T cell fraction information of patient blood to classify mild or severe COVID-19 with an AUROC of 80% that can serve as a biomarker of disease stage. DISCERN can be easily integrated into existing single-cell sequencing workflow. CONCLUSIONS Thus, DISCERN is a flexible tool for reconstructing missing single-cell gene expression using a reference dataset and can easily be applied to a variety of data sets yielding novel insights, e.g., into disease mechanisms.
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Affiliation(s)
- Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Can Ergen
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Mohamed Marouf
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Samuel Huber
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Pierre Machart
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
- Hamburg Center for Translational Immunology (HCTI), I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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7
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Lu C, Li S, Qing P, Zhang Q, Ji X, Tang Z, Chen C, Wu T, Hu Y, Zhao Y, Zhang X, He Q, Fox DA, Tan C, Luo Y, Liu Y. Single-cell transcriptome analysis and protein profiling reveal broad immune system activation in IgG4-related disease. JCI Insight 2023; 8:e167602. [PMID: 37561593 PMCID: PMC10544205 DOI: 10.1172/jci.insight.167602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
IgG4-related disease (IgG4-RD) is a systemic autoimmune disease with unclear pathogenesis. We performed single-cell RNA-seq and surface proteome analyses on 61,379 PBMCs from 9 treatment-naive IgG4-RD patients and 7 age- and sex-matched healthy controls. Integrative analyses were performed for altered gene expression in IgG4-RD, and flow cytometry and immunofluorescence were used for validation. We observed expansion of plasmablasts with enhanced protein processing and activation, which correlated with the number of involved organs in IgG4-RD. Increased proportions of CD4+ cytotoxic T lymphocytes (CTLs), CD8+ CTLs-GNLY (granulysin), and γδT cells with enhanced chemotaxis and cytotoxicity but with suppressed inhibitory receptors characterize IgG4-RD. Prominent infiltration of lymphocytes with distinct compositions were found in different organs of IgG4-RD patients. Transcription factors (TFs), including PRDM1/XBP1 and RUNX3, were upregulated in IgG4-RD, promoting the differentiation of plasmablasts and CTLs, respectively. Monocytes in IgG4-RD have stronger expression of genes related to cell adhesion and chemotaxis, which may give rise to profibrotic macrophages in lesions. The gene activation pattern in peripheral immune cells indicated activation of multiple interaction pathways between cell types, in part through chemokines or growth factors and their receptors. Specific upregulation of TFs and expansion of plasmablasts and CTLs may be involved in the pathogenesis of IgG4-RD, and each of these populations are candidate targets for therapeutic interventions in this disease.
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Affiliation(s)
- Chenyang Lu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
- Division of Rheumatology, Department of Internal Medicine, and
| | - Shasha Li
- Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Pingying Qing
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiuping Zhang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Xing Ji
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhigang Tang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Chunyan Chen
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Tong Wu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yidan Hu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Zhao
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohui Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qi He
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - David A. Fox
- Division of Rheumatology and Clinical Autoimmunity Center of Excellence, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Chunyu Tan
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yubin Luo
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
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8
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Khired ZA, Kattan SW, Alzahrani AK, Milebary AJ, Hussein MH, Qusti SY, Alshammari EM, Toraih EA, Fawzy MS. Analysis of MIR27A (rs11671784) Variant Association with Systemic Lupus Erythematous. Life (Basel) 2023; 13:701. [PMID: 36983856 PMCID: PMC10058767 DOI: 10.3390/life13030701] [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: 01/29/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Multiple microRNAs (miRs) are associated with systemic autoimmune disease susceptibility/phenotype, including systemic lupus erythematosus (SLE). With this work, we aimed to unravel the association of the miR-27a gene (MIR27A) rs11671784G/A variant with SLE risk/severity. One-hundred sixty-three adult patients with SLE and matched controls were included. A TaqMan allelic discrimination assay was applied for MIR27A genotyping. Logistic regression models were run to test the association with SLE susceptibility/risk. Genotyping of 326 participants revealed that the heterozygote form was the most common genotype among the study cohort, accounting for 72% of the population (n = 234), while A/A and G/G represented 15% (n = 49) and 13% (n = 43), respectively. Similarly, the most prevalent genotype among cases was the A/G genotype, which was present in approximately 93.3% of cases (n = 152). In contrast, only eight and three patients had A/A and G/G genotypes, respectively. The MIR27A rs11671784 variant conferred protection against the development of SLE in several genetic models, including heterozygous (G/A vs. A/A; OR = 0.10, 95% CI = 0.05-0.23), dominant (G/A + G/G vs. AA; OR = 0.15, 95% CI = 0.07-0.34), and overdominant (G/A vs. A/A + G/G; OR = 0.07, 95% CI = 0.04-0.14) models. However, the G/G genotype was associated with increased SLE risk in the recessive model (G/G vs. A/A+ G/G; OR = 17.34, 95% CI = 5.24-57.38). Furthermore, the variant showed significant associations with musculoskeletal and mucocutaneous manifestations in the patient cohort (p = 0.035 and 0.009, respectively) and platelet and white blood cell counts (p = 0.034 and 0.049, respectively). In conclusion, the MIR27A rs11671784 variant showed a potentially significant association with SLE susceptibility/risk in the studied population. Larger-scale studies on multiethnic populations are recommended to verify the results.
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Affiliation(s)
- Zenat Ahmed Khired
- Department of Surgery, College of Medicine, Jazan University, Jazan 45142, Saudi Arabia
| | - Shahad W. Kattan
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu 46423, Saudi Arabia
| | - Ahmad Khuzaim Alzahrani
- Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar 91431, Saudi Arabia
| | - Ahmad J. Milebary
- Department of Medical Laboratory, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammad H. Hussein
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Safaa Y. Qusti
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Eida M. Alshammari
- Department of Chemistry, College of Sciences, University of Ha’il, Ha’il 2440, Saudi Arabia
| | - Eman A. Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Medical Genetics Unit, Department of Histology and Cell Biology, Suez Canal University, Ismailia 41522, Egypt
| | - Manal S. Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 1321, Saudi Arabia
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9
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Crosstalk of Transcriptional Regulators of Adaptive Immune System and microRNAs: An Insight into Differentiation and Development. Cells 2023; 12:cells12040635. [PMID: 36831302 PMCID: PMC9953855 DOI: 10.3390/cells12040635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
MicroRNAs (miRNAs), as small regulatory RNA molecules, are involved in gene expression at the post-transcriptional level. Hence, miRNAs contribute to gene regulation of various steps of different cell subsets' differentiation, maturation, and activation. The adaptive immune system arm, which exhibits the most specific immune responses, is also modulated by miRNAs. The generation and maturation of various T-cell subsets concomitant with B-cells is under precise regulation of miRNAs which function directly on the hallmark genes of each cell subset or indirectly through regulation of signaling pathway mediators and/or transcription factors involved in this maturation journey. In this review, we first discussed the origination process of common lymphocyte progenitors from hematopoietic stem cells, which further differentiate into various T-cell subsets under strict regulation of miRNAs and transcription factors. Subsequently, the differentiation of B-cells from common lymphocyte progenitors in bone marrow and periphery were discussed in association with a network of miRNAs and transcription factors.
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10
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Thelen B, Schipperges V, Knörlein P, Hummel JF, Arnold F, Kupferschmid L, Klose CSN, Arnold SJ, Boerries M, Tanriver Y. Eomes is sufficient to regulate IL-10 expression and cytotoxic effector molecules in murine CD4 + T cells. Front Immunol 2023; 14:1058267. [PMID: 36756120 PMCID: PMC9901365 DOI: 10.3389/fimmu.2023.1058267] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
The T-box transcription factors T-bet and Eomesodermin regulate type 1 immune responses in innate and adaptive lymphocytes. T-bet is widely expressed in the immune system but was initially identified as the lineage-specifying transcription factor of Th1 CD4+ T cells, where it governs expression of the signature cytokine IFN- γ and represses alternative cell fates like Th2 and Th17. T-bet's paralog Eomes is less abundantly expressed and Eomes+ CD4+ T cells are mostly found in the context of persistent antigen exposure, like bone marrow transplantation, chronic infection or inflammation as well as malignant disorders. However, it has remained unresolved whether Eomes executes similar transcriptional activities as T-bet in CD4+ T cells. Here we use a novel genetic approach to show that Eomes expression in CD4+ T cells drives a distinct transcriptional program that shows only partial overlap with T-bet. We found that Eomes is sufficient to induce the expression of the immunoregulatory cytokine IL-10 and, together with T-bet, promotes a cytotoxic effector profile, including Prf1, Gzmb, Gzmk, Nkg7 and Ccl5, while repressing alternative cell fates. Our results demonstrate that Eomes+ CD4+ T cells, which are often found in the context of chronic antigen stimulation, are likely to be a unique CD4+ T cell subset that limits inflammation and immunopathology as well as eliminates antigen-presenting and malignant cells.
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Affiliation(s)
- Benedikt Thelen
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Vincent Schipperges
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Paulina Knörlein
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jonas F. Hummel
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frederic Arnold
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany,Department of Internal Medicine IV, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,Berta-Ottenstein-Programme, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laurence Kupferschmid
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph S. N. Klose
- Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sebastian J. Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,German Cancer Consortium (Deutsches Konsortium für Translationale Krebsforschung, DKTK), Partner Site Freiburg, and German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Yakup Tanriver
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany,Department of Internal Medicine IV, Faculty of Medicine, Medical Center - University of Freiburg, University of Freiburg, Freiburg, Germany,*Correspondence: Yakup Tanriver,
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11
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Liu C, Omilusik K, Toma C, Kurd NS, Chang JT, Goldrath AW, Wang W. Systems-level identification of key transcription factors in immune cell specification. PLoS Comput Biol 2022; 18:e1010116. [PMID: 36156073 PMCID: PMC9536753 DOI: 10.1371/journal.pcbi.1010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/06/2022] [Accepted: 08/10/2022] [Indexed: 01/30/2023] Open
Abstract
Transcription factors (TFs) are crucial for regulating cell differentiation during the development of the immune system. However, the key TFs for orchestrating the specification of distinct immune cells are not fully understood. Here, we integrated the transcriptomic and epigenomic measurements in 73 mouse and 61 human primary cell types, respectively, that span the immune cell differentiation pathways. We constructed the cell-type-specific transcriptional regulatory network and assessed the global importance of TFs based on the Taiji framework, which is a method we have previously developed that can infer the global impact of TFs using integrated transcriptomic and epigenetic data. Integrative analysis across cell types revealed putative driver TFs in cell lineage-specific differentiation in both mouse and human systems. We have also identified TF combinations that play important roles in specific developmental stages. Furthermore, we validated the functions of predicted novel TFs in murine CD8+ T cell differentiation and showed the importance of Elf1 and Prdm9 in the effector versus memory T cell fate specification and Kdm2b and Tet3 in promoting differentiation of CD8+ tissue resident memory (Trm) cells, validating the approach. Thus, we have developed a bioinformatic approach that provides a global picture of the regulatory mechanisms that govern cellular differentiation in the immune system and aids the discovery of novel mechanisms in cell fate decisions.
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Affiliation(s)
- Cong Liu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Kyla Omilusik
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Clara Toma
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Nadia S. Kurd
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - John T. Chang
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
| | - Ananda W. Goldrath
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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12
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Hoeks C, Duran G, Hellings N, Broux B. When Helpers Go Above and Beyond: Development and Characterization of Cytotoxic CD4+ T Cells. Front Immunol 2022; 13:951900. [PMID: 35903098 PMCID: PMC9320319 DOI: 10.3389/fimmu.2022.951900] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Once regarded as an experimental artefact, cytotoxic CD4+ T cells (CD4 CTL) are presently recognized as a biologically relevant T cell subset with important functions in anti-viral, anti-tumor, and autoimmune responses. Despite the potentially large impact on their micro-environment, the absolute cell counts of CD4 CTL within the peripheral circulation are relatively low. With the rise of single cell analysis techniques, detection of these cells is greatly facilitated. This led to a renewed appraisal of CD4 CTL and an increased insight into their heterogeneous nature and ontogeny. In this review, we summarize the developmental path from naïve CD4+ T cells to terminally differentiated CD4 CTL, and present markers that can be used to detect or isolate CD4 CTL and their precursors. Subsets of CD4 CTL and their divergent functionalities are discussed. Finally, the importance of local cues as triggers for CD4 CTL differentiation is debated, posing the question whether CD4 CTL develop in the periphery and migrate to site of inflammation when called for, or that circulating CD4 CTL reflect cells that returned to the circulation following differentiation at the local inflammatory site they previously migrated to. Even though much remains to be learned about this intriguing T cell subset, it is clear that CD4 CTL represent interesting therapeutic targets for several pathologies.
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Affiliation(s)
- Cindy Hoeks
- Neuro Immune Connections & Repair Lab, Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Gayel Duran
- Neuro Immune Connections & Repair Lab, Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Niels Hellings
- Neuro Immune Connections & Repair Lab, Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Bieke Broux
- Neuro Immune Connections & Repair Lab, Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
- *Correspondence: Bieke Broux,
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13
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Jonkman TH, Dekkers KF, Slieker RC, Grant CD, Ikram MA, van Greevenbroek MMJ, Franke L, Veldink JH, Boomsma DI, Slagboom PE, Consortium BIOS, Heijmans BT. Functional genomics analysis identifies T and NK cell activation as a driver of epigenetic clock progression. Genome Biol 2022; 23:24. [PMID: 35031073 PMCID: PMC8759260 DOI: 10.1186/s13059-021-02585-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/20/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Epigenetic clocks use DNA methylation (DNAm) levels of specific sets of CpG dinucleotides to accurately predict individual chronological age. A popular application of these clocks is to explore whether the deviation of predicted age from chronological age is associated with disease phenotypes, where this deviation is interpreted as a potential biomarker of biological age. This wide application, however, contrasts with the limited insight in the processes that may drive the running of epigenetic clocks. RESULTS We perform a functional genomics analysis on four epigenetic clocks, including Hannum's blood predictor and Horvath's multi-tissue predictor, using blood DNA methylome and transcriptome data from 3132 individuals. The four clocks result in similar predictions of individual chronological age, and their constituting CpGs are correlated in DNAm level and are enriched for similar histone modifications and chromatin states. Interestingly, DNAm levels of CpGs from the clocks are commonly associated with gene expression in trans. The gene sets involved are highly overlapping and enriched for T cell processes. Further analysis of the transcriptome and methylome of sorted blood cell types identifies differences in DNAm between naive and activated T and NK cells as a probable contributor to the clocks. Indeed, within the same donor, the four epigenetic clocks predict naive cells to be up to 40 years younger than activated cells. CONCLUSIONS The ability of epigenetic clocks to predict chronological age involves their ability to detect changes in proportions of naive and activated immune blood cells, an established feature of immuno-senescence. This finding may contribute to the interpretation of associations between clock-derived measures and age-related health outcomes.
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Affiliation(s)
- Thomas H Jonkman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Koen F Dekkers
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Department of Epidemiology and Biostatistics, Amsterdam Public Health Institute, Amsterdam Cardiovascular Sciences Institute, Amsterdam UMC, location VUmc, Amsterdam, The Netherlands
| | - Crystal D Grant
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine and School for Cardiovascular Diseases, Maastricht University Medical Center, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Van der Boechorststraat 1, 1081 BT, Amsterdam, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | | | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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14
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Zhang J, Rousseaux N, Walzer T. Eomes and T‐bet, a dynamic duo regulating NK cell differentiation. Bioessays 2022; 44:e2100281. [DOI: 10.1002/bies.202100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jiang Zhang
- Department of Dermatology Brigham and Women's Hospital Harvard Medical School Boston Massachusetts USA
| | - Noémi Rousseaux
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
| | - Thierry Walzer
- CIRI Centre International de Recherche en Infectiologie CNRS, UMR5308, ENS de Lyon Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1 Lyon France
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15
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Granne I, Shen M, Rodriguez-Caro H, Chadha G, O’Donnell E, Brosens JJ, Quenby S, Child T, Southcombe JH. Characterisation of peri-implantation endometrial Treg and identification of an altered phenotype in recurrent pregnancy loss. Mucosal Immunol 2022; 15:120-129. [PMID: 34552206 PMCID: PMC8732268 DOI: 10.1038/s41385-021-00451-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/31/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023]
Abstract
Recurrent Pregnancy Loss (RPL) affects 2-4% of couples, and with increasing numbers of pregnancy losses the risk of miscarrying a euploid pregnancy is increased, suggesting RPL is a pathology distinct from sporadic miscarriage that is due largely to lethal embryonic aneuploidy. There are a number of conditions associated with RPL including unspecified "immune" pathologies; one of the strongest candidates for dysregulation remains T regulatory cells as depletion in the very early stages of pregnancy in mice leads to pregnancy loss. Human endometrial Treg and conventional CD4T cells were isolated during the peri-implantation period of the menstrual cycle in normal women. We identified an endometrial Treg transcriptomic signature and validated an enhanced regulatory phenotype compared to peripheral blood Treg. Parous women had an altered endometrial Treg transcriptome compared to nulliparity, indicating acquired immune memory of pregnancy within the Treg population, by comparison endometrial conventional CD4T cells were not altered. We compared primary and secondary RPL to nulliparous or parous controls respectively. Both RPL subgroups displayed differentially expressed Treg gene transcriptomes compared to controls. We found increased cell surface S1PR1 and decreased TIGIT protein expression by Treg in primary RPL, confirming the presence of altered Treg in the peri-implantation RPL endometrium.
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Affiliation(s)
- Ingrid Granne
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Mengni Shen
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Helena Rodriguez-Caro
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Gurmeher Chadha
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Elizabeth O’Donnell
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jan J. Brosens
- grid.7372.10000 0000 8809 1613Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV2 2DX UK ,grid.15628.380000 0004 0393 1193Tommy’s National Centre for Miscarriage Research, University Hospitals Coventry & Warwickshire NHS Trust, Coventry, CV2 2DX UK
| | - Siobhan Quenby
- grid.7372.10000 0000 8809 1613Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV2 2DX UK ,grid.15628.380000 0004 0393 1193Tommy’s National Centre for Miscarriage Research, University Hospitals Coventry & Warwickshire NHS Trust, Coventry, CV2 2DX UK
| | - Tim Child
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK ,grid.477692.90000 0004 0379 0597Oxford Fertility, The Fertility Partnership, Oxford, OX4 2HW UK
| | - Jennifer H. Southcombe
- grid.4991.50000 0004 1936 8948Nuffield Department of Women’s and Reproductive Health, L3 Women’s Centre, John Radcliffe Hospital, University of Oxford, Oxford, UK
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16
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Duurland CL, Santegoets SJ, Abdulrahman Z, Loof NM, Sturm G, Wesselink TH, Arens R, Boekestijn S, Ehsan I, van Poelgeest MIE, Finotello F, Hackl H, Trajanoski Z, Ten Dijke P, Braud VM, Welters MJP, van der Burg SH. CD161 expression and regulation defines rapidly responding effector CD4+ T cells associated with improved survival in HPV16-associated tumors. J Immunother Cancer 2022; 10:e003995. [PMID: 35039463 PMCID: PMC8765066 DOI: 10.1136/jitc-2021-003995] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Expression of killer cell lectin-like receptor B1 (KLRB1), the gene encoding the cell surface molecule CD161, is associated with favorable prognosis in many cancers. CD161 is expressed by several lymphocyte populations, but its role and regulation on tumor-specific CD4+ T cells is unknown. METHODS We examined the clinical impact of CD4+CD161+ T cells in human papillomavirus (HPV)16+ oropharyngeal squamous cell carcinoma (OPSCC), analyzed their contribution in a cohort of therapeutically vaccinated patients and used HPV16-specific CD4+CD161+ tumor-infiltrating lymphocytes and T cell clones for in-depth mechanistic studies. RESULTS Central and effector memory CD4+ T cells express CD161, but only CD4+CD161+ effector memory T cells (Tem) are associated with improved survival in OPSCC. Therapeutic vaccination activates and expands type 1 cytokine-producing CD4+CD161+ effector T cells. The expression of CD161 is dynamic and follows a pattern opposite of the checkpoint molecules PD1 and CD39. CD161 did not function as an immune checkpoint molecule as demonstrated using multiple experimental approaches using antibodies to block CD161 and gene editing to knockout CD161 expression. Single-cell transcriptomics revealed KLRB1 expression in many T cell clusters suggesting differences in their activation. Indeed, CD4+CD161+ effector cells specifically expressed the transcriptional transactivator SOX4, known to enhance T cell receptor (TCR) signaling via CD3ε. Consistent with this observation, CD4+CD161+ cells respond more vigorously to limiting amounts of cognate antigen in presence of interleukin (IL)-12 and IL-18 compared to their CD161- counterparts. The expression of CD161/KLRB1 and SOX4 was downregulated upon TCR stimulation and this effect was boosted by transforming growth factor (TGF)β1. CONCLUSION High levels of CD4+CD161+ Tem are associated with improved survival and our data show that CD161 is dynamically regulated by cell intrinsic and extrinsic factors. CD161 expressing CD4+ T cells rapidly respond to suboptimal antigen stimulation suggesting that CD161, similar to SOX4, is involved in the amplification of TCR signals in CD4+ T cells.
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Affiliation(s)
- Chantal L Duurland
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ziena Abdulrahman
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Nikki M Loof
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Tom H Wesselink
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sanne Boekestijn
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilina Ehsan
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Molecular Biology, University of Innsbruck, Innsbruck, Austria
- Digital Science Center (DiSC), University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Ten Dijke
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Veronique M Braud
- Institut de Pharmacologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Université Côte d'Azur, UMR7275, 06560 Valbonne, Sophia Antipolis, France
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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17
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Solé P, Santamaria P. Re-Programming Autoreactive T Cells Into T-Regulatory Type 1 Cells for the Treatment of Autoimmunity. Front Immunol 2021; 12:684240. [PMID: 34335585 PMCID: PMC8320845 DOI: 10.3389/fimmu.2021.684240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022] Open
Abstract
Systemic delivery of peptide-major histocompatibility complex (pMHC) class II-based nanomedicines can re-program cognate autoantigen-experienced CD4+ T cells into disease-suppressing T-regulatory type 1 (TR1)-like cells. In turn, these TR1-like cells trigger the formation of complex regulatory cell networks that can effectively suppress organ-specific autoimmunity without impairing normal immunity. In this review, we summarize our current understanding of the transcriptional, phenotypic and functional make up of TR1-like cells as described in the literature. The true identity and direct precursors of these cells remain unclear, in particular whether TR1-like cells comprise a single terminally-differentiated lymphocyte population with distinct transcriptional and epigenetic features, or a collection of phenotypically different subsets sharing key regulatory properties. We propose that detailed transcriptional and epigenetic characterization of homogeneous pools of TR1-like cells will unravel this conundrum.
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Affiliation(s)
- Patricia Solé
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Pere Santamaria
- Institut D'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain.,Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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18
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Chen L, Li M, Sun F, Qian J, Du M, Wang S, Li D. Eomesodermin regulate decidual CD4 +T cell function during human early pregnancy. J Reprod Immunol 2021; 146:103290. [PMID: 33637323 DOI: 10.1016/j.jri.2021.103290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022]
Abstract
Decidual CD4+T (dCD4+T) cells play pivotal roles in inducing and maintaining maternal-fetal tolerance. Dysfunctional dCD4+T cells are associated with miscarriage. In the present study, we demonstrated that the T-box transcription factor protein eomesodermin (Eomes) was involved in the functional regulation of dCD4+T cells during early pregnancy. We concluded the higher Eomes expression dCD4+T cells during normal pregnancy, and the Eomes+dCD4+T cells displayed an active status and produced more Th2- and Treg type cytokines. Decreased number and altered function of Eomes+dCD4+T cells were observed in miscarriage. Progesterone, the traditional treatment for miscarriage, had no effect on Eomes expression by dCD4+T cells from normal pregnancy, but increased Eomes expression by dCD4+T cells from miscarriage. We also found the higher frequency of Eomes+dCD4+T cells from miscarriage in response to cyclosporine, tacrolimus, Trophoblasts, and HTR8/SVneo cell line, might provide new strategy for therapy to promote maternal-fetal tolerance and prevent pregnancy loss. These results indicated that Eomes might be promising early warming targets of miscarriage, though further studies are required to determine that the altered number and function of Eomes+dCD4+T cells are the cause or consequence of miscarriage.
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Affiliation(s)
- Lanting Chen
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China
| | - Mengdie Li
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China
| | - Fengrun Sun
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China
| | - Jinfeng Qian
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China
| | - Meirong Du
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China
| | - Songcun Wang
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China.
| | - Dajin Li
- Laboratory for Reproductive Immunology, Hospital of Obstetrics and Gynecology, Fudan University Shanghai Medical College, Shanghai, PR China.
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19
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Multiplex Immunofluorescence Histology for Immune Cell Infiltrates in Melanoma-Associated Tertiary Lymphoid Structures. Methods Mol Biol 2021; 2265:573-587. [PMID: 33704741 DOI: 10.1007/978-1-0716-1205-7_40] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The presence of tertiary lymphoid structures (TLS) is correlated with prolonged patient survival in a variety of solid cancers, including melanoma. However, few methods have been described that could enable a more comprehensive understanding of the organization and functionality of TLS in solid cancers. In this chapter, we describe multiplex immunohistochemistry and microscopy approaches for identifying, characterizing, and quantifying TLS and intra-tumoral immune infiltrates in melanoma. The described methods are not limited to melanoma alone and could be used to evaluate tertiary lymphoid structures in a wide variety of human cancers.
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20
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Du Bruyn E, Ruzive S, Lindestam Arlehamn CS, Sette A, Sher A, Barber DL, Wilkinson RJ, Riou C. Mycobacterium tuberculosis-specific CD4 T cells expressing CD153 inversely associate with bacterial load and disease severity in human tuberculosis. Mucosal Immunol 2021; 14:491-499. [PMID: 32678272 PMCID: PMC7855386 DOI: 10.1038/s41385-020-0322-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 02/04/2023]
Abstract
Recent data from mice and non-human primate models of tuberculosis suggested that CD153, a TNF super family member, plays an important role in Mycobacterium tuberculosis (Mtb) control. However, this molecule has not been comprehensively evaluated in humans. Here, we show that the proportion of Mtb-specific CD4 T cells expressing CD153 was significantly reduced in active TB patients compared to latently infected persons. Importantly, the CD153+ Mtb-specific CD4 response inversely correlated with lung bacterial load, inferred by Xpert cycle threshold, irrespective of HIV status. Antitubercular treatment partially restored CD153 expression on Mtb-specific CD4 T cells. This is the first report of a subset of Mtb-specific CD4 T cells showing strong negative correlation with bacterial burden. Building on substantial evidence from animal models implicating CD153 as a mediator of host protection, our findings suggest it may play a similar role in humans and its measurement may be useful to evaluate TB vaccine efficacy.
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Affiliation(s)
- Elsa Du Bruyn
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa
| | - Sheena Ruzive
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa
| | | | - Alessandro Sette
- grid.185006.a0000 0004 0461 3162Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, La Jolla, CA USA
| | - Alan Sher
- grid.419681.30000 0001 2164 9667Immunobiology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Daniel L. Barber
- grid.419681.30000 0001 2164 9667T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Robert J. Wilkinson
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.7445.20000 0001 2113 8111Department of Infectious Diseases, Imperial College London, London, W2 1PG UK ,grid.7836.a0000 0004 1937 1151Department of Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, NW1 1AT UK
| | - Catherine Riou
- grid.7836.a0000 0004 1937 1151Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925 South Africa ,grid.7836.a0000 0004 1937 1151Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
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21
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Lian J, Liu S, Yue Y, Yang Q, Zhang Z, Yang S, Zhang Y. Eomes promotes esophageal carcinoma progression by recruiting Treg cells through the CCL20-CCR6 pathway. Cancer Sci 2020; 112:144-154. [PMID: 33113266 PMCID: PMC7780006 DOI: 10.1111/cas.14712] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/13/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eomesodermin (Eomes) is a T‐box transcription factor that drives the differentiation and function of cytotoxic lymphocytes. However, the underlying function and mechanism of Eomes in tumor cells remains elusive. Here, we studied the role of Eomes in human esophageal squamous cell carcinoma (ESCC). Using 2 human ESCC cell lines, we found that Eomes knockdown reduced esophageal cancer cell proliferation and that the esophageal cancer cell cycle was blocked in the G2/M phase. Mechanistically, we identified CCL20 as the main downstream target of Eomes. Furthermore, we found that CCL20 could chemoregulate regulatory T cells (Tregs) through their specific receptor CCR6, then promoting the proliferation of esophageal cancer cells. Eomes knockdown also delayed the growth of human ESCC xenografts in BALB/c nude mice. Importantly, in 133 human ESCC tissues, high Eomes levels were associated with poor clinical prognosis. Overall, our findings suggested that the Eomes‐CCL20‐CCR6 pathway plays a vital role in human ESCC progress. Therefore, targeting this pathway may represent a promising strategy for controlling human ESCC.
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Affiliation(s)
- Jingyao Lian
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Saisai Liu
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Ying Yue
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Clinical Laboratory, Henan Medical College Hospital Workers, Zhengzhou, China
| | - Qingshan Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Zhen Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
| | - Shengli Yang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yi Zhang
- Biotherapy Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou, China
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22
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Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma. Cell Res 2020; 30:1024-1042. [PMID: 32686767 PMCID: PMC7784929 DOI: 10.1038/s41422-020-0374-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/27/2020] [Indexed: 02/07/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumor microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7581 malignant cells and 40,285 immune cells from fifteen primary NPC tumors and one normal sample. We revealed malignant signatures capturing intratumoral transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as CLEC9A+ dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell–cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs), CLEC9A+ DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for precision therapies in NPC.
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