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Zhao F, Cui Z, Wang P, Zhao Z, Zhu K, Bai Y, Jin X, Wang L, Lu L. GRP75-dependent mitochondria-ER contacts ensure cell survival during early mouse thymocyte development. Dev Cell 2024:S1534-5807(24)00385-X. [PMID: 38981469 DOI: 10.1016/j.devcel.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 04/25/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
Mitochondria and endoplasmic reticulum contacts (MERCs) control multiple cellular processes, including cell survival and differentiation. Based on the observations that MERCs were specifically enriched in the CD4-CD8- double-negative (DN) stage, we studied their role in early mouse thymocyte development. We found that T cell-specific knockout of Hspa9, which encodes GRP75, a protein that mediates MERC formation by assembling the IP3R-GRP75-VDAC complex, impaired DN3 thymocyte viability and resulted in thymocyte developmental arrest at the DN3-DN4 transition. Mechanistically, GRP75 deficiency induced mitochondrial stress, releasing mitochondrial DNA (mtDNA) into the cytosol and triggering the type I interferon (IFN-I) response. The IFN-I pathway contributed to both the impairment of cell survival and DN3-DN4 transition blockage, while increased lipid peroxidation (LPO) played a major role downstream of IFN-I. Thus, our study identifies the essential role of GRP75-dependent MERCs in early thymocyte development and the governing facts of cell survival and differentiation in the DN stage.
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Affiliation(s)
- Fan Zhao
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zejin Cui
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Pengfei Wang
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Zhishan Zhao
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Kaixiang Zhu
- Department of Cardiology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yadan Bai
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China
| | - Xuexiao Jin
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lie Wang
- Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China; Bone Marrow Transplantation Center and Institute of Immunology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Linrong Lu
- Institute of Immunology and Department of Rheumatology at Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Future Health Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing 314100, China.
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Das AS, Basu A, Mukhopadhyay R. Ribosomal proteins: the missing piece in the inflammation puzzle? Mol Cell Biochem 2024:10.1007/s11010-024-05050-9. [PMID: 38951378 DOI: 10.1007/s11010-024-05050-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/09/2024] [Indexed: 07/03/2024]
Abstract
Ribosomal proteins (RPs) are constituents of macromolecular machinery, ribosome that translates genetic information into proteins. Besides ribosomal functions, RPs are now getting appreciated for their 'moonlighting'/extra-ribosomal functions modulating many cellular processes. Accumulating evidence suggests that a number of RPs are involved in inflammation. Though acute inflammation is a part of the innate immune response, uncontrolled inflammation is a driving factor for several chronic inflammatory diseases. An in-depth understanding of inflammation regulation has always been valued for the better management of associated diseases. Hence, this review first outlines the common livelihood of RPs and then provides a comprehensive account of five RPs that significantly contribute to the inflammation process. Finally, we discuss the possible therapeutic uses of RPs against chronic inflammatory diseases.
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Affiliation(s)
- Anindhya Sundar Das
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, 02912, USA.
| | - Anandita Basu
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India
- Division of Surgical Research, Department of Surgery, Rhode Island Hospital, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, 02903, USA
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam, 784028, India.
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Sankaran DG, Zhu H, Maymi VI, Forlastro IM, Jiang Y, Laniewski N, Scheible KM, Rudd BD, Grimson AW. Gene Regulatory Programs that Specify Age-Related Differences during Thymocyte Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599011. [PMID: 38948840 PMCID: PMC11212896 DOI: 10.1101/2024.06.14.599011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
T cell development is fundamental to immune system establishment, yet how this development changes with age remains poorly understood. Here, we construct a transcriptional and epigenetic atlas of T cell developmental programs in neonatal and adult mice, revealing the ontogeny of divergent gene regulatory programs and their link to age-related differences in phenotype and function. Specifically, we identify a gene module that diverges with age from the earliest stages of genesis and includes programs that govern effector response and cell cycle regulation. Moreover, we reveal that neonates possess more accessible chromatin during early thymocyte development, likely establishing poised gene expression programs that manifest later in thymocyte development. Finally, we leverage this atlas, employing a CRISPR-based perturbation approach coupled with single-cell RNA sequencing as a readout to uncover a conserved transcriptional regulator, Zbtb20, that contributes to age-dependent differences in T cell development. Altogether, our study defines transcriptional and epigenetic programs that regulate age-specific differences in T cell development.
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Belean A, Xue E, Cisneros B, Roberson EDO, Paley MA, Bigley TM. Transcriptomic profiling of thymic dysregulation and viral tropism after neonatal roseolovirus infection. Front Immunol 2024; 15:1375508. [PMID: 38895117 PMCID: PMC11183875 DOI: 10.3389/fimmu.2024.1375508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Introduction Herpesviruses, including the roseoloviruses, have been linked to autoimmune disease. The ubiquitous and chronic nature of these infections have made it difficult to establish a causal relationship between acute infection and subsequent development of autoimmunity. We have shown that murine roseolovirus (MRV), which is highly related to human roseoloviruses, induces thymic atrophy and disruption of central tolerance after neonatal infection. Moreover, neonatal MRV infection results in development of autoimmunity in adult mice, long after resolution of acute infection. This suggests that MRV induces durable immune dysregulation. Methods In the current studies, we utilized single-cell RNA sequencing (scRNAseq) to study the tropism of MRV in the thymus and determine cellular processes in the thymus that were disrupted by neonatal MRV infection. We then utilized tropism data to establish a cell culture system. Results Herein, we describe how MRV alters the thymic transcriptome during acute neonatal infection. We found that MRV infection resulted in major shifts in inflammatory, differentiation and cell cycle pathways in the infected thymus. We also observed shifts in the relative number of specific cell populations. Moreover, utilizing expression of late viral transcripts as a proxy of viral replication, we identified the cellular tropism of MRV in the thymus. This approach demonstrated that double negative, double positive, and CD4 single positive thymocytes, as well as medullary thymic epithelial cells were infected by MRV in vivo. Finally, by applying pseudotime analysis to viral transcripts, which we refer to as "pseudokinetics," we identified viral gene transcription patterns associated with specific cell types and infection status. We utilized this information to establish the first cell culture systems susceptible to MRV infection in vitro. Conclusion Our research provides the first complete picture of roseolovirus tropism in the thymus after neonatal infection. Additionally, we identified major transcriptomic alterations in cell populations in the thymus during acute neonatal MRV infection. These studies offer important insight into the early events that occur after neonatal MRV infection that disrupt central tolerance and promote autoimmune disease.
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Affiliation(s)
- Andrei Belean
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Eden Xue
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Benjamin Cisneros
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Elisha D. O. Roberson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Michael A. Paley
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Tarin M. Bigley
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, United States
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5
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Tong Q, Yao L, Su M, Yang YG, Sun L. Thymocyte migration and emigration. Immunol Lett 2024; 267:106861. [PMID: 38697225 DOI: 10.1016/j.imlet.2024.106861] [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: 09/08/2023] [Revised: 12/15/2023] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
Hematopoietic precursors (HPCs) entering into the thymus undergo a sequential process leading to the generation of a variety of T cell subsets. This developmental odyssey unfolds in distinct stages within the thymic cortex and medulla, shaping the landscape of T cell receptor (TCR) expression and guiding thymocytes through positive and negative selection. Initially, early thymic progenitors (ETPs) take residence in the thymic cortex, where thymocytes begin to express their TCR and undergo positive selection. Subsequently, thymocytes transition to the thymic medulla, where they undergo negative selection. Both murine and human thymocyte development can be broadly classified into distinct stages based on the expression of CD4 and CD8 coreceptors, resulting in categorizations as double negative (DN), double positive (DP) or single positive (SP) cells. Thymocyte migration to the appropriate thymic microenvironment at the right differentiation stage is pivotal for the development and the proper functioning of T cells, which is critical for adaptive immune responses. The journey of lymphoid progenitor cells into the T cell developmental pathway hinges on an ongoing dialogue between the differentiating cell and the signals emanating from the thymus niche. Herein, we review the contribution of the key factors mentioned above for the localization, migration and emigration of thymocytes.
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Affiliation(s)
- Qingyue Tong
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Liyu Yao
- Department of Pediatric Surgery, The First Hospital of Jilin University, Changchun, China
| | - Mengting Su
- National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China
| | - Yong-Guang Yang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China.
| | - Liguang Sun
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, Jilin, China; National-local Joint Engineering Laboratory of Animal Models for Human Diseases, Changchun, China.
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6
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Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A, Lamoliatte F, Marin-Rubio JL, Woodbine L, Lemos H, Swan DJ, Pintar V, Sayes K, Ruiz-Morales ER, Eastham S, Dixon D, Prete M, Prigmore E, Jeggo P, Boyes J, Mellor A, Huang L, van der Burg M, Engelhardt KR, Stray-Pedersen A, Erichsen HC, Gennery AR, Trost M, Adams DJ, Anderson G, Lorenc A, Trynka G, Hambleton S. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome. Sci Immunol 2024; 9:eade5705. [PMID: 38787962 DOI: 10.1126/sciimmunol.ade5705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 11 affected patients across four consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain-containing 3 (NUDCD3). Two infants had severe combined immunodeficiency with the complete absence of T and B cells (T -B- SCID), whereas nine showed classical features of Omenn syndrome (OS). Restricted antigen receptor gene usage by residual T lymphocytes suggested impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, which was associated with pathologic sequestration of RAG1 in the nucleoli. Although impaired V(D)J recombination in a mouse model bearing the homologous variant led to milder immunologic abnormalities, NUDCD3 is absolutely required for healthy T and B cell development in humans.
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Affiliation(s)
- Rui Chen
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Elena Lukianova
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | | | - Joseph D P Willet
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Helen Griffin
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Akshada Gajbhiye
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Jose L Marin-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Henrique Lemos
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Swan
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Valeria Pintar
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kamal Sayes
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | | | - Simon Eastham
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Joan Boyes
- Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, UK
| | - Andrew Mellor
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Karin R Engelhardt
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo 0424, Norway
| | - Hans Christian Erichsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo 0424, Norway
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Anna Lorenc
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
- Open Targets, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
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O'Connor KW, Kishimoto K, Kuzma IO, Wagner KP, Selway JS, Roderick JE, Karna KK, Gallagher KM, Hu K, Liu H, Li R, Brehm MA, Zhu LJ, Curtis DJ, Tremblay CS, Kelliher MA. The role of quiescent thymic progenitors in TAL/LMO2-induced T-ALL chemotolerance. Leukemia 2024; 38:951-962. [PMID: 38553571 PMCID: PMC11073972 DOI: 10.1038/s41375-024-02232-8] [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: 01/29/2024] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/08/2024]
Abstract
Relapse in T-cell acute lymphoblastic leukemia (T-ALL) may signify the persistence of leukemia-initiating cells (L-ICs). Ectopic TAL1/LMO expression defines the largest subset of T-ALL, but its role in leukemic transformation and its impact on relapse-driving L-ICs remain poorly understood. In TAL1/LMO mouse models, double negative-3 (DN3; CD4-CD8-CD25+CD44-) thymic progenitors harbored L-ICs. However, only a subset of DN3 leukemic cells exhibited L-IC activity, and studies linking L-ICs and chemotolerance are needed. To investigate L-IC heterogeneity, we used mouse models and applied single-cell RNA-sequencing and nucleosome labeling techniques in vivo. We identified a DN3 subpopulation with a cell cycle-restricted profile and heightened TAL1/LMO2 activity, that expressed genes associated with stemness and quiescence. This dormant DN3 subset progressively expanded throughout leukemogenesis, displaying intrinsic chemotolerance and enrichment in genes linked to minimal residual disease. Examination of TAL/LMO patient samples revealed a similar pattern in CD7+CD1a- thymic progenitors, previously recognized for their L-IC activity, demonstrating cell cycle restriction and chemotolerance. Our findings substantiate the emergence of dormant, chemotolerant L-ICs during leukemogenesis, and demonstrate that Tal1 and Lmo2 cooperate to promote DN3 quiescence during the transformation process. This study provides a deeper understanding of TAL1/LMO-induced T-ALL and its clinical implications in therapy failure.
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Affiliation(s)
- Kevin W O'Connor
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kensei Kishimoto
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Irena O Kuzma
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kelsey P Wagner
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Jonathan S Selway
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Justine E Roderick
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Keshab K Karna
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kayleigh M Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Kai Hu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Haibo Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Rui Li
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Michael A Brehm
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Cedric S Tremblay
- Department of Immunology, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0T5, Canada
- Paul Albrechtsen Research Institute CCMB, CancerCare Manitoba (CCMB), Winnipeg, MB, R3E 0V9, Canada
| | - Michelle A Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA.
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8
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Miccoli A, Pianese V, Bidoli C, Fausto AM, Scapigliati G, Picchietti S. Transcriptome profiling of microdissected cortex and medulla unravels functional regionalization in the European sea bass Dicentrarchus labrax thymus. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109319. [PMID: 38145782 DOI: 10.1016/j.fsi.2023.109319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
The thymus is a sophisticated primary lymphoid organ in jawed vertebrates, but knowledge on teleost thymus remains scarce. In this study, for the first time in the European sea bass, laser capture microdissection was leveraged to collect two thymic regions based on histological features, namely the cortex and the medulla. The two regions were then processed by RNAseq and in-depth functional transcriptome analyses with the aim of revealing differential gene expression patterns and gene sets enrichments, ultimately unraveling unique microenvironments imperative for the development of functional T cells. The sea bass cortex emerged as a hub of T cell commitment, somatic recombination, chromatin remodeling, cell cycle regulation, and presentation of self antigens from autophagy-, proteasome- or proteases-processed proteins. The cortex therefore accommodated extensive thymocyte proliferation and differentiation up to the checkpoint of positive selection. The medulla instead appeared as the center stage in autoimmune regulation by negative selection and deletion of autoreactive T cells, central tolerance mechanisms and extracellular matrix organization. Region-specific canonical markers of T and non-T lineage cells as well as signals for migration to/from, and trafficking within, the thymus were identified, shedding light on the highly coordinated and exquisitely complex bi-directional interactions among thymocytes and stromal components. Markers ascribable to thymic nurse cells and poorly characterized post-aire mTEC populations were found in the cortex and medulla, respectively. An in-depth data mining also exposed previously un-annotated genomic resources with differential signatures. Overall, our findings contribute to a broader understanding of the relationship between regional organization and function in the European sea bass thymus, and provide essential insights into the molecular mechanisms underlying T-cell mediated adaptive immune responses in teleosts.
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Affiliation(s)
- A Miccoli
- National Research Council, Institute for Marine Biological Resources and Biotechnology (IRBIM), 60125, Ancona, Italy
| | - V Pianese
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - C Bidoli
- Dept. of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - A M Fausto
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - G Scapigliati
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - S Picchietti
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy.
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Harris B, Singh DK, Verma M, Fahl SP, Rhodes M, Sprinkle SR, Wang M, Zhang Y, Perrigoue J, Kessel R, Peri S, West J, Giricz O, Boultwood J, Pellagatti A, Ramesh KH, Montagna C, Pradhan K, Tyner JW, Kennedy BK, Holinstat M, Steidl U, Sykes S, Verma A, Wiest DL. Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543132. [PMID: 37398007 PMCID: PMC10312568 DOI: 10.1101/2023.05.31.543132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We report here that expression of the ribosomal protein, RPL22, is frequently reduced in human myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML); reduced RPL22 expression is associated with worse outcomes. Mice null for Rpl22 display characteristics of an MDS-like syndrome and develop leukemia at an accelerated rate. Rpl22-deficient mice also display enhanced hematopoietic stem cell (HSC) self-renewal and obstructed differentiation potential, which arises not from reduced protein synthesis but from increased expression of the Rpl22 target, ALOX12, an upstream regulator of fatty acid oxidation (FAO). The increased FAO mediated by Rpl22-deficiency also persists in leukemia cells and promotes their survival. Altogether, these findings reveal that Rpl22 insufficiency enhances the leukemia potential of HSC via non-canonical de-repression of its target, ALOX12, which enhances FAO, a process that may serve as a therapeutic vulnerability of Rpl22 low MDS and AML leukemia cells. Highlights RPL22 insufficiency is observed in MDS/AML and is associated with reduced survivalRpl22-deficiency produces an MDS-like syndrome and facilitates leukemogenesisRpl22-deficiency does not impair global protein synthesis by HSCRpl22 controls leukemia cell survival by non-canonical regulation of lipid oxidation eTOC: Rpl22 controls the function and transformation potential of hematopoietic stem cells through effects on ALOX12 expression, a regulator of fatty acid oxidation.
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10
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Oh S, Liu X, Tomei S, Luo M, Skinner JP, Berzins SP, Naik SH, Gray DHD, Chong MMW. Distinct subpopulations of DN1 thymocytes exhibit preferential γδ T lineage potential. Front Immunol 2023; 14:1106652. [PMID: 37077921 PMCID: PMC10106834 DOI: 10.3389/fimmu.2023.1106652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
The αβ and γδ T cell lineages both differentiate in the thymus from common uncommitted progenitors. The earliest stage of T cell development is known as CD4-CD8- double negative 1 (DN1), which has previously been shown to be a heterogenous mixture of cells. Of these, only the CD117+ fraction has been proposed to be true T cell progenitors that progress to the DN2 and DN3 thymocyte stages, at which point the development of the αβ and γδ T cell lineages diverge. However, recently, it has been shown that at least some γδ T cells may be derived from a subset of CD117- DN thymocytes. Along with other ambiguities, this suggests that T cell development may not be as straightforward as previously thought. To better understand early T cell development, particularly the heterogeneity of DN1 thymocytes, we performed a single cell RNA sequence (scRNAseq) of mouse DN and γδ thymocytes and show that the various DN stages indeed comprise a transcriptionally diverse subpopulations of cells. We also show that multiple subpopulations of DN1 thymocytes exhibit preferential development towards the γδ lineage. Furthermore, specific γδ-primed DN1 subpopulations preferentially develop into IL-17 or IFNγ-producing γδ T cells. We show that DN1 subpopulations that only give rise to IL-17-producing γδ T cells already express many of the transcription factors associated with type 17 immune cell responses, while the DN1 subpopulations that can give rise to IFNγ-producing γδ T cell already express transcription factors associated with type 1 immune cell responses.
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Affiliation(s)
- Seungyoul Oh
- St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Department of Medicine (St Vincent’s), University of Melbourne, Fitzroy, VIC, Australia
| | - Xin Liu
- St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Sara Tomei
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Mengxiao Luo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | | | - Stuart P. Berzins
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
- Institute of Innovation, Science and Sustainability, Federation University Australia, Ballarat, VIC, Australia
| | - Shalin H. Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Daniel H. D. Gray
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Mark M. W. Chong
- St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Department of Medicine (St Vincent’s), University of Melbourne, Fitzroy, VIC, Australia
- *Correspondence: Mark M. W. Chong,
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11
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Zhao J, Ding C, Li HB. N 6 - Methyladenosine defines a new checkpoint in γδ T cell development. Bioessays 2023; 45:e2300002. [PMID: 36942692 DOI: 10.1002/bies.202300002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023]
Abstract
T cells, which are derived from hematopoietic stem cells (HSCs), are the most important components of adaptive immune system. Based on the expression of αβ and γδ receptors, T cells are mainly divided into αβ and γδ T cells. In the thymus, they share common progenitor cells, while undergoing a series of well-characterized and different developmental processes. N6 -Methyladenosine (m6 A), one of the most abundant modifications in mRNAs, plays critical roles in cell development and maintenance of function. Recently, we have demonstrated that the depletion of m6 A demethylase ALKBH5 in lymphocytes specifically induces an expansion of γδ T cells through the regulation of Jag1/Notch2 signaling, but not αβ T cells, indicating a checkpoint role of ALKBH5 and m6 A modification in the early development of γδ T cells. Based on previous studies, many key pathway molecules, which exert dominant roles in γδ T cell fate determination, have been identified as the targets regulated by m6 A modification. In this review, we mainly summarize the potential regulation between m6 A modification and these key signaling molecules in the γδ T cell lineage commitment, to provide new perspectives in the checkpoint of γδ T cell development.
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Affiliation(s)
- Jiachen Zhao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenbo Ding
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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12
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Perucho L, Icardi L, Di Simone E, Basso V, Agresti A, Vilas Zornoza A, Lozano T, Prosper F, Lasarte JJ, Mondino A. The transcriptional regulator Sin3A balances IL-17A and Foxp3 expression in primary CD4 T cells. EMBO Rep 2023; 24:e55326. [PMID: 36929576 PMCID: PMC10157306 DOI: 10.15252/embr.202255326] [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: 04/29/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 03/18/2023] Open
Abstract
The Sin3 transcriptional regulator homolog A (Sin3A) is the core member of a multiprotein chromatin-modifying complex. Its inactivation at the CD4/CD8 double-negative stage halts further thymocyte development. Among various functions, Sin3A regulates STAT3 transcriptional activity, central to the differentiation of Th17 cells active in inflammatory disorders and opportunistic infections. To further investigate the consequences of conditional Sin3A inactivation in more mature precursors and post-thymic T cell, we have generated CD4-Cre and CD4-CreERT2 Sin3AF/F mice. Sin3A inactivation in vivo hinders both thymocyte development and peripheral T-cell survival. In vitro, in Th17 skewing conditions, Sin3A-deficient cells proliferate and acquire memory markers and yet fail to properly upregulate Il17a, Il23r, and Il22. Instead, IL-2+ and FOXP3+ are mostly enriched for, and their inhibition partially rescues IL-17A+ T cells. Notably, Sin3A deletion also causes an enrichment of genes implicated in the mTORC1 signaling pathway, overt STAT3 activation, and aberrant cytoplasmic RORγt accumulation. Thus, together our data unveil a previously unappreciated role for Sin3A in shaping critical signaling events central to the acquisition of immunoregulatory T-cell phenotypes.
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Affiliation(s)
- Laura Perucho
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Icardi
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisabetta Di Simone
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Veronica Basso
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Agresti
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Amaia Vilas Zornoza
- Departamento de Hematología, Clínica Universidad de Navarra and CCUN, IDISNA, Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Teresa Lozano
- Immunology and Immunotherapy Program, Center for Applied Medical Research (CIMA), CCUN, IDISNA, University of Navarra, Pamplona, Spain
| | - Felipe Prosper
- Departamento de Hematología, Clínica Universidad de Navarra and CCUN, IDISNA, Universidad de Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Pamplona, Spain
| | - Juan José Lasarte
- Immunology and Immunotherapy Program, Center for Applied Medical Research (CIMA), CCUN, IDISNA, University of Navarra, Pamplona, Spain
| | - Anna Mondino
- Lymphocyte Activation Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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13
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Shin B, Rothenberg EV. Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells. Front Immunol 2023; 14:1108368. [PMID: 36817475 PMCID: PMC9928580 DOI: 10.3389/fimmu.2023.1108368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023] Open
Abstract
T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose "stem-ness" from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
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Affiliation(s)
- Boyoung Shin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Ellen V. Rothenberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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14
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Dauphars DJ, Wu G, Bassing CH, Krangel MS. Methods for Study of Mouse T Cell Receptor α and β Gene Rearrangements. Methods Mol Biol 2023; 2580:261-282. [PMID: 36374463 DOI: 10.1007/978-1-0716-2740-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Quantitative real-time PCR and next-generation sequencing (NGS) are invaluable techniques to analyze T cell receptor (Tcr) gene rearrangements in mouse lymphocyte populations. Although these approaches are powerful, they also have limitations that must be accounted for in experimental design and data interpretation. Here, we provide relevant background required for understanding these limitations and then outline established quantitative real-time PCR and NGS methods that can be used for analysis of mouse Tcra and Tcrb gene rearrangements in mice.
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Affiliation(s)
- Danielle J Dauphars
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Glendon Wu
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael S Krangel
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA.
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15
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Bosselut R. A Beginner's Guide to T Cell Development. Methods Mol Biol 2023; 2580:3-24. [PMID: 36374448 DOI: 10.1007/978-1-0716-2740-2_1] [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] [Indexed: 06/16/2023]
Abstract
T lymphocytes (T cells) are essential components of the adaptive immune system; they serve multiple functions in responses to pathogens and to ensure immune homeostasis. Written for readers first entering this field of study, this chapter is a brief overview of the development of T cells in the thymus, from the entry of thymus-settling bone marrow-derived precursors to the egress of mature T cells. Surveyed topics include the differentiation and expansion of early precursors, the generation of the T cell antigen receptor repertoire, the selection of αβ T cell precursors, and their acquisition of functional competency.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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16
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Werlen G, Li ML, Tottone L, da Silva-Diz V, Su X, Herranz D, Jacinto E. Dietary glucosamine overcomes the defects in αβ-T cell ontogeny caused by the loss of de novo hexosamine biosynthesis. Nat Commun 2022; 13:7404. [PMID: 36456551 PMCID: PMC9715696 DOI: 10.1038/s41467-022-35014-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/14/2022] [Indexed: 12/02/2022] Open
Abstract
T cell development requires the coordinated rearrangement of T cell receptor (TCR) gene segments and the expression of either αβ or γδ TCR. However, whether and how de novo synthesis of nutrients contributes to thymocyte commitment to either lineage remains unclear. Here, we find that T cell-specific deficiency in glutamine:fructose-6-phosphate aminotransferase 1 (GFAT1), the rate-limiting enzyme of the de novo hexosamine biosynthesis pathway (dn-HBP), attenuates hexosamine levels, blunts N-glycosylation of TCRβ chains, reduces surface expression of key developmental receptors, thus impairing αβ-T cell ontogeny. GFAT1 deficiency triggers defects in N-glycans, increases the unfolded protein response, and elevates γδ-T cell numbers despite reducing γδ-TCR diversity. Enhancing TCR expression or PI3K/Akt signaling does not reverse developmental defects. Instead, dietary supplementation with the salvage metabolite, glucosamine, and an α-ketoglutarate analogue partially restores αβ-T cell development in GFAT1T-/- mice, while fully rescuing it in ex vivo fetal thymic organ cultures. Thus, dn-HBP fulfils, while salvage nutrients partially satisfy, the elevated demand for hexosamines during early T cell development.
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Affiliation(s)
- Guy Werlen
- grid.430387.b0000 0004 1936 8796Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State Univ. of New Jersey, Piscataway, NJ 08854 USA
| | - Mei-Ling Li
- grid.430387.b0000 0004 1936 8796Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State Univ. of New Jersey, Piscataway, NJ 08854 USA
| | - Luca Tottone
- grid.430387.b0000 0004 1936 8796Dept. of Pharmacology and Pediatrics, Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, Rutgers, The State Univ. of New Jersey, New Brunswick, NJ 08901 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, FL Miami, 33136 USA
| | - Victoria da Silva-Diz
- grid.430387.b0000 0004 1936 8796Dept. of Pharmacology and Pediatrics, Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, Rutgers, The State Univ. of New Jersey, New Brunswick, NJ 08901 USA
| | - Xiaoyang Su
- grid.430387.b0000 0004 1936 8796Dept. of Medicine, Div. of Endocrinology, Child Health Inst. of New Jersey, Rutgers, The State Univ. of New Jersey, New Brunswick, NJ 08901 USA
| | - Daniel Herranz
- grid.430387.b0000 0004 1936 8796Dept. of Pharmacology and Pediatrics, Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, Rutgers, The State Univ. of New Jersey, New Brunswick, NJ 08901 USA
| | - Estela Jacinto
- grid.430387.b0000 0004 1936 8796Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State Univ. of New Jersey, Piscataway, NJ 08854 USA
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17
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Yamashita M, Taniuchi I. Fine-tuning Notch1 by the stage-specific enhancer. Nat Immunol 2022; 23:1509-1511. [DOI: 10.1038/s41590-022-01341-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Boehme L, Roels J, Taghon T. Development of γδ T cells in the thymus - A human perspective. Semin Immunol 2022; 61-64:101662. [PMID: 36374779 DOI: 10.1016/j.smim.2022.101662] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 12/14/2022]
Abstract
γδ T cells are increasingly emerging as crucial immune regulators that can take on innate and adaptive roles in the defence against pathogens. Although they arise within the thymus from the same hematopoietic precursors as conventional αβ T cells, the development of γδ T cells is less well understood. In this review, we focus on summarising the current state of knowledge about the cellular and molecular processes involved in the generation of γδ T cells in human.
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Affiliation(s)
- Lena Boehme
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Juliette Roels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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19
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Kashiwagi M, Figueroa DS, Ay F, Morgan BA, Georgopoulos K. A double-negative thymocyte-specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and β-selection. Nat Immunol 2022; 23:1628-1643. [PMID: 36316479 PMCID: PMC10187983 DOI: 10.1038/s41590-022-01322-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
T cell differentiation requires Notch1 signaling. In the present study, we show that an enhancer upstream of Notch1 active in double-negative (DN) mouse thymocytes is responsible for raising Notch1 signaling intrathymically. This enhancer is required to expand multipotent progenitors intrathymically while delaying early differentiation until lineage restrictions have been established. Early thymic progenitors lacking the enhancer show accelerated differentiation through the DN stages and increased frequency of B, innate lymphoid (IL) and natural killer (NK) cell differentiation. Transcription regulators for T cell lineage restriction and commitment are expressed normally, but IL and NK cell gene expression persists after T cell lineage commitment and T cell receptor β VDJ recombination, Cd3 expression and β-selection have been impaired. This Notch1 enhancer is inactive in double-positive (DP) thymocytes. Its aberrant reactivation at this stage in Ikaros mutants is required for leukemogenesis. Thus, the DN-specific Notch1 enhancer harnesses the regulatory architecture of DN and DP thymocytes to achieve carefully orchestrated changes in Notch1 signaling required for early lineage restrictions and normal T cell differentiation.
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20
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Chann AS, Charnley M, Newton LM, Newbold A, Wiede F, Tiganis T, Humbert PO, Johnstone RW, Russell SM. Stepwise progression of β-selection during T cell development involves histone deacetylation. Life Sci Alliance 2022; 6:6/1/e202201645. [PMID: 36283704 PMCID: PMC9595210 DOI: 10.26508/lsa.202201645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/02/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
During T cell development, the first step in creating a unique T cell receptor (TCR) is genetic recombination of the TCRβ chain. The quality of the new TCRβ is assessed at the β-selection checkpoint. Most cells fail this checkpoint and die, but the coordination of fate at the β-selection checkpoint is not yet understood. We shed new light on fate determination during β-selection using a selective inhibitor of histone deacetylase 6, ACY1215. ACY1215 disrupted the β-selection checkpoint. Characterising the basis for this disruption revealed a new, pivotal stage in β-selection, bookended by up-regulation of TCR co-receptors, CD28 and CD2, respectively. Within this "DN3bPre" stage, CD5 and Lef1 are up-regulated to reflect pre-TCR signalling, and their expression correlates with proliferation. These findings suggest a refined model of β-selection in which a coordinated increase in expression of pre-TCR, CD28, CD5 and Lef1 allows for modulating TCR signalling strength and culminates in the expression of CD2 to enable exit from the β-selection checkpoint.
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Affiliation(s)
- Anchi S Chann
- Optical Sciences Centre, School of Science, Swinburne University of Technology, Hawthorn, Australia,Peter MacCallum Cancer Centre, Melbourne, Australia,Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Mirren Charnley
- Optical Sciences Centre, School of Science, Swinburne University of Technology, Hawthorn, Australia,Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Lucas M Newton
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Andrea Newbold
- Peter MacCallum Cancer Centre, Melbourne, Australia,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Florian Wiede
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Tony Tiganis
- Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Patrick O Humbert
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Australia,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia,Department of Clinical Pathology, University of Melbourne, Melbourne, Australia
| | - Ricky W Johnstone
- Peter MacCallum Cancer Centre, Melbourne, Australia,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Sarah M Russell
- Optical Sciences Centre, School of Science, Swinburne University of Technology, Hawthorn, Australia .,Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
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21
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Ratiu JJ, Barclay WE, Lin E, Wang Q, Wellford S, Mehta N, Harnois MJ, DiPalma D, Roy S, Contreras AV, Shinohara ML, Wiest D, Zhuang Y. Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes. Nat Commun 2022; 13:5901. [PMID: 36202870 PMCID: PMC9537144 DOI: 10.1038/s41467-022-33610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Production of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.
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Affiliation(s)
- Jeremy J Ratiu
- Duke University, Department of Immunology, Durham, NC, 27710, USA.
| | | | - Elliot Lin
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Qun Wang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Naren Mehta
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Devon DiPalma
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Sumedha Roy
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Alejandra V Contreras
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Mari L Shinohara
- Duke University, Department of Immunology, Durham, NC, 27710, USA
- Duke University, Department of Molecular Genetics and Microbiology, Durham, NC, 27710, USA
| | - David Wiest
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Yuan Zhuang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
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22
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Rodríguez-Caparrós A, Tani-ichi S, Casal Á, López-Ros J, Suñé C, Ikuta K, Hernández-Munain C. Interleukin-7 receptor signaling is crucial for enhancer-dependent TCRδ germline transcription mediated through STAT5 recruitment. Front Immunol 2022; 13:943510. [PMID: 36059467 PMCID: PMC9437428 DOI: 10.3389/fimmu.2022.943510] [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: 05/13/2022] [Accepted: 08/03/2022] [Indexed: 11/29/2022] Open
Abstract
γδ T cells play important roles in immune responses by rapidly producing large quantities of cytokines. Recently, γδ T cells have been found to be involved in tissue homeostatic regulation, playing roles in thermogenesis, bone regeneration and synaptic plasticity. Nonetheless, the mechanisms involved in γδ T-cell development, especially the regulation of TCRδ gene transcription, have not yet been clarified. Previous studies have established that NOTCH1 signaling plays an important role in the Tcrg and Tcrd germline transcriptional regulation induced by enhancer activation, which is mediated through the recruitment of RUNX1 and MYB. In addition, interleukin-7 signaling has been shown to be required for Tcrg germline transcription, VγJγ rearrangement and γδ T-lymphocyte generation as well as for promoting T-cell survival. In this study, we discovered that interleukin-7 is required for the activation of enhancer-dependent Tcrd germline transcription during thymocyte development. These results indicate that the activation of both Tcrg and Tcrd enhancers during γδ T-cell development in the thymus depends on the same NOTCH1- and interleukin-7-mediated signaling pathways. Understanding the regulation of the Tcrd enhancer during thymocyte development might lead to a better understanding of the enhancer-dependent mechanisms involved in the genomic instability and chromosomal translocations that cause leukemia.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Shizue Tani-ichi
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Áurea Casal
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”- Spanish Scientific Research Council (IPBLN-CSIC), Technological Park of Health Sciences (PTS), Granada, Spain
- *Correspondence: Cristina Hernández-Munain,
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23
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Roels J, Van Hulle J, Lavaert M, Kuchmiy A, Strubbe S, Putteman T, Vandekerckhove B, Leclercq G, Van Nieuwerburgh F, Boehme L, Taghon T. Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development. Front Immunol 2022; 13:960918. [PMID: 35967340 PMCID: PMC9366357 DOI: 10.3389/fimmu.2022.960918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/05/2022] [Indexed: 12/05/2022] Open
Abstract
T cells are generated from hematopoietic stem cells through a highly organized developmental process, in which stage-specific molecular events drive maturation towards αβ and γδ T cells. Although many of the mechanisms that control αβ- and γδ-lineage differentiation are shared between human and mouse, important differences have also been observed. Here, we studied the regulatory dynamics of the E and ID protein encoding genes during pediatric human T cell development by evaluating changes in chromatin accessibility, histone modifications and bulk and single cell gene expression. We profiled patterns of ID/E protein activity and identified up- and downstream regulators and targets, respectively. In addition, we compared transcription of E and ID protein encoding genes in human versus mouse to predict both shared and unique activities in these species, and in prenatal versus pediatric human T cell differentiation to identify regulatory changes during development. This analysis showed a putative involvement of TCF3/E2A in the development of γδ T cells. In contrast, in αβ T cell precursors a pivotal pre-TCR-driven population with high ID gene expression and low predicted E protein activity was identified. Finally, in prenatal but not postnatal thymocytes, high HEB/TCF12 levels were found to counteract high ID levels to sustain thymic development. In summary, we uncovered novel insights in the regulation of E and ID proteins on a cross-species and cross-developmental level.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Child
- Epigenesis, Genetic
- Hematopoietic Stem Cells/metabolism
- Humans
- Mice
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Transcription Factors/metabolism
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Affiliation(s)
- Juliette Roels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jolien Van Hulle
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marieke Lavaert
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Anna Kuchmiy
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tom Putteman
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Lena Boehme
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- *Correspondence: Lena Boehme, ; Tom Taghon,
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- *Correspondence: Lena Boehme, ; Tom Taghon,
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24
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Huseby ES, Teixeiro E. The perception and response of T cells to a changing environment are based on the law of initial value. Sci Signal 2022; 15:eabj9842. [PMID: 35639856 PMCID: PMC9290192 DOI: 10.1126/scisignal.abj9842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
αβ T cells are critical components of the adaptive immune system and are capable of inducing sterilizing immunity after pathogen infection and eliminating transformed tumor cells. The development and function of T cells are controlled through the T cell antigen receptor, which recognizes peptides displayed on major histocompatibility complex (MHC) molecules. Here, we review how T cells generate the ability to recognize self-peptide-bound MHC molecules and use signals derived from these interactions to instruct cellular development, activation thresholds, and functional specialization in the steady state and during immune responses. We argue that the basic tenants of T cell development and function follow Weber-Fetcher's law of just noticeable differences and Wilder's law of initial value. Together, these laws argue that the ability of a system to respond and the quality of that response are scalable to the basal state of that system. Manifestation of these laws in T cells generates clone-specific activation thresholds that are based on perceivable differences between homeostasis and pathogen encounter (self versus nonself discrimination), as well as poised states for subsequent differentiation into specific effector cell lineages.
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Affiliation(s)
- Eric S. Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
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25
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Li Z, Yang Q, Tang X, Chen Y, Wang S, Qi X, Zhang Y, Liu Z, Luo J, Liu H, Ba Y, Guo L, Wu B, Huang F, Cao G, Yin Z. Single-cell RNA-seq and chromatin accessibility profiling decipher the heterogeneity of mouse γδ T cells. Sci Bull (Beijing) 2022; 67:408-426. [PMID: 36546093 DOI: 10.1016/j.scib.2021.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/06/2023]
Abstract
The distinct characteristics of γδ T cells determine their vital roles in the formation of local immune responses and contribute to tissue homeostasis. However, the heterogeneity of γδ T cells across tissues remains unclear. By combining transcriptional and chromatin analyses with a truly unbiased fashion, we constructed a single-cell transcriptome and chromatin accessibility landscape of mouse γδ T cells in the lymph, spleen, and thymus. We also revealed the heterogeneity of γδ T1 and γδ T17 cells across these tissues and inferred their potential regulatory mechanisms. In the thymus, we reconstructed the developmental trajectory and gained further insights into the signature genes from the mature stage, intermediate stage, and immature stage of γδ T cells on the basis of single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing data. Notably, a novel Gzma+ γδ T cell subset was identified with immature properties and only localized to the thymus. Finally, NR1D1, a circadian transcription factor (TF), was validated as a key and negative regulator of γδ T17 cell differentiation by performing a combined analysis of TF motif enrichment, regulon enrichment, and Nr1d1 knockout mice. In summary, our data represent a comprehensive mapping on the transcriptome and chromatin accessibility dynamics of mouse γδ T cells, providing a valuable resource and reference for future studies on γδ T cells.
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Affiliation(s)
- Zhenhua Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Quanli Yang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Xin Tang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China; The First Affiliated Hospital, Faculty of Medical Science, Jinan University, Guangzhou 510000, China
| | - Yiming Chen
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Shanshan Wang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Xiaojie Qi
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Yawen Zhang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Zonghua Liu
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China
| | - Jing Luo
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China; The First Affiliated Hospital, Faculty of Medical Science, Jinan University, Guangzhou 510000, China
| | - Hui Liu
- Emergency Department, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou 510000, China
| | - Yongbing Ba
- OE Biotech Co., Ltd., Shanghai 201114, China
| | - Lianxia Guo
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou 510700, China
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou 510700, China
| | - Fang Huang
- Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Jinan University, Zhuhai 519000, China
| | - Guangchao Cao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China.
| | - Zhinan Yin
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai 519000, China; The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou 510632, China.
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26
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Rodríguez-Caparrós A, Álvarez-Santiago J, López-Castellanos L, Ruiz-Rodríguez C, Valle-Pastor MJ, López-Ros J, Angulo Ú, Andrés-León E, Suñé C, Hernández-Munain C. Differently Regulated Gene-Specific Activity of Enhancers Located at the Boundary of Subtopologically Associated Domains: TCRα Enhancer. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:910-928. [PMID: 35082160 DOI: 10.4049/jimmunol.2000864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/05/2021] [Indexed: 11/19/2022]
Abstract
Enhancers activate transcription through long-distance interactions with their cognate promoters within a particular subtopologically associated domain (sub-TAD). The TCRα enhancer (Eα) is located at the sub-TAD boundary between the TCRα and DAD1 genes and regulates transcription toward both sides in an ∼1-Mb region. Analysis of Eα activity in transcribing the unrearranged TCRα gene at the 5'-sub-TAD has defined Eα as inactive in CD4-CD8- thymocytes, active in CD4+CD8+ thymocytes, and strongly downregulated in CD4+ and CD8+ thymocytes and αβ T lymphocytes. Despite its strongly reduced activity, Eα is still required for high TCRα transcription and expression of TCRαβ in mouse and human T lymphocytes, requiring collaboration with distant sequences for such functions. Because VαJα rearrangements in T lymphocytes do not induce novel long-range interactions between Eα and other genomic regions that remain in cis after recombination, strong Eα connectivity with the 3'-sub-TAD might prevent reduced transcription of the rearranged TCRα gene. Our analyses of transcriptional enhancer dependence during T cell development and non-T lineage tissues at the 3'-sub-TAD revealed that Eα can activate the transcription of specific genes, even when it is inactive to transcribe the TCRα gene at the 5'-sub-TAD. Hence distinct requirements for Eα function are necessary at specific genes at both sub-TADs, implying that enhancers do not merely function as chromatin loop anchors that nucleate the formation of factor condensates to increase gene transcription initiated at their cognate promoters. The observed different regulated Eα activity for activating specific genes at its flanking sub-TADs may be a general feature for enhancers located at sub-TAD boundaries.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jesús Álvarez-Santiago
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Laura López-Castellanos
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Candela Ruiz-Rodríguez
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - María Jesús Valle-Pastor
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Úrsula Angulo
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
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27
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Scaramuzzino S, Potier D, Ordioni R, Grenot P, Payet-Bornet D, Luche H, Malissen B. Single-cell transcriptomics uncovers an instructive T-cell receptor role in adult γδ T-cell lineage commitment. EMBO J 2022; 41:e110023. [PMID: 35128689 PMCID: PMC8886544 DOI: 10.15252/embj.2021110023] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/18/2021] [Accepted: 01/03/2022] [Indexed: 01/05/2023] Open
Abstract
After entering the adult thymus, bipotent T‐cell progenitors give rise to αβ or γδ T cells. To determine whether the γδ T‐cell receptor (TCR) has an instructive role in γδ T‐cell lineage commitment or only “confirms” a pre‐established γδ Τ‐cell lineage state, we exploited mice lacking expression of LAT, an adaptor required for γδ TCR signaling. Although these mice showed a T‐cell development block at the CD4−CD8− double‐negative third (DN3) stage, 0.3% of their DN3 cells expressed intermediate levels of γδ TCR (further referred to as γδint) at their surface. Single‐cell transcriptomics of LAT‐deficient DN3 γδint cells demonstrated no sign of commitment to the γδ T‐cell lineage, apart from γδ TCR expression. Although the lack of LAT is thought to tightly block DN3 cell development, we unexpectedly found that 25% of LAT‐deficient DN3 γδint cells were actively proliferating and progressed up to the DN4 stage. However, even those cells failed to turn on the transcriptional program associated with the γδ T‐cell lineage. Therefore, the γδ TCR‐LAT signaling axis builds upon a γδ T‐cell uncommitted lineage state to fully instruct adult γδ T‐cell lineage specification.
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Affiliation(s)
- Sara Scaramuzzino
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS UMR, Marseille, France.,Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Delphine Potier
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Robin Ordioni
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS UMR, Marseille, France
| | - Pierre Grenot
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS UMR, Marseille, France
| | - Dominique Payet-Bornet
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Hervé Luche
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS UMR, Marseille, France
| | - Bernard Malissen
- Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS UMR, Marseille, France.,Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France
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28
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Zhang W, Pajulas A, Kaplan MH. γδ T Cells in Skin Inflammation. Crit Rev Immunol 2022; 42:43-56. [PMID: 37075018 PMCID: PMC10439530 DOI: 10.1615/critrevimmunol.2022047288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Gamma delta (γδ) T cells are a subset of T lymphocytes that express T cell receptor γ and 5 chains and display structural and functional heterogeneity. γδ T cells are typically of low abundance in the body and account for 1-5% of the blood lymphocytes and peripheral lymphoid tissues. As a bridge between innate and adaptive immunity, γδ T cells are uniquely poised to rapidly respond to stimulation and can regulate immune responses in peripheral tissues. The dendritic epidermal T cells in the skin epidermis can secrete growth factors to regulate skin homeostasis and re-epithelization and release inflammatory factors to mediate wound healing during skin inflammatory responses. Dermal γδ T cells can regulate the inflammatory process by producing interleukin-17 and other cytokines or chemokines. Here, we offer a review of the immune functions of γδ T cells, intending to understand their role in regulating skin barrier integrity and skin wound healing, which may be crucial for the development of novel therapeutics in skin diseases like atopic dermatitis and psoriasis.
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Affiliation(s)
- Wenwu Zhang
- Department of Microbiology & Immunology, Indiana University School Medicine, Indianapolis, IN 46202
| | - Abigail Pajulas
- Department of Microbiology & Immunology, Indiana University School Medicine, Indianapolis, IN 46202
| | - Mark H Kaplan
- Department of Microbiology & Immunology, Indiana University School Medicine, Indianapolis, IN 46202
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29
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Argenty J, Rouquié N, Bories C, Mélique S, Duplan-Eche V, Saoudi A, Fazilleau N, Lesourne R. A selective LIS1 requirement for mitotic spindle assembly discriminates distinct T-cell division mechanisms within the T-cell lineage. eLife 2022; 11:80277. [PMID: 36519536 PMCID: PMC9797186 DOI: 10.7554/elife.80277] [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: 05/13/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
The ability to proliferate is a common feature of most T-cell populations. However, proliferation follows different cell-cycle dynamics and is coupled to different functional outcomes according to T-cell subsets. Whether the mitotic machineries supporting these qualitatively distinct proliferative responses are identical remains unknown. Here, we show that disruption of the microtubule-associated protein LIS1 in mouse models leads to proliferative defects associated with a blockade of T-cell development after β-selection and of peripheral CD4+ T-cell expansion after antigen priming. In contrast, cell divisions in CD8+ T cells occurred independently of LIS1 following T-cell antigen receptor stimulation, although LIS1 was required for proliferation elicited by pharmacological activation. In thymocytes and CD4+ T cells, LIS1 deficiency did not affect signaling events leading to activation but led to an interruption of proliferation after the initial round of division and to p53-induced cell death. Proliferative defects resulted from a mitotic failure, characterized by the presence of extra-centrosomes and the formation of multipolar spindles, causing abnormal chromosomes congression during metaphase and separation during telophase. LIS1 was required to stabilize dynein/dynactin complexes, which promote chromosome attachment to mitotic spindles and ensure centrosome integrity. Together, these results suggest that proliferative responses are supported by distinct mitotic machineries across T-cell subsets.
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Affiliation(s)
- Jérémy Argenty
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nelly Rouquié
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Cyrielle Bories
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Suzanne Mélique
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Valérie Duplan-Eche
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Abdelhadi Saoudi
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Nicolas Fazilleau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
| | - Renaud Lesourne
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291, CNRS UMR5051, University Toulouse IIIToulouseFrance
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30
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Hiwa R, Nielsen HV, Mueller JL, Mandla R, Zikherman J. NR4A family members regulate T cell tolerance to preserve immune homeostasis and suppress autoimmunity. JCI Insight 2021; 6:e151005. [PMID: 34343134 PMCID: PMC8492309 DOI: 10.1172/jci.insight.151005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
The NR4A family of orphan nuclear receptors (Nr4a1–3) plays redundant roles to establish and maintain Treg identity; deletion of multiple family members in the thymus results in Treg deficiency and a severe inflammatory disease. Consequently, it has been challenging to unmask redundant functions of the NR4A family in other immune cells. Here we use a competitive bone marrow chimera strategy, coupled with conditional genetic tools, to rescue Treg homeostasis and unmask such functions. Unexpectedly, chimeras harboring Nr4a1–/– Nr4a3–/– (double-knockout, DKO) bone marrow developed autoantibodies and a systemic inflammatory disease despite a replete Treg compartment of largely WT origin. This disease differs qualitatively from that seen with Treg deficiency and is B cell extrinsic. Negative selection of DKO thymocytes is profoundly impaired in a cell-intrinsic manner. Consistent with escape of self-reactive T cells into the periphery, DKO T cells with functional, phenotypic, and transcriptional features of anergy accumulated in chimeric mice. Nevertheless, we observed upregulation of genes encoding inflammatory mediators in anergic DKO T cells, and DKO T cells exhibited enhanced capacity for IL-2 production. These studies reveal cell-intrinsic roles for the NR4A family in both central and peripheral T cell tolerance and demonstrate that each is essential to preserve immune homeostasis.
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Affiliation(s)
- Ryosuke Hiwa
- Department of Medicine, UCSF Medical Center, San Francisco, United States of America
| | - Hailyn V Nielsen
- Department of Medicine, UCSF Medical Center, San Francisco, United States of America
| | - James L Mueller
- Department of Medicine, UCSF Medical Center, San Francisco, United States of America
| | - Ravi Mandla
- Department of Medicine, UCSF Medical Center, San Francisco, United States of America
| | - Julie Zikherman
- Department of Medicine, UCSF Medical Center, San Francisco, United States of America
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31
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New insights into TCR β-selection. Trends Immunol 2021; 42:735-750. [PMID: 34261578 DOI: 10.1016/j.it.2021.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022]
Abstract
T cell receptor (TCR) β-selection (herein referred to as β-selection) is a pivotal checkpoint in mammalian T cell development when immature CD4-CD8- T-cells (thymocytes) express pre-TCR following successful Tcrb gene rearrangement. At this stage, αβ T cell lineage commitment and allelic exclusion to restrict one β-chain per cell take place and thymocytes undergo a proliferative burst. β-selection is known to be crucially dependent upon synchronized Notch and pre-TCR signaling; however, other necessary inputs have been identified over the past decade, expanding our knowledge and understanding of the β-selection process. In this review, we discuss recent mechanistic findings that have enabled a more detailed decoding of the molecular dynamics of the β-selection checkpoint and have helped to elucidate its role in early T cell development.
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32
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Kobayashi S, Phung HT, Kagawa Y, Miyazaki H, Takahashi Y, Asao A, Maruyama T, Yoshimura A, Ishii N, Owada Y. Fatty acid-binding protein 3 controls contact hypersensitivity through regulating skin dermal Vγ4 + γ/δ T cell in a murine model. Allergy 2021; 76:1776-1788. [PMID: 33090507 PMCID: PMC8246717 DOI: 10.1111/all.14630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fatty acid-binding protein 3 (FABP3) is a cytosolic carrier protein of polyunsaturated fatty acids (PUFAs) and regulates cellular metabolism. However, the physiological functions of FABP3 in immune cells and how FABP3 regulates inflammatory responses remain unclear. METHODS Contact hypersensitivity (CHS) induced by 2,4-dinitrofluorobenzene (DNFB) and fluorescein isothiocyanate was applied to the skin wild-type and Fabp3-/- mice. Skin inflammation was assessed using FACS, histological, and qPCR analyses. The development of γ/δ T cells was evaluated by a co-culture system with OP9/Dll1 cells in the presence or absence of transgene of FABP3. RESULTS Fabp3-deficient mice exhibit a more severe phenotype of contact hypersensitivity (CHS) accompanied by infiltration of IL-17-producing Vγ4+ γ/δ T cells that critically control skin inflammation. In Fabp3-/- mice, we found a larger proportion of Vγ4+ γ/δ T cells in the skin, even though the percentage of total γ/δ T cells did not change at steady state. Similarly, juvenile Fabp3-/- mice also contained a higher amount of Vγ4+ γ/δ T cells not only in the skin but in the thymus when compared with wild-type mice. Furthermore, thymic double-negative (DN) cells expressed FABP3, and FABP3 negatively regulates the development of Vγ4+ γ/δ T cells in the thymus. CONCLUSIONS These findings suggest that FABP3 functions as a negative regulator of skin inflammation through limiting pathogenic Vγ4+ γ/δ T-cell generation in the thymus.
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Affiliation(s)
- Shuhei Kobayashi
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Hai The Phung
- Department of Microbiology and ImmunologyTohoku University Graduate School of MedicineSendaiJapan
| | - Yoshiteru Kagawa
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Hirofumi Miyazaki
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Yu Takahashi
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Atsuko Asao
- Department of Microbiology and ImmunologyTohoku University Graduate School of MedicineSendaiJapan
| | - Takashi Maruyama
- Mucosal Immunology UnitNational Institute of Dental and Craniofacial ResearchNational Institutes of HealthBethesdaMDUSA
| | - Akihiko Yoshimura
- Department of Microbiology and ImmunologyKeio University School of MedicineTokyoJapan
| | - Naoto Ishii
- Department of Microbiology and ImmunologyTohoku University Graduate School of MedicineSendaiJapan
| | - Yuji Owada
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
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33
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Werlen G, Jain R, Jacinto E. MTOR Signaling and Metabolism in Early T Cell Development. Genes (Basel) 2021; 12:genes12050728. [PMID: 34068092 PMCID: PMC8152735 DOI: 10.3390/genes12050728] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
The mechanistic target of rapamycin (mTOR) controls cell fate and responses via its functions in regulating metabolism. Its role in controlling immunity was unraveled by early studies on the immunosuppressive properties of rapamycin. Recent studies have provided insights on how metabolic reprogramming and mTOR signaling impact peripheral T cell activation and fate. The contribution of mTOR and metabolism during early T-cell development in the thymus is also emerging and is the subject of this review. Two major T lineages with distinct immune functions and peripheral homing organs diverge during early thymic development; the αβ- and γδ-T cells, which are defined by their respective TCR subunits. Thymic T-regulatory cells, which have immunosuppressive functions, also develop in the thymus from positively selected αβ-T cells. Here, we review recent findings on how the two mTOR protein complexes, mTORC1 and mTORC2, and the signaling molecules involved in the mTOR pathway are involved in thymocyte differentiation. We discuss emerging views on how metabolic remodeling impacts early T cell development and how this can be mediated via mTOR signaling.
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34
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Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells 2021; 10:1074. [PMID: 33946533 PMCID: PMC8147249 DOI: 10.3390/cells10051074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
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Affiliation(s)
- Veronica Della Chiara
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), 2300 RC Leiden, The Netherlands; (V.D.C.); (L.D.)
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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35
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Paiva RA, Sousa AGG, Ramos CV, Ávila M, Lilue J, Paixão T, Martins VC. Self-renewal of double-negative 3 early thymocytes enables thymus autonomy but compromises the β-selection checkpoint. Cell Rep 2021; 35:108967. [PMID: 33852867 DOI: 10.1016/j.celrep.2021.108967] [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: 09/29/2020] [Revised: 01/29/2021] [Accepted: 03/18/2021] [Indexed: 10/21/2022] Open
Abstract
T lymphocyte differentiation in the steady state is characterized by high cellular turnover whereby thymocytes do not self-renew. However, if deprived of competent progenitors, the thymus can temporarily maintain thymopoiesis autonomously. This bears a heavy cost, because prolongation of thymus autonomy causes leukemia. Here, we show that, at an early stage, thymus autonomy relies on double-negative 3 early (DN3e) thymocytes that acquire stem-cell-like properties. Following competent progenitor deprivation, DN3e thymocytes become long lived, are required for thymus autonomy, differentiate in vivo, and include DNA-label-retaining cells. At the single-cell level, the transcriptional programs of thymopoiesis in autonomy and the steady state are similar. However, a new cell population emerges in autonomy that expresses an aberrant Notch target gene signature and bypasses the β-selection checkpoint. In summary, DN3e thymocytes have the potential to self-renew and differentiate in vivo if cell competition is impaired, but this generates atypical cells, probably the precursors of leukemia.
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Affiliation(s)
- Rafael A Paiva
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - António G G Sousa
- Bioinformatics Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Camila V Ramos
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Mariana Ávila
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Jingtao Lilue
- Bioinformatics Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Tiago Paixão
- Quantitative and Digital Science Unit, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal
| | - Vera C Martins
- Lymphocyte Development and Leukemogenesis Laboratory, Instituto Gulbenkian de Ciência, Calouste Gulbenkian Foundation, Oeiras 2780-156, Portugal.
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36
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Li Y, Li K, Zhu L, Li B, Zong D, Cai P, Jiang C, Du P, Lin J, Qu K. Development of double-positive thymocytes at single-cell resolution. Genome Med 2021; 13:49. [PMID: 33771202 PMCID: PMC8004397 DOI: 10.1186/s13073-021-00861-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/25/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND T cells generated from thymopoiesis are essential for the immune system, and recent single-cell studies have contributed to our understanding of the development of thymocytes at the genetic and epigenetic levels. However, the development of double-positive (DP) T cells, which comprise the majority of thymocytes, has not been well investigated. METHODS We applied single-cell sequencing to mouse thymocytes and analyzed the transcriptome data using Seurat. By applying unsupervised clustering, we defined thymocyte subtypes and validated DP cell subtypes by flow cytometry. We classified the cell cycle phases of each cell according to expression of cell cycle phase-specific genes. For immune synapse detection, we used immunofluorescent staining and ImageStream-based flow cytometry. We studied and integrated human thymocyte data to verify the conservation of our findings and also performed cross-species comparisons to examine species-specific gene regulation. RESULTS We classified blast, rearrangement, and selection subtypes of DP thymocytes and used the surface markers CD2 and Ly6d to identify these subtypes by flow cytometry. Based on this new classification, we found that the proliferation of blast DP cells is quite different from that of double-positive cells and other cell types, which tend to exit the cell cycle after a single round. At the DP cell selection stage, we observed that CD8-associated immune synapses formed between thymocytes, indicating that CD8sp selection occurred among thymocytes themselves. Moreover, cross-species comparison revealed species-specific transcription factors (TFs) that contribute to the transcriptional differences of thymocytes from humans and mice. CONCLUSIONS Our study classified DP thymocyte subtypes of different developmental stages and provided new insight into the development of DP thymocytes at single-cell resolution, furthering our knowledge of the fundamental immunological process of thymopoiesis.
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Affiliation(s)
- Young Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Kun Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Lianbang Zhu
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Bin Li
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Dandan Zong
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengfei Cai
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Chen Jiang
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Pengcheng Du
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Jun Lin
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China
| | - Kun Qu
- Department of oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, Anhui, China.
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230021, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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37
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Qi C, Wang Y, Li P, Zhao J. Gamma Delta T Cells and Their Pathogenic Role in Psoriasis. Front Immunol 2021; 12:627139. [PMID: 33732249 PMCID: PMC7959710 DOI: 10.3389/fimmu.2021.627139] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
γδT cells are an unconventional population of T lymphocytes that play an indispensable role in host defense, immune surveillance, and homeostasis of the immune system. They display unique developmental, distributional, and functional patterns and rapidly respond to various insults and contribute to diverse diseases. Although γδT cells make up only a small portion of the total T cell pool, emerging evidence suggest that aberrantly activated γδT cells may play a role in the pathogenesis of psoriasis. Dermal γδT cells are the major IL-17-producing cells in the skin that respond to IL-23 stimulation. Furthermore, γδT cells exhibit memory-cell-like characteristics that mediate repeated episodes of psoriatic inflammation. This review discusses the differentiation, development, distribution, and biological function of γδT cells and the mechanisms by which they contribute to psoriasis. Potential therapeutic approaches targeting these cells in psoriasis have also been detailed.
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Affiliation(s)
- Cong Qi
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Clinic and Basic Research with Traditional Chinese Medicine on Psoriasis, Beijing Institute of Traditional Chinese Medicine, Beijing, China
| | - Yazhuo Wang
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Clinic and Basic Research with Traditional Chinese Medicine on Psoriasis, Beijing Institute of Traditional Chinese Medicine, Beijing, China
| | - Ping Li
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Clinic and Basic Research with Traditional Chinese Medicine on Psoriasis, Beijing Institute of Traditional Chinese Medicine, Beijing, China
| | - Jingxia Zhao
- Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Clinic and Basic Research with Traditional Chinese Medicine on Psoriasis, Beijing Institute of Traditional Chinese Medicine, Beijing, China
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38
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Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function. Int J Mol Sci 2020; 21:ijms21228478. [PMID: 33187197 PMCID: PMC7696796 DOI: 10.3390/ijms21228478] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The adaptive immune response in vertebrates depends on the expression of antigen-specific receptors in lymphocytes. T-cell receptor (TCR) gene expression is exquisitely regulated during thymocyte development to drive the generation of αβ and γδ T lymphocytes. The TCRα, TCRβ, TCRγ, and TCRδ genes exist in two different configurations, unrearranged and rearranged. A correctly rearranged configuration is required for expression of a functional TCR chain. TCRs can take the form of one of three possible heterodimers, pre-TCR, TCRαβ, or TCRγδ which drive thymocyte maturation into αβ or γδ T lymphocytes. To pass from an unrearranged to a rearranged configuration, global and local three dimensional (3D) chromatin changes must occur during thymocyte development to regulate gene segment accessibility for V(D)J recombination. During this process, enhancers play a critical role by modifying the chromatin conformation and triggering noncoding germline transcription that promotes the recruitment of the recombination machinery. The different signaling that thymocytes receive during their development controls enhancer activity. Here, we summarize the dynamics of long-distance interactions established through chromatin regulatory elements that drive transcription and V(D)J recombination and how different signaling pathways are orchestrated to regulate the activity of enhancers to precisely control TCR gene expression during T-cell maturation.
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39
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Loontiens S, Dolens AC, Strubbe S, Van de Walle I, Moore FE, Depestel L, Vanhauwaert S, Matthijssens F, Langenau DM, Speleman F, Van Vlierberghe P, Durinck K, Taghon T. PHF6 Expression Levels Impact Human Hematopoietic Stem Cell Differentiation. Front Cell Dev Biol 2020; 8:599472. [PMID: 33251223 PMCID: PMC7672048 DOI: 10.3389/fcell.2020.599472] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 01/10/2023] Open
Abstract
Transcriptional control of hematopoiesis involves complex regulatory networks and functional perturbations in one of these components often results in malignancies. Loss-of-function mutations in PHF6, encoding a presumed epigenetic regulator, have been primarily described in T cell acute lymphoblastic leukemia (T-ALL) and the first insights into its function in normal hematopoiesis only recently emerged from mouse modeling experiments. Here, we investigated the role of PHF6 in human blood cell development by performing knockdown studies in cord blood and thymus-derived hematopoietic precursors to evaluate the impact on lineage differentiation in well-established in vitro models. Our findings reveal that PHF6 levels differentially impact the differentiation of human hematopoietic progenitor cells into various blood cell lineages, with prominent effects on lymphoid and erythroid differentiation. We show that loss of PHF6 results in accelerated human T cell development through reduced expression of NOTCH1 and its downstream target genes. This functional interaction in developing thymocytes was confirmed in vivo using a phf6-deficient zebrafish model that also displayed accelerated developmental kinetics upon reduced phf6 or notch1 activation. In summary, our work reveals that appropriate control of PHF6 expression is important for normal human hematopoiesis and provides clues towards the role of PHF6 in T-ALL development.
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Affiliation(s)
- Siebe Loontiens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Finola E. Moore
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
| | - Lisa Depestel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Filip Matthijssens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - David M. Langenau
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
- Harvard Stem Cell Institute, Cambridge, MA, United States
| | - Frank Speleman
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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40
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Anderson MK, Selvaratnam JS. Interaction between γδTCR signaling and the E protein-Id axis in γδ T cell development. Immunol Rev 2020; 298:181-197. [PMID: 33058287 DOI: 10.1111/imr.12924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/24/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023]
Abstract
γδ T cells acquire their functional properties in the thymus, enabling them to exert rapid innate-like responses. To understand how distinct γδ T cell subsets are generated, we have developed a Two-Stage model for γδ T cell development. This model is predicated on the finding that γδTCR signal strength impacts E protein activity through graded upregulation of Id3. Our model proposes that cells enter Stage 1 in response to a γδTCR signaling event in the cortex that activates a γδ T cell-specific gene network. Part of this program includes the upregulation of chemokine receptors that guide them to the medulla. In the medulla, Stage 1 cells receive distinct combinations of γδTCR, cytokine, and/co-stimulatory signals that induce their transit into Stage 2, either toward the γδT1 or the γδT17 lineage. The intersection between γδTCR and cytokine signals can tune Id3 expression, leading to different outcomes even in the presence of strong γδTCR signals. The thymic signaling niches required for γδT17 development are segregated in time and space, providing transient windows of opportunity during ontogeny. Understanding the regulatory context in which E proteins operate at different stages will be key in defining how their activity levels impose functional outcomes.
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Affiliation(s)
- Michele K Anderson
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Johanna S Selvaratnam
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada.,Department of Immunology, University of Toronto, Toronto, ON, Canada
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41
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Köchl R, Vanes L, Llorian Sopena M, Chakravarty P, Hartweger H, Fountain K, White A, Cowan J, Anderson G, Tybulewicz VL. Critical role of WNK1 in MYC-dependent early mouse thymocyte development. eLife 2020; 9:56934. [PMID: 33051000 PMCID: PMC7591260 DOI: 10.7554/elife.56934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
WNK1, a kinase that controls kidney salt homeostasis, also regulates adhesion and migration in CD4+ T cells. Wnk1 is highly expressed in thymocytes, and since migration is important for thymocyte maturation, we investigated a role for WNK1 in mouse thymocyte development. We find that WNK1 is required for the transition of double negative (DN) thymocytes through the β-selection checkpoint and subsequent proliferation and differentiation into double positive (DP) thymocytes. Furthermore, we show that WNK1 negatively regulates LFA1-mediated adhesion and positively regulates CXCL12-induced migration in DN thymocytes. Despite this, migration defects of WNK1-deficient thymocytes do not account for the developmental arrest. Instead, we show that in DN thymocytes WNK1 transduces pre-TCR signals via OXSR1 and STK39 kinases, and the SLC12A2 ion co-transporter that are required for post-transcriptional upregulation of MYC and subsequent proliferation and differentiation into DP thymocytes. Thus, a pathway regulating ion homeostasis is a critical regulator of thymocyte development.
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Affiliation(s)
- Robert Köchl
- The Francis Crick Institute, London, United Kingdom.,Kings College London, London, United Kingdom
| | - Lesley Vanes
- The Francis Crick Institute, London, United Kingdom
| | | | | | | | | | - Andrea White
- University of Birmingham, Birmingham, United Kingdom
| | | | | | - Victor Lj Tybulewicz
- The Francis Crick Institute, London, United Kingdom.,Imperial College, London, United Kingdom
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42
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Montel-Hagen A, Sun V, Casero D, Tsai S, Zampieri A, Jackson N, Li S, Lopez S, Zhu Y, Chick B, He C, de Barros SC, Seet CS, Crooks GM. In Vitro Recapitulation of Murine Thymopoiesis from Single Hematopoietic Stem Cells. Cell Rep 2020; 33:108320. [PMID: 33113379 PMCID: PMC7727762 DOI: 10.1016/j.celrep.2020.108320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/01/2020] [Accepted: 10/06/2020] [Indexed: 12/16/2022] Open
Abstract
We report a serum-free, 3D murine artificial thymic organoid (M-ATO)
system that mimics normal murine thymopoiesis with the production of all T cell
stages, from early thymic progenitors to functional single-positive (CD8SP and
CD4SP) TCRαβ and TCRγδ cells. RNA sequencing aligns
M-ATO-derived populations with phenotypically identical primary thymocytes.
M-ATOs initiated with Rag1−/− marrow
produce the same differentiation block as seen in the endogenous thymus, and
Notch signaling patterns in M-ATOs mirror primary thymopoiesis. M-ATOs initiated
with defined hematopoietic stem cells (HSCs) and lymphoid progenitors from
marrow and thymus generate each of the downstream differentiation stages,
allowing the kinetics of T cell differentiation to be tracked. Remarkably,
single HSCs deposited into each M-ATO generate the complete trajectory of T cell
differentiation, producing diverse TCR repertoires across clones that largely
match endogenous thymus. M-ATOs represent a highly reproducible and efficient
experimental platform for the interrogation of clonal thymopoiesis from
HSCs. Montel-Hagen et al. develop a murine artificial thymic organoid (M-ATO)
system to reproduce thymopoiesis in vitro from bone marrow stem
and progenitor cells (HSPCs). This method efficiently recapitulates the
phenotypic and transcriptional features of normal murine T cell development even
when initiated with a single HSC.
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Affiliation(s)
- Amélie Montel-Hagen
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Victoria Sun
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Molecular Biology Interdepartmental Program, UCLA, Los Angeles, CA, USA
| | - David Casero
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Steven Tsai
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Alexandre Zampieri
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Nicholas Jackson
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Suwen Li
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
| | - Shawn Lopez
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Yuhua Zhu
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Brent Chick
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Chongbin He
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Stéphanie C de Barros
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Christopher S Seet
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Gay M Crooks
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA; Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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43
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Astori A, Tingvall-Gustafsson J, Kuruvilla J, Coyaud E, Laurent EMN, Sunnerhagen M, Åhsberg J, Ungerbäck J, Strid T, Sigvardsson M, Raught B, Somasundaram R. ARID1a Associates with Lymphoid-Restricted Transcription Factors and Has an Essential Role in T Cell Development. THE JOURNAL OF IMMUNOLOGY 2020; 205:1419-1432. [PMID: 32747500 DOI: 10.4049/jimmunol.1900959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/29/2020] [Indexed: 11/19/2022]
Abstract
Maturation of lymphoid cells is controlled by the action of stage and lineage-restricted transcription factors working in concert with the general transcription and chromatin remodeling machinery to regulate gene expression. To better understand this functional interplay, we used Biotin Identification in human embryonic kidney cells to identify proximity interaction partners for GATA3, TCF7 (TCF1), SPI1, HLF, IKZF1, PAX5, ID1, and ID2. The proximity interaction partners shared among the lineage-restricted transcription factors included ARID1a, a BRG1-associated factor complex component. CUT&RUN analysis revealed that ARID1a shared binding with TCF7 and GATA3 at a substantial number of putative regulatory elements in mouse T cell progenitors. In support of an important function for ARID1a in lymphocyte development, deletion of Arid1a in early lymphoid progenitors in mice resulted in a pronounced developmental arrest in early T cell development with a reduction of CD4+CD8+ cells and a 20-fold reduction in thymic cellularity. Exploring gene expression patterns in DN3 cells from Wt and Arid1a-deficient mice suggested that the developmental block resided in the DN3a to DN3b transition, indicating a deficiency in β-selection. Our work highlights the critical importance of functional interactions between stage and lineage-restricted factors and the basic transcription machinery during lymphocyte differentiation.
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Affiliation(s)
- Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | | | - Jacob Kuruvilla
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden; and
| | - Josefine Åhsberg
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
| | - Tobias Strid
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, 22184 Lund, Sweden; .,Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 3K1, Canada
| | - Rajesh Somasundaram
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
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44
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Roels J, Kuchmiy A, De Decker M, Strubbe S, Lavaert M, Liang KL, Leclercq G, Vandekerckhove B, Van Nieuwerburgh F, Van Vlierberghe P, Taghon T. Distinct and temporary-restricted epigenetic mechanisms regulate human αβ and γδ T cell development. Nat Immunol 2020; 21:1280-1292. [PMID: 32719521 DOI: 10.1038/s41590-020-0747-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/24/2020] [Indexed: 01/08/2023]
Abstract
The development of TCRαβ and TCRγδ T cells comprises a step-wise process in which regulatory events control differentiation and lineage outcome. To clarify these mechanisms, we employed RNA-sequencing, ATAC-sequencing and ChIPmentation on well-defined thymocyte subsets that represent the continuum of human T cell development. The chromatin accessibility dynamics show clear stage specificity and reveal that human T cell-lineage commitment is marked by GATA3- and BCL11B-dependent closing of PU.1 sites. A temporary increase in H3K27me3 without open chromatin modifications is unique for β-selection, whereas emerging γδ T cells, which originate from common precursors of β-selected cells, show large chromatin accessibility changes due to strong T cell receptor (TCR) signaling. Furthermore, we unravel distinct chromatin landscapes between CD4+ and CD8+ αβ-lineage cells that support their effector functions and reveal gene-specific mechanisms that define mature T cells. This resource provides a framework for studying gene regulatory mechanisms that drive normal and malignant human T cell development.
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Affiliation(s)
- Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Anna Kuchmiy
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | | | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Marieke Lavaert
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Kai Ling Liang
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Cancer Research Institute Ghent, Ghent, Belgium.,Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium. .,Cancer Research Institute Ghent, Ghent, Belgium.
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45
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Machado A, Pouzolles M, Gailhac S, Fritz V, Craveiro M, López-Sánchez U, Kondo T, Pala F, Bosticardo M, Notarangelo LD, Petit V, Taylor N, Zimmermann VS. Phosphate Transporter Profiles in Murine and Human Thymi Identify Thymocytes at Distinct Stages of Differentiation. Front Immunol 2020; 11:1562. [PMID: 32793218 PMCID: PMC7387685 DOI: 10.3389/fimmu.2020.01562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Abstract
Thymocyte differentiation is dependent on the availability and transport of metabolites in the thymus niche. As expression of metabolite transporters is a rate-limiting step in nutrient utilization, cell surface transporter levels generally reflect the cell's metabolic state. The GLUT1 glucose transporter is upregulated on actively dividing thymocytes, identifying thymocytes with an increased metabolism. However, it is not clear whether transporters of essential elements such as phosphate are modulated during thymocyte differentiation. While PiT1 and PiT2 are both phosphate transporters in the SLC20 family, we show here that they exhibit distinct expression profiles on both murine and human thymocytes. PiT2 expression distinguishes thymocytes with high metabolic activity, identifying immature murine double negative (CD4−CD8−) DN3b and DN4 thymocyte blasts as well as immature single positive (ISP) CD8 thymocytes. Notably, the absence of PiT2 expression on RAG2-deficient thymocytes, blocked at the DN3a stage, strongly suggests that high PiT2 expression is restricted to thymocytes having undergone a productive TCRβ rearrangement at the DN3a/DN3b transition. Similarly, in the human thymus, PiT2 was upregulated on early post-β selection CD4+ISP and TCRαβ−CD4hiDP thymocytes co-expressing the CD71 transferrin receptor, a marker of metabolic activity. In marked contrast, expression of the PiT1 phosphate importer was detected on mature CD3+ murine and human thymocytes. Notably, PiT1 expression on CD3+DN thymocytes was identified as a biomarker of an aging thymus, increasing from 8.4 ± 1.5% to 42.4 ± 9.4% by 1 year of age (p < 0.0001). We identified these cells as TCRγδ and, most significantly, NKT, representing 77 ± 9% of PiT1+DN thymocytes by 1 year of age (p < 0.001). Thus, metabolic activity and thymic aging are associated with distinct expression profiles of the PiT1 and PiT2 phosphate transporters.
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Affiliation(s)
- Alice Machado
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marie Pouzolles
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Sarah Gailhac
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Vanessa Fritz
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marco Craveiro
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Uriel López-Sánchez
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Taisuke Kondo
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | | | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Valérie S Zimmermann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, United States.,Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
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46
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Vanderbeck A, Maillard I. Notch signaling at the crossroads of innate and adaptive immunity. J Leukoc Biol 2020; 109:535-548. [PMID: 32557824 DOI: 10.1002/jlb.1ri0520-138r] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Notch signaling is an evolutionarily conserved cell-to-cell signaling pathway that regulates cellular differentiation and function across multiple tissue types and developmental stages. In this review, we discuss our current understanding of Notch signaling in mammalian innate and adaptive immunity. The importance of Notch signaling is pervasive throughout the immune system, as it elicits lineage and context-dependent effects in a wide repertoire of cells. Although regulation of binary cell fate decisions encompasses many of the functions first ascribed to Notch in the immune system, recent advances in the field have refined and expanded our view of the Notch pathway beyond this initial concept. From establishing T cell identity in the thymus to regulating mature T cell function in the periphery, the Notch pathway is an essential, recurring signal for the T cell lineage. Among B cells, Notch signaling is required for the development and maintenance of marginal zone B cells in the spleen. Emerging roles for Notch signaling in innate and innate-like lineages such as classical dendritic cells and innate lymphoid cells are likewise coming into view. Lastly, we speculate on the molecular underpinnings that shape the activity and versatility of the Notch pathway.
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Affiliation(s)
- Ashley Vanderbeck
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Veterinary Medical Scientist Training Program, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Ivan Maillard
- Immunology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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47
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Dolens A, Durinck K, Lavaert M, Van der Meulen J, Velghe I, De Medts J, Weening K, Roels J, De Mulder K, Volders P, De Preter K, Kerre T, Vandekerckhove B, Leclercq G, Vandesompele J, Mestdagh P, Van Vlierberghe P, Speleman F, Taghon T. Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development. EMBO Rep 2020; 21:e49006. [PMID: 32255245 PMCID: PMC7202205 DOI: 10.15252/embr.201949006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/03/2020] [Accepted: 03/12/2020] [Indexed: 12/22/2022] Open
Abstract
γδ and αβ T cells have unique roles in immunity and both originate in the thymus from T-lineage committed precursors through distinct but unclear mechanisms. Here, we show that Notch1 activation is more stringently required for human γδ development compared to αβ-lineage differentiation and performed paired mRNA and miRNA profiling across 11 discrete developmental stages of human T cell development in an effort to identify the potential Notch1 downstream mechanism. Our data suggest that the miR-17-92 cluster is a Notch1 target in immature thymocytes and that miR-17 can restrict BCL11B expression in these Notch-dependent T cell precursors. We show that enforced miR-17 expression promotes human γδ T cell development and, consistently, that BCL11B is absolutely required for αβ but less for γδ T cell development. This study suggests that human γδ T cell development is mediated by a stage-specific Notch-driven negative feedback loop through which miR-17 temporally restricts BCL11B expression and provides functional insights into the developmental role of the disease-associated genes BCL11B and the miR-17-92 cluster in a human context.
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Affiliation(s)
| | - Kaat Durinck
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Marieke Lavaert
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | - Imke Velghe
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Jelle De Medts
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Karin Weening
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | - Juliette Roels
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | | | | | | | - Tessa Kerre
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
| | | | | | - Jo Vandesompele
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Pieter Mestdagh
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | | | - Frank Speleman
- Department of Biomolecular MedicineGhent UniversityGhentBelgium
| | - Tom Taghon
- Department of Diagnostic SciencesGhent UniversityGhentBelgium
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48
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Lee HW, Chung YS, Kim TJ. Heterogeneity of Human γδ T Cells and Their Role in Cancer Immunity. Immune Netw 2020; 20:e5. [PMID: 32158593 PMCID: PMC7049581 DOI: 10.4110/in.2020.20.e5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/04/2020] [Accepted: 02/08/2020] [Indexed: 12/24/2022] Open
Abstract
The γδ T cells are unconventional lymphocytes that function in both innate and adaptive immune responses against various intracellular and infectious stresses. The γδ T cells can be exploited as cancer-killing effector cells since γδ TCRs recognize MHC-like molecules and growth factor receptors that are upregulated in cancer cells, and γδ T cells can differentiate into cytotoxic effector cells. However, γδ T cells may also promote tumor progression by secreting IL-17 or other cytokines. Therefore, it is essential to understand how the differentiation and homeostasis of γδ T cells are regulated and whether distinct γδ T cell subsets have different functions. Human γδ T cells are classified into Vδ2 and non-Vδ2 γδ T cells. The majority of Vδ2 γδ T cells are Vγ9δ2 T cells that recognize pyrophosphorylated isoprenoids generated by the dysregulated mevalonate pathway. In contrast, Vδ1 T cells expand from initially diverse TCR repertoire in patients with infectious diseases and cancers. The ligands of Vδ1 T cells are diverse and include the growth factor receptors such as endothelial protein C receptor. Both Vδ1 and Vδ2 γδ T cells are implicated to have immunotherapeutic potentials for cancers, but the detailed elucidation of the distinct characteristics of 2 populations will be required to enhance the immunotherapeutic potential of γδ T cells. Here, we summarize recent progress regarding cancer immunology of human γδ T cells, including their development, heterogeneity, and plasticity, the putative mechanisms underlying ligand recognition and activation, and their dual effects on tumor progression in the tumor microenvironment.
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Affiliation(s)
- Hye Won Lee
- Department of Hospital Medicine, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Yun Shin Chung
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Tae Jin Kim
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
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49
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Parker ME, Ciofani M. Regulation of γδ T Cell Effector Diversification in the Thymus. Front Immunol 2020; 11:42. [PMID: 32038664 PMCID: PMC6992645 DOI: 10.3389/fimmu.2020.00042] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/08/2020] [Indexed: 12/27/2022] Open
Abstract
γδ T cells are the first T cell lineage to develop in the thymus and take up residence in a wide variety of tissues where they can provide fast, innate-like sources of effector cytokines for barrier defense. In contrast to conventional αβ T cells that egress the thymus as naïve cells, γδ T cells can be programmed for effector function during development in the thymus. Understanding the molecular mechanisms that determine γδ T cell effector fate is of great interest due to the wide-spread tissue distribution of γδ T cells and their roles in pathogen clearance, immunosurveillance, cancer, and autoimmune diseases. In this review, we will integrate the current understanding of the role of the T cell receptor, environmental signals, and transcription factor networks in controlling mouse innate-like γδ T cell effector commitment.
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Affiliation(s)
| | - Maria Ciofani
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
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50
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Kim SM, Park M, Yee SM, Ji KY, Lee EH, Nguyen TV, Nguyen THL, Jang J, Kim EM, Choi HR, Yun CH, Kang HS. Axl is a key regulator of intestinal γδ T-cell homeostasis. FASEB J 2019; 33:13386-13397. [DOI: 10.1096/fj.201901356r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Su-Man Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Min Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Su-Min Yee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Kon-Young Ji
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Eun-Hee Lee
- Deagu-Gyeongbuk Medical Innovation Foundation, Daegu, South Korea
| | - Thi-Van Nguyen
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Thi Hong-Loan Nguyen
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Jin Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Eun-Mi Kim
- Predictive Model Research Center, Korea Institute of Toxicology, Daejeon, South Korea
| | - Ha-Rim Choi
- Department of Nursing, Nambu University, Gwangju, South Korea
| | - Chul-Ho Yun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Hyung-Sik Kang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
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