1
|
Sun L, He X, Kong J, Yu H, Wang Y. Menstrual blood-derived stem cells exosomal miR-let-7 to ameliorate pulmonary fibrosis through inhibiting ferroptosis by Sp3/HDAC2/Nrf2 signaling pathway. Int Immunopharmacol 2024; 126:111316. [PMID: 38056200 DOI: 10.1016/j.intimp.2023.111316] [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: 07/23/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a serious, lifelong lung disease with high morbidity and high mortality. Menstrual blood-derived stem cells (MenSCs) derived exosomes (MenSCs-Exo) emerge as an attractive tool for the treatment of acute lung injury and fibrosis-related diseases. However, more comprehensive mechanism over how MenSCs derived exosomes exhibits anti-pulmonary fibrosis needs to be elucidated. In this study, TGF-β was used to construct cell fibrosis model, and bleomycin (BLM) was applied to induce lung tissue fibrosis mice model. BLM- and TGF-β1-induced cellular reactive oxygen species (ROS), mitochondrial DNA (mtDNA) damage, and lung epithelial cell apoptosis were alleviated by MenSCs-Exo treatment in vivo and in vitro. Besides, it was found that MenSCs-Exo delivered miR-let-7 into MLE-12 cells/lung epithelial cell and the reduction of miR-let-7 blocked the improvement produced by MenSCs-Exo. Mechanistically, miR-let-7 directly bound to Sp3 and negatively regulated its expression. Sp3 elevation promoted the expression of ferroptosis-related protein and mitochondrial DNA (mtDNA) damage markers via recruiting HDAC2, thereby inactivating keap1/Nrf2 signal cascade, which were confirmed in BLM-induced pulmonary fibrosis mice model under the combination therapy of the MenSCs-Exo and let-7 inhibitor. Collectively, MenSCs derived exosomes could transmit miR-let-7 into MLE-12 cells to inhibit the expression of Sp3, thereby weakening the recruitment effect of Sp3 on HDAC2, lifting the deacetylation restriction of HDAC2 on Nrf2, and enhancing the Nrf2 pathway. These changes further declined ferroptosis and delayed the pathological process of oxidative damage and lung epithelial cell apoptosis in PF.
Collapse
Affiliation(s)
- Lifang Sun
- Department of Tuberculosis, Zhejiang Hospital of Integrated Traditional Chinese and Western Medicine, Hangzhou 310003, PR China; Department of Tuberculosis, Hangzhou Red Cross Hospital, Hangzhou 310003, PR China
| | - Xinxin He
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou 311399, PR China
| | - Jiao Kong
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, PR China
| | - Huan Yu
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, PR China
| | - Yunguang Wang
- Department of Nephrology, the First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou, Zhejiang 310000, PR China.
| |
Collapse
|
2
|
Schmidt H, Raj T, O'Neill TJ, Muschaweckh A, Giesert F, Negraschus A, Hoefig KP, Behrens G, Esser L, Baumann C, Feederle R, Plaza-Sirvent C, Geerlof A, Gewies A, Isay SE, Ruland J, Schmitz I, Wurst W, Korn T, Krappmann D, Heissmeyer V. Unrestrained cleavage of Roquin-1 by MALT1 induces spontaneous T cell activation and the development of autoimmunity. Proc Natl Acad Sci U S A 2023; 120:e2309205120. [PMID: 37988467 PMCID: PMC10691344 DOI: 10.1073/pnas.2309205120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 11/23/2023] Open
Abstract
Constitutive activation of the MALT1 paracaspase in conventional T cells of Malt1TBM/TBM (TRAF6 Binding Mutant = TBM) mice causes fatal inflammation and autoimmunity, but the involved targets and underlying molecular mechanisms are unknown. We genetically rendered a single MALT1 substrate, the RNA-binding protein (RBP) Roquin-1, insensitive to MALT1 cleavage. These Rc3h1Mins/Mins mice showed normal immune homeostasis. Combining Rc3h1Mins/Mins alleles with those encoding for constitutively active MALT1 (TBM) prevented spontaneous T cell activation and restored viability of Malt1TBM/TBM mice. Mechanistically, we show how antigen/MHC recognition is translated by MALT1 into Roquin cleavage and derepression of Roquin targets. Increasing T cell receptor (TCR) signals inactivated Roquin more effectively, and only high TCR strength enabled derepression of high-affinity targets to promote Th17 differentiation. Induction of experimental autoimmune encephalomyelitis (EAE) revealed increased cleavage of Roquin-1 in disease-associated Th17 compared to Th1 cells in the CNS. T cells from Rc3h1Mins/Mins mice did not efficiently induce the high-affinity Roquin-1 target IκBNS in response to TCR stimulation, showed reduced Th17 differentiation, and Rc3h1Mins/Mins mice were protected from EAE. These data demonstrate how TCR signaling and MALT1 activation utilize graded cleavage of Roquin to differentially regulate target mRNAs that control T cell activation and differentiation as well as the development of autoimmunity.
Collapse
Affiliation(s)
- Henrik Schmidt
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Timsse Raj
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Thomas J. O'Neill
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Andreas Muschaweckh
- Institute for Experimental Neuroimmunology, Technical University of Munich, School of Medicine, Munich81675, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Arlinda Negraschus
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Kai P. Hoefig
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
| | - Gesine Behrens
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Lena Esser
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Christina Baumann
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Carlos Plaza-Sirvent
- Department of Molecular Immunology, ZKF2, Ruhr-University Bochum, Bochum44801, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Andreas Gewies
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Sophie E. Isay
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich81675, Germany
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich81675, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich81675, Germany
| | - Ingo Schmitz
- Department of Molecular Immunology, ZKF2, Ruhr-University Bochum, Bochum44801, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
- Max-Planck-Institute of Psychiatry, Munich80804, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising85354, Germany
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Technical University of Munich, School of Medicine, Munich81675, Germany
- Munich Cluster for Systems Neurology, Munich81377, Germany
| | - Daniel Krappmann
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
| |
Collapse
|
3
|
Nizharadze T, Becker NB, Höfer T. Quantitating CD8 + T cell memory development. Trends Immunol 2023; 44:519-529. [PMID: 37277233 DOI: 10.1016/j.it.2023.05.004] [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: 04/17/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
In acute immune responses to infection, memory T cells develop that can spawn recall responses. This process has not been observable directly in vivo. Here we highlight the utility of mathematical inference to derive quantitatively testable models of mammalian CD8+ T cell memory development from complex experimental data. Previous inference studies suggested that precursors of memory T cells arise early during the immune response. Recent work has both validated a crucial prediction of this T cell diversification model and refined the model. While multiple developmental routes to distinct memory subsets might exist, a branch point occurs early in proliferating T cell blasts, from which separate differentiation pathways emerge for slowly dividing precursors of re-expandable memory cells and rapidly dividing effectors.
Collapse
Affiliation(s)
- Tamar Nizharadze
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Nils B Becker
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.
| |
Collapse
|
4
|
Jones MC, Castonguay C, Nanaware PP, Weaver GC, Stadinski B, Kugler-Umana OA, Huseby ES, Stern LJ, McKinstry KK, Strutt TM, Devarajan P, Swain SL. CD4 Effector TCR Avidity for Peptide on APC Determines the Level of Memory Generated. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1950-1961. [PMID: 37093656 PMCID: PMC10247507 DOI: 10.4049/jimmunol.2200337] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 03/30/2023] [Indexed: 04/25/2023]
Abstract
Initial TCR affinity for peptide Ag is known to impact the generation of memory; however, its contributions later, when effectors must again recognize Ag at 5-8 d postinfection to become memory, is unclear. We examined whether the effector TCR affinity for peptide at this "effector checkpoint" dictates the extent of memory and degree of protection against rechallenge. We made an influenza A virus nucleoprotein (NP)-specific TCR transgenic mouse strain, FluNP, and generated NP-peptide variants that are presented by MHC class II to bind to the FluNP TCR over a broad range of avidity. To evaluate the impact of avidity in vivo, we primed naive donor FluNP in influenza A virus-infected host mice, purified donor effectors at the checkpoint, and cotransferred them with the range of peptides pulsed on activated APCs into second uninfected hosts. Higher-avidity peptides yielded higher numbers of FluNP memory cells in spleen and most dramatically in lung and draining lymph nodes and induced better protection against lethal influenza infection. Avidity determined memory cell number, not cytokine profile, and already impacted donor cell number within several days of transfer. We previously found that autocrine IL-2 production at the checkpoint prevents default effector apoptosis and supports memory formation. Here, we find that peptide avidity determines the level of IL-2 produced by these effectors and that IL-2Rα expression by the APCs enhances memory formation, suggesting that transpresentation of IL-2 by APCs further amplifies IL-2 availability. Secondary memory generation was also avidity dependent. We propose that this regulatory pathway selects CD4 effectors of highest affinity to progress to memory.
Collapse
Affiliation(s)
- Michael C. Jones
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Catherine Castonguay
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Padma P. Nanaware
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Grant C. Weaver
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Brian Stadinski
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Olivia A. Kugler-Umana
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Eric S. Huseby
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Lawrence J. Stern
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karl Kai McKinstry
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL. 32827,USA
| | - Tara M. Strutt
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL. 32827,USA
| | - Priyadharshini Devarajan
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Susan L. Swain
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| |
Collapse
|
5
|
Zander R, Khatun A, Kasmani MY, Chen Y, Cui W. Delineating the transcriptional landscape and clonal diversity of virus-specific CD4 + T cells during chronic viral infection. eLife 2022; 11:e80079. [PMID: 36255051 PMCID: PMC9629829 DOI: 10.7554/elife.80079] [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: 05/07/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
Although recent evidence indicates that CD4+ T cells responding to chronic viral infection are functionally heterogenous, our understanding of the developmental relationships between these subsets, and a determination of how their transcriptional landscape compares to their acute infection counterparts remains unclear. Additionally, whether cell-intrinsic factors such as TCR usage influence CD4+ T cell fate commitment during persistent infection has not previously been studied. Herein, we perform single-cell RNA sequencing (scRNA-seq) combined with single-cell T cell receptor sequencing (scTCR-seq) on virus-specific CD4+ T cells isolated from mice infected with chronic lymphocytic choriomeningitis virus (LCMV) infection. We identify several transcriptionally distinct states among the Th1, Tfh, and memory-like T cell subsets that form at the peak of infection, including the presence of a previously unrecognized Slamf7+ subset with cytolytic features. We further show that the relative distribution of these populations differs substantially between acute and persistent LCMV infection. Moreover, while the progeny of most T cell clones displays membership within each of these transcriptionally unique populations, overall supporting a one cell-multiple fate model, a small fraction of clones display a biased cell fate decision, suggesting that TCR usage may impact CD4+ T cell development during chronic infection. Importantly, comparative analyses further reveal both subset-specific and core gene expression programs that are differentially regulated between CD4+ T cells responding to acute and chronic LCMV infection. Together, these data may serve as a useful framework and allow for a detailed interrogation into the clonal distribution and transcriptional circuits underlying CD4+ T cell differentiation during chronic viral infection.
Collapse
Affiliation(s)
- Ryan Zander
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
| | - Achia Khatun
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Moujtaba Y Kasmani
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Yao Chen
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Weiguo Cui
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| |
Collapse
|
6
|
Yi J, Miller AT, Archambault AS, Jones AJ, Bradstreet TR, Bandla S, Hsu YS, Edelson BT, Zhou YW, Fremont DH, Egawa T, Singh N, Wu GF, Hsieh CS. Antigen-specific depletion of CD4 + T cells by CAR T cells reveals distinct roles of higher- and lower-affinity TCRs during autoimmunity. Sci Immunol 2022; 7:eabo0777. [PMID: 36206355 PMCID: PMC9867937 DOI: 10.1126/sciimmunol.abo0777] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Both higher- and lower-affinity self-reactive CD4+ T cells are expanded in autoimmunity; however, their individual contribution to disease remains unclear. We addressed this question using peptide-MHCII chimeric antigen receptor (pMHCII-CAR) T cells to specifically deplete peptide-reactive T cells in mice. Integration of improvements in CAR engineering with TCR repertoire analysis was critical for interrogating in vivo the role of TCR affinity in autoimmunity. Our original MOG35-55 pMHCII-CAR, which targeted only higher-affinity TCRs, could prevent the induction of experimental autoimmune encephalomyelitis (EAE). However, pMHCII-CAR enhancements to pMHCII stability, as well as increased survivability via overexpression of a dominant-negative Fas, were required to target lower-affinity MOG-specific T cells and reverse ongoing clinical EAE. Thus, these data suggest a model in which higher-affinity autoreactive T cells are required to provide the "activation energy" for initiating neuroinflammatory injury, but lower-affinity cells are sufficient to maintain ongoing disease.
Collapse
Affiliation(s)
- Jaeu Yi
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Co-first authors
| | - Aidan T. Miller
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Co-first authors
| | - Angela S. Archambault
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Andrew J. Jones
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA
| | - Tara R. Bradstreet
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sravanthi Bandla
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Yu-Sung Hsu
- Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Brian T. Edelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - You W. Zhou
- Wugen Inc, 4340 Duncan Ave, St Louis MO 63110, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan Singh
- Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63105, USA
| | - Gregory F. Wu
- Department of Neurology, Washington University in St. Louis, St. Louis, MO 63110, USA,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA,Correspondence: and
| | - Chyi-Song Hsieh
- Department of Internal Medicine, Division of Rheumatology, Washington University of Medicine, St. Louis, MO 63110, USA,Correspondence: and
| |
Collapse
|
7
|
Robinson AM, Higgins BW, Shuparski AG, Miller KB, McHeyzer-Williams LJ, McHeyzer-Williams MG. Evolution of antigen-specific follicular helper T cell transcription from effector function to memory. Sci Immunol 2022; 7:eabm2084. [PMID: 36206356 PMCID: PMC9881730 DOI: 10.1126/sciimmunol.abm2084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Understanding how follicular helper T cells (TFH) regulate the specialization, maturation, and differentiation of adaptive B cell immunity is crucial for developing durable high-affinity immune protection. Using indexed single-cell molecular strategies, we reveal a skewed intraclonal assortment of higher-affinity T cell receptors and the distinct molecular programming of the localized TFH compartment compared with emigrant conventional effector TH cells. We find a temporal shift in B cell receptor class switch, which permits identification of inflammatory and anti-inflammatory modules of transcriptional programming that subspecialize TFH function before and during the germinal center (GC) reaction. Late collapse of this local primary GC reaction reveals a persistent post-GC TFH population that discloses a putative memory TFH program. These studies define subspecialized antigen-specific TFH transcriptional programs that progressively change with antibody class-specific evolution of high-affinity B cell immunity and a memory TFH transcriptional program that emerges upon local GC resolution.
Collapse
|
8
|
Richard AC. Divide and Conquer: Phenotypic and Temporal Heterogeneity Within CD8+ T Cell Responses. Front Immunol 2022; 13:949423. [PMID: 35911755 PMCID: PMC9334874 DOI: 10.3389/fimmu.2022.949423] [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: 05/20/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of technologies that can characterize the phenotypes, functions and fates of individual cells has revealed extensive and often unexpected levels of diversity between cells that are nominally of the same subset. CD8+ T cells, also known as cytotoxic T lymphocytes (CTLs), are no exception. Investigations of individual CD8+ T cells both in vitro and in vivo have highlighted the heterogeneity of cellular responses at the levels of activation, differentiation and function. This review takes a broad perspective on the topic of heterogeneity, outlining different forms of variation that arise during a CD8+ T cell response. Specific attention is paid to the impact of T cell receptor (TCR) stimulation strength on heterogeneity. In particular, this review endeavors to highlight connections between variation at different cellular stages, presenting known mechanisms and key open questions about how variation between cells can arise and propagate.
Collapse
|
9
|
Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4 + T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. eLife 2022; 11:76339. [PMID: 35829695 PMCID: PMC9323004 DOI: 10.7554/elife.76339] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Using single-cell transcriptomics, we characterized the diversity of CD4+ T cells responding to self-resolving and chronic viral infections in mice. We built a comprehensive map of virus-specific CD4+ T cells and their evolution over time, and identified six major cell states consistently observed in acute and chronic infections. During the course of acute infections, T cell composition progressively changed from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, in persistent infections T cells acquired distinct, chronicity-associated programs. By single-cell T cell receptor (TCR) analysis, we characterized the clonal structure of virus-specific CD4+ T cells across individuals. Virus-specific CD4+ T cell responses were essentially private across individuals and most T cells differentiated into both Tfh and Th1 subtypes irrespective of their TCR. Finally, we showed that our CD4+ T cell map can be used as a reference to accurately interpret cell states in external single-cell datasets across tissues and disease models. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis.
Collapse
Affiliation(s)
- Massimo Andreatta
- Agora Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| | - Ariel Tjitropranoto
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Zachary Sherman
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Michael C Kelly
- Frederick National Laboratory for Cancer Research, Fregerick, United States
| | - Thomas Ciucci
- Department of Microbiology and Immunology, University of Rochester, Rochester, United States
| | - Santiago J Carmona
- Agora Cancer Research Center, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
10
|
Heritable changes in division speed accompany the diversification of single T cell fate. Proc Natl Acad Sci U S A 2022; 119:2116260119. [PMID: 35217611 PMCID: PMC8892279 DOI: 10.1073/pnas.2116260119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 11/18/2022] Open
Abstract
Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. Bayesian inference of tree-structured data reveals that clonal expansion is divided into a homogenously fast burst phase encompassing two to three divisions and a subsequent diversification phase during which T cells segregate into quickly dividing effector T cells and more slowly cycling memory precursors. Our work highlights cell cycle speed as a major heritable property that is regulated in parallel to key lineage decisions of activated T cells. Rapid clonal expansion of antigen-specific T cells is a fundamental feature of adaptive immune responses. It enables the outgrowth of an individual T cell into thousands of clonal descendants that diversify into short-lived effectors and long-lived memory cells. Clonal expansion is thought to be programmed upon priming of a single naive T cell and then executed by homogenously fast divisions of all of its descendants. However, the actual speed of cell divisions in such an emerging “T cell family” has never been measured with single-cell resolution. Here, we utilize continuous live-cell imaging in vitro to track the division speed and genealogical connections of all descendants derived from a single naive CD8+ T cell throughout up to ten divisions of activation-induced proliferation. This comprehensive mapping of T cell family trees identifies a short burst phase, in which division speed is homogenously fast and maintained independent of external cytokine availability or continued T cell receptor stimulation. Thereafter, however, division speed diversifies, and model-based computational analysis using a Bayesian inference framework for tree-structured data reveals a segregation into heritably fast- and slow-dividing branches. This diversification of division speed is preceded already during the burst phase by variable expression of the interleukin-2 receptor alpha chain. Later it is accompanied by selective expression of memory marker CD62L in slower dividing branches. Taken together, these data demonstrate that T cell clonal expansion is structured into subsequent burst and diversification phases, the latter of which coincides with specification of memory versus effector fate.
Collapse
|
11
|
Ciucci T, Vacchio MS, Chen T, Nie J, Chopp LB, McGavern DB, Kelly MC, Bosselut R. Dependence on Bcl6 and Blimp1 drive distinct differentiation of murine memory and follicular helper CD4+ T cells. J Exp Med 2022; 219:e20202343. [PMID: 34792530 PMCID: PMC8605495 DOI: 10.1084/jem.20202343] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022] Open
Abstract
During the immune response, CD4+ T cells differentiate into distinct effector subtypes, including follicular helper T (Tfh) cells that help B cells, and into memory cells. Tfh and memory cells are required for long-term immunity; both depend on the transcription factor Bcl6, raising the question whether they differentiate through similar mechanisms. Here, using single-cell RNA and ATAC sequencing, we show that virus-responding CD4+ T cells lacking both Bcl6 and Blimp1 can differentiate into cells with transcriptomic, chromatin accessibility, and functional attributes of memory cells but not of Tfh cells. Thus, Bcl6 promotes memory cell differentiation primarily through its repression of Blimp1. These findings demonstrate that distinct mechanisms underpin the differentiation of memory and Tfh CD4+ cells and define the Bcl6-Blimp1 axis as a potential target for promoting long-term memory T cell differentiation.
Collapse
Affiliation(s)
- Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Melanie S. Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ting Chen
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jia Nie
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura B. Chopp
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Immunology Graduate Group, University of Pennsylvania Medical School, Philadelphia, PA
| | - Dorian B. McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Michael C. Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
12
|
Grassmann S, Sun JC, Buchholz VR. Retrogenic Color-Barcoding for Fate Mapping of Single Innate Lymphocytes. Methods Mol Biol 2022; 2463:117-127. [PMID: 35344171 DOI: 10.1007/978-1-0716-2160-8_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lymphocyte fate mapping using single-cell transfers has been used to study T and B cell differentiation. Recently, retrogenic color-barcoding has allowed the extension of this approach to single innate lymphocytes such as NK cells. This new and versatile technology is based on the transduction of hematopoietic stem cells (HSCs) with a collection of retroviruses encoding distinct fluorescent proteins. Through combinatorial transduction, fluorescent protein barcodes are generated, which are inherited by the progeny of HSCs after transfer. By sorting individual cells expressing unique color-barcodes from the mature lymphocyte populations derived from these HSCs, it is now possible to track the fate of innate lymphocytes in vivo.
Collapse
Affiliation(s)
- Simon Grassmann
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich, Germany.
| |
Collapse
|
13
|
Thapa P, Guyer RS, Yang AY, Parks CA, Brusko TM, Brusko M, Connors TJ, Farber DL. Infant T cells are developmentally adapted for robust lung immune responses through enhanced T cell receptor signaling. Sci Immunol 2021; 6:eabj0789. [PMID: 34890254 PMCID: PMC8765725 DOI: 10.1126/sciimmunol.abj0789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Infants require coordinated immune responses to prevent succumbing to multiple infectious challenges during early life, particularly in the respiratory tract. The mechanisms by which infant T cells are functionally adapted for these responses are not well understood. Here, we demonstrated using an in vivo mouse cotransfer model that infant T cells generated greater numbers of lung-homing effector cells in response to influenza infection compared with adult T cells in the same host, due to augmented T cell receptor (TCR)–mediated signaling. Mouse infant T cells showed increased sensitivity to low antigen doses, originating at the interface between T cells and antigen-bearing accessory cells—through actin-mediated mobilization of signaling molecules to the immune synapse. This enhanced signaling was also observed in human infant versus adult T cells. Our findings provide a mechanism for how infants control pathogen load and dissemination, which is important for designing developmentally targeted strategies for promoting immune responses at this vulnerable life stage.
Collapse
Affiliation(s)
- Puspa Thapa
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Rebecca S. Guyer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Alexander Y. Yang
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Christopher A. Parks
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032
| | - Todd M. Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611
| | - Thomas J. Connors
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032
| | - Donna L. Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032
| |
Collapse
|
14
|
Rogers D, Sood A, Wang H, van Beek JJP, Rademaker TJ, Artusa P, Schneider C, Shen C, Wong DC, Bhagrath A, Lebel MÈ, Condotta SA, Richer MJ, Martins AJ, Tsang JS, Barreiro LB, François P, Langlais D, Melichar HJ, Textor J, Mandl JN. Pre-existing chromatin accessibility and gene expression differences among naive CD4 + T cells influence effector potential. Cell Rep 2021; 37:110064. [PMID: 34852223 DOI: 10.1016/j.celrep.2021.110064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/26/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.
Collapse
Affiliation(s)
- Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Aditi Sood
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Microbiology, Immunology, and Infectious Disease, Université de Montréal, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Jasper J P van Beek
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Patricio Artusa
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Caitlin Schneider
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Connie Shen
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Dylan C Wong
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Aanya Bhagrath
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Paul François
- Department of Physics, McGill University, Montreal, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University Genome Centre, Montreal, QC, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
| |
Collapse
|
15
|
Staggered starts in the race to T cell activation. Trends Immunol 2021; 42:994-1008. [PMID: 34649777 PMCID: PMC7612485 DOI: 10.1016/j.it.2021.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023]
Abstract
How T lymphocytes tune their responses to different strengths of stimulation is a fundamental question in immunology. Recent work using new optogenetic, single-cell genomic, and live-imaging approaches has revealed that stimulation strength controls the rate of individual cell responses within a population. Moreover, these responses have been found to use shared molecular programs, regardless of stimulation strength. However, additional data indicate that stimulation duration or cytokine feedback can impact later gene expression phenotypes of activated cells. In-depth molecular studies have suggested mechanisms by which stimulation strength might modulate the probability of T cell activation. This emerging model allows activating T cells to achieve a wide range of population responses through probabilistic control within individual cells.
Collapse
|
16
|
Kretschmer L, Busch DH, Buchholz VR. A Single-Cell Perspective on Memory T-Cell Differentiation. Cold Spring Harb Perspect Biol 2021; 13:a038067. [PMID: 33903160 PMCID: PMC8411955 DOI: 10.1101/cshperspect.a038067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Memory differentiation of CD4 and CD8 T-cell populations has been extensively studied and many key molecular players and transcriptional networks have been identified. But how regulatory principles, identified on this population level, translate to immune responses that originate from single antigen-specific T cells is only now being elucidated. Here, we provide a short summary of the approaches used for mapping the fate of individual T cells and their progeny in vivo. We then highlight which major questions, with respect to memory T-cell differentiation, have been addressed by studying the development of single-cell-derived T-cell families during infection or vaccination. We discuss how fate decisions of single T cells are modulated by the affinity of their TCR and further shaped through a coregulation of T-cell differentiation and T-cell proliferation. These current findings indicate the early segregation into slowly dividing T central memory precursors (CMPs) and rapidly dividing non-CMPs, as a key event that separates the developmental paths of long- and short-lived T cells.
Collapse
Affiliation(s)
- Lorenz Kretschmer
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich 81675, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich (TUM), Munich 81675 , Germany
| |
Collapse
|
17
|
Niebuhr M, Belde J, Fähnrich A, Serge A, Irla M, Ellebrecht CT, Hammers CM, Bieber K, Westermann J, Kalies K. Receptor repertoires of murine follicular T helper cells reveal a high clonal overlap in separate lymph nodes in autoimmunity. eLife 2021; 10:70053. [PMID: 34402793 PMCID: PMC8370764 DOI: 10.7554/elife.70053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Follicular T helper cells (Tfh) are a specialized subset of CD4 effector T cells that are crucial for germinal center (GC) reactions and for selecting B cells to undergo affinity maturation. Despite this central role for humoral immunity, only few data exist about their clonal distribution when multiple lymphoid organs are exposed to the same antigen (Ag) as it is the case in autoimmunity. Here, we used an autoantibody-mediated disease model of the skin and injected one auto-Ag into the two footpads of the same mouse and analyzed the T cell receptor (TCR)β sequences of Tfh located in GCs of both contralateral draining lymph nodes. We found that over 90% of the dominant GC-Tfh clonotypes were shared in both lymph nodes but only transiently. The initially dominant Tfh clonotypes especially declined after establishment of chronic disease while GC reaction and autoimmune disease continued. Our data demonstrates a dynamic behavior of Tfh clonotypes under autoimmune conditions and emphasizes the importance of the time point for distinguishing auto-Ag-specific Tfh clonotypes from potential bystander activated ones.
Collapse
Affiliation(s)
- Markus Niebuhr
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Julia Belde
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Arnauld Serge
- Laboratoire Adhésion et Inflammation, Inserm U1067 CNRS, Aix-Marseille Université, Marseille, France
| | - Magali Irla
- Centre d'Immunologie de Marseille Luminy (CIML), INSERM U1104, Aix-Marseille Université UM2, Marseille, France
| | - Christoph T Ellebrecht
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Pennsylvania, Philadelphia, United States
| | - Christoph M Hammers
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| |
Collapse
|
18
|
Khatun A, Kasmani MY, Zander R, Schauder DM, Snook JP, Shen J, Wu X, Burns R, Chen YG, Lin CW, Williams MA, Cui W. Single-cell lineage mapping of a diverse virus-specific naive CD4 T cell repertoire. J Exp Med 2021; 218:e20200650. [PMID: 33201171 PMCID: PMC7676493 DOI: 10.1084/jem.20200650] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/24/2020] [Accepted: 10/22/2020] [Indexed: 12/21/2022] Open
Abstract
Tracking how individual naive T cells from a natural TCR repertoire clonally expand, differentiate, and make lineage choices in response to an infection has not previously been possible. Here, using single-cell sequencing technology to identify clones by their unique TCR sequences, we were able to trace the clonal expansion, differentiation trajectory, and lineage commitment of individual virus-specific CD4 T cells during an acute lymphocytic choriomeningitis virus (LCMV) infection. Notably, we found previously unappreciated clonal diversity and cellular heterogeneity among virus-specific helper T cells. Interestingly, although most naive CD4 T cells gave rise to multiple lineages at the clonal level, ∼28% of naive cells exhibited a preferred lineage choice toward either Th1 or TFH cells. Mechanistically, we found that TCR structure, in particular the CDR3 motif of the TCR α chain, skewed lineage decisions toward the TFH cell fate.
Collapse
Affiliation(s)
- Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Moujtaba Y. Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Ryan Zander
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - David M. Schauder
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Jeremy P. Snook
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Jian Shen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
- Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI
| | - Chien-Wei Lin
- Institute for Health and Equity, Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI
| | - Matthew A. Williams
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| |
Collapse
|
19
|
Kervevan J, Chakrabarti LA. Role of CD4+ T Cells in the Control of Viral Infections: Recent Advances and Open Questions. Int J Mol Sci 2021; 22:E523. [PMID: 33430234 PMCID: PMC7825705 DOI: 10.3390/ijms22020523] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/26/2022] Open
Abstract
CD4+ T cells orchestrate adaptive immune responses through their capacity to recruit and provide help to multiple immune effectors, in addition to exerting direct effector functions. CD4+ T cells are increasingly recognized as playing an essential role in the control of chronic viral infections. In this review, we present recent advances in understanding the nature of CD4+ T cell help provided to antiviral effectors. Drawing from our studies of natural human immunodeficiency virus (HIV) control, we then focus on the role of high-affinity T cell receptor (TCR) clonotypes in mediating antiviral CD4+ T cell responses. Last, we discuss the role of TCR affinity in determining CD4+ T cell differentiation, reviewing the at times divergent studies associating TCR signal strength to the choice of a T helper 1 (Th1) or a T follicular helper (Tfh) cell fate.
Collapse
Affiliation(s)
- Jérôme Kervevan
- Control of Chronic Viral Infections Group (CIVIC), Virus and Immunity Unit, Institut Pasteur, 75724 Paris, France;
- CNRS UMR, 3569 Paris, France
| | - Lisa A. Chakrabarti
- Control of Chronic Viral Infections Group (CIVIC), Virus and Immunity Unit, Institut Pasteur, 75724 Paris, France;
- CNRS UMR, 3569 Paris, France
| |
Collapse
|
20
|
Grassmann S, Mihatsch L, Mir J, Kazeroonian A, Rahimi R, Flommersfeld S, Schober K, Hensel I, Leube J, Pachmayr LO, Kretschmer L, Zhang Q, Jolly A, Chaudhry MZ, Schiemann M, Cicin-Sain L, Höfer T, Busch DH, Flossdorf M, Buchholz VR. Early emergence of T central memory precursors programs clonal dominance during chronic viral infection. Nat Immunol 2020; 21:1563-1573. [DOI: 10.1038/s41590-020-00807-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/14/2020] [Indexed: 12/13/2022]
|
21
|
Sheikh AA, Groom JR. Transcription tipping points for T follicular helper cell and T-helper 1 cell fate commitment. Cell Mol Immunol 2020; 18:528-538. [PMID: 32999454 PMCID: PMC7525231 DOI: 10.1038/s41423-020-00554-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
During viral infection, immune cells coordinate the induction of inflammatory responses that clear infection and humoral responses that promote protection. CD4+ T-cell differentiation sits at the center of this axis. Differentiation toward T-helper 1 (Th1) cells mediates inflammation and pathogen clearance, while T follicular helper (Tfh) cells facilitate germinal center (GC) reactions for the generation of high-affinity antibodies and immune memory. While Th1 and Tfh differentiation occurs in parallel, these CD4+ T-cell identities are mutually exclusive, and progression toward these ends is determined via the upregulation of T-bet and Bcl6, respectively. These lineage-defining transcription factors act in concert with multiple networks of transcriptional regulators that tip the T-bet and Bcl6 axis in CD4+ T-cell progenitors to either a Th1 or Tfh fate. It is now clear that these transcriptional networks are guided by cytokine cues that are not only varied between distinct viral infections but also dynamically altered throughout the duration of infection. Thus, multiple intrinsic and extrinsic factors combine to specify the fate, plasticity, and function of Th1 and Tfh cells during infection. Here, we review the current information on the mode of action of the lineage-defining transcription factors Bcl6 and T-bet and how they act individually and in complex to govern CD4+ T-cell ontogeny. Furthermore, we outline the multifaceted transcriptional regulatory networks that act upstream and downstream of Bcl6 and T-bet to tip the differentiation equilibrium toward either a Tfh or Th1 fate and how these are impacted by dynamic inflammatory cues.
Collapse
Affiliation(s)
- Amania A Sheikh
- Divisions of Immunology and Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joanna R Groom
- Divisions of Immunology and Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
22
|
Bhattacharyya ND, Feng CG. Regulation of T Helper Cell Fate by TCR Signal Strength. Front Immunol 2020; 11:624. [PMID: 32508803 PMCID: PMC7248325 DOI: 10.3389/fimmu.2020.00624] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
T cells are critical in orchestrating protective immune responses to cancer and an array of pathogens. The interaction between a peptide MHC (pMHC) complex on antigen presenting cells (APCs) and T cell receptors (TCRs) on T cells initiates T cell activation, division, and clonal expansion in secondary lymphoid organs. T cells must also integrate multiple T cell-intrinsic and extrinsic signals to acquire the effector functions essential for the defense against invading microbes. In the case of T helper cell differentiation, while innate cytokines have been demonstrated to shape effector CD4+ T lymphocyte function, the contribution of TCR signaling strength to T helper cell differentiation is less understood. In this review, we summarize the signaling cascades regulated by the strength of TCR stimulation. Various mechanisms in which TCR signal strength controls T helper cell expansion and differentiation are also discussed.
Collapse
Affiliation(s)
- Nayan D Bhattacharyya
- Immunology and Host Defense Group, Discipline of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Carl G Feng
- Immunology and Host Defense Group, Discipline of Infectious Diseases and Immunology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Tuberculosis Research Program, Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
23
|
Abstract
One of the hallmarks of the vertebrate adaptive immune system is the prolific expansion of individual cell clones that encounter their cognate antigen. More recently, however, there is growing evidence for the clonal expansion of innate lymphocytes, particularly in the context of pathogen challenge. Clonal expansion not only serves to amplify the number of specific lymphocytes to mount a robust protective response to the pathogen at hand but also results in selection and differentiation of the responding lymphocytes to generate a multitude of cell fates. Here, we summarize the evidence for clonal expansion in innate lymphocytes, which has primarily been observed in natural killer (NK) cells responding to cytomegalovirus infection, and consider the requirements for such a response in NK cells in light of those for T cells. Furthermore, we discuss multiple aspects of heterogeneity that both contribute to and result from the fundamental immunological process of clonal expansion, highlighting the parallels between innate and adaptive lymphocytes, with a particular focus on NK cells and CD8+ T cells.
Collapse
|
24
|
Abadie K, Pease NA, Wither MJ, Kueh HY. Order by chance: origins and benefits of stochasticity in immune cell fate control. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 18:95-103. [PMID: 33791444 PMCID: PMC8009491 DOI: 10.1016/j.coisb.2019.10.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To protect against diverse challenges, the immune system must continuously generate an arsenal of specialized cell types, each of which can mount a myriad of effector responses upon detection of potential threats. To do so, it must generate multiple differentiated cell populations with defined sizes and proportions, often from rare starting precursor cells. Here, we discuss the emerging view that inherently probabilistic mechanisms, involving rare, rate-limiting regulatory events in single cells, control fate decisions and population sizes and fractions during immune development and function. We first review growing evidence that key fate control points are gated by stochastic signaling and gene regulatory events that occur infrequently over decision-making timescales, such that initially homogeneous cells can adopt variable outcomes in response to uniform signals. We next discuss how such stochastic control can provide functional capabilities that are harder to achieve with deterministic control strategies, and may be central to robust immune system function.
Collapse
Affiliation(s)
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington
- Molecular and Cellular Biology Program, University of Washington
| | | | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington
| |
Collapse
|
25
|
Hawse WF, Cattley RT, Wendell SG. Cutting Edge: TCR Signal Strength Regulates Acetyl-CoA Metabolism via AKT. THE JOURNAL OF IMMUNOLOGY 2019; 203:2771-2775. [PMID: 31628154 DOI: 10.4049/jimmunol.1900749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/25/2019] [Indexed: 12/17/2022]
Abstract
TCR signaling activates kinases including AKT/mTOR that engage metabolic networks to support the energetic demands of a T cell during an immune response. It is realized that CD4+ T cell subsets have different metabolic requirements. Yet, how TCR signaling is coupled to the regulation of intermediate metabolites and how changes in metabolite flux contribute to T cell differentiation are less established. We find that TCR signaling regulates acetyl-CoA metabolism via AKT in murine CD4+ T cells. Weak TCR signals promote AKT-catalyzed phosphorylation and inhibition of citrate synthase, elevated acetyl-CoA levels, and hyperacetylation of mitochondrial proteins. Genetic knockdown of citrate synthase promotes increased nuclear acetyl-CoA levels, increased histone acetylation at the FOXP3 promotor and induction of FOXP3 transcription. These data identify a circuit between AKT signaling and acetyl-CoA metabolism regulated via TCR signal strength and that transient fluctuations in acetyl-CoA levels function in T cell fate decisions.
Collapse
Affiliation(s)
- William F Hawse
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Richard T Cattley
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261; and
| | - Stacy G Wendell
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261
| |
Collapse
|
26
|
T cell engineering for adoptive T cell therapy: safety and receptor avidity. Cancer Immunol Immunother 2019; 68:1701-1712. [PMID: 31542797 DOI: 10.1007/s00262-019-02395-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 09/10/2019] [Indexed: 12/13/2022]
Abstract
Since the first bone marrow transplantation, adoptive T cell therapy (ACT) has developed over the last 80 years to a highly efficient and specific therapy for infections and cancer. Genetic engineering of T cells with antigen-specific receptors now provides the possibility of generating highly defined and efficacious T cell products. The high sensitivity of engineered T cells towards their targets, however, also bears the risk of severe off-target toxicities. Therefore, different safety strategies for engineered T cells have been developed that enable removal of the transferred cells in case of adverse events, control of T cell activity or improvement of target selectivity. Receptor avidity is a crucial component in the balance between safety and efficacy of T cell products. In clinical trials, T cells equipped with high avidity T cell receptor (TCR)/chimeric antigen receptor (CAR) have been mostly used so far because of their faster and better response to antigen recognition. However, over-activation can trigger T cell exhaustion/death as well as side effects due to excessive cytokine production. Low avidity T cells, on the other hand, are less susceptible to over-activation and could possess better selectivity in case of tumor antigens shared with healthy tissues, but complete tumor eradication may not be guaranteed. In this review we describe how 'optimal' TCR/CAR affinity can increase the safety/efficacy balance of engineered T cells, and discuss simultaneous or sequential infusion of high and low avidity receptors as further options for efficacious but safe T cell therapy.
Collapse
|
27
|
Sood A, Lebel MÈ, Fournier M, Rogers D, Mandl JN, Melichar HJ. Differential interferon-gamma production potential among naïve CD4 + T cells exists prior to antigen encounter. Immunol Cell Biol 2019; 97:931-940. [PMID: 31420892 DOI: 10.1111/imcb.12287] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/08/2019] [Accepted: 08/15/2019] [Indexed: 12/14/2022]
Abstract
Individual CD4+ T cells can become one of a number of helper (Th) lineages with distinct effector functions. However, whether biases in Th potential exist prior to antigen encounter is unknown. Studies have identified cell-intrinsic functional heterogeneity among naïve T cells that can be parsed based on the strength of T-cell receptor (TCR) interactions with self-peptide. Here, using CD5 levels as a surrogate for the strength of these basal TCR signals, we sought to identify pre-existing effector biases in the CD4+ T-cell lineage. We show that ex vivo-activated CD5lo CD4+ T cells produce greater amounts of the Th1 cytokine interferon-gamma (IFNγ) than their CD5hi counterparts. In addition, a greater percentage of CD5lo effector CD4+ T cells produce IFNγ in both polyclonal and monoclonal CD4+ T-cell populations after antigen challenge in vivo. These results suggest that differential IFNγ production potential exists among CD4+ T cells prior to activation and independent of TCR affinity for foreign antigen.
Collapse
Affiliation(s)
- Aditi Sood
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, H1T 2M4, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, H3T 1J4, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, H1T 2M4, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, H3T 1J4, Canada
| | - Marilaine Fournier
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, H1T 2M4, Canada
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, Quebec, H3G 0B1, Canada
| | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, Quebec, H3G 0B1, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec, H1T 2M4, Canada.,Département de médecine, Université de Montréal, Montreal, Quebec, H3T 1J4, Canada
| |
Collapse
|
28
|
Grassmann S, Pachmayr LO, Leube J, Mihatsch L, Andrae I, Flommersfeld S, Oduro J, Cicin-Sain L, Schiemann M, Flossdorf M, Buchholz VR. Distinct Surface Expression of Activating Receptor Ly49H Drives Differential Expansion of NK Cell Clones upon Murine Cytomegalovirus Infection. Immunity 2019; 50:1391-1400.e4. [DOI: 10.1016/j.immuni.2019.04.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/08/2019] [Accepted: 04/25/2019] [Indexed: 12/25/2022]
|
29
|
Pei W, Wang X, Rössler J, Feyerabend TB, Höfer T, Rodewald HR. Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice. Nat Protoc 2019; 14:1820-1840. [PMID: 31110297 DOI: 10.1038/s41596-019-0163-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/12/2019] [Indexed: 01/02/2023]
Abstract
Fate mapping is a powerful genetic tool for linking stem or progenitor cells with their progeny, and hence for defining cell lineages in vivo. The resolution of fate mapping depends on the numbers of distinct markers that are introduced in the beginning into stem or progenitor cells; ideally, numbers should be sufficiently large to allow the tracing of output from individual cells. Highly diverse genetic barcodes can serve this purpose. We recently developed an endogenous genetic barcoding system, termed Polylox. In Polylox, random DNA recombination can be induced by transient activity of Cre recombinase in a 2.1-kb-long artificial recombination substrate that has been introduced into a defined locus in mice (Rosa26Polylox reporter mice). Here, we provide a step-by-step protocol for the use of Polylox, including barcode induction and estimation of induction efficiency, barcode retrieval with single-molecule real-time (SMRT) DNA sequencing followed by computational barcode identification, and the calculation of barcode-generation probabilities, which is key for estimations of single-cell labeling for a given number of stem cells. Thus, Polylox barcoding enables high-resolution fate mapping in essentially all tissues in mice for which inducible Cre driver lines are available. Alternative methods include ex vivo cell barcoding, inducible transposon insertion and CRISPR-Cas9-based barcoding; Polylox currently allows combining non-invasive and cell-type-specific labeling with high label diversity. The execution time of this protocol is ~2-3 weeks for experimental data generation and typically <2 d for computational Polylox decoding and downstream analysis.
Collapse
Affiliation(s)
- Weike Pei
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Xi Wang
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Jens Rössler
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany.,Bioquant Center, University of Heidelberg, Heidelberg, Germany
| | - Thorsten B Feyerabend
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, Heidelberg, Germany. .,Bioquant Center, University of Heidelberg, Heidelberg, Germany.
| | - Hans-Reimer Rodewald
- Division of Cellular Immunology, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
30
|
Pandit A, De Boer RJ. Stochastic Inheritance of Division and Death Times Determines the Size and Phenotype of CD8 + T Cell Families. Front Immunol 2019; 10:436. [PMID: 30923522 PMCID: PMC6426761 DOI: 10.3389/fimmu.2019.00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
After antigen stimulation cognate naïve CD8+ T cells undergo rapid proliferation and ultimately their progeny differentiates into short-lived effectors and longer-lived memory T cells. Although the expansion of individual cells is very heterogeneous, the kinetics are reproducible at the level of the total population of cognate cells. After the expansion phase, the population contracts, and if antigen is cleared, a population of memory T cells remains behind. Different markers like CD62L, CD27, and KLRG1 have been used to define several T cell subsets (or cell fates) developing from individual naïve CD8+ T cells during the expansion phase. Growing evidence from high-throughput experiments, like single cell RNA sequencing, epigenetic profiling, and lineage tracing, highlights the need to model this differentiation process at the level of single cells. We model CD8+ T cell proliferation and differentiation as a competitive process between the division and death probabilities of individual cells (like in the Cyton model). We use an extended form of the Cyton model in which daughter cells inherit the division and death times from their mother cell in a stochastic manner (using lognormal distributions). We show that this stochastic model reproduces the dynamics of CD8+ T cells both at the population and at the single cell level. Modeling the expression of the CD62L, CD27, and KLRG1 markers of each individual cell, we find agreement with the changing phenotypic distributions of these markers in single cell RNA sequencing data. Retrospectively re-defining conventional T-cell subsets by “gating” on these markers, we find agreement with published population data, without having to assume that these subsets have different properties, i.e., correspond to different fates.
Collapse
Affiliation(s)
- Aridaman Pandit
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Rob J De Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
31
|
Snook JP, Kim C, Williams MA. TCR signal strength controls the differentiation of CD4 + effector and memory T cells. Sci Immunol 2019; 3:3/25/eaas9103. [PMID: 30030369 DOI: 10.1126/sciimmunol.aas9103] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022]
Abstract
CD4+ T cell responses are composed of heterogeneous T cell receptor (TCR) signals that influence the acquisition of effector and memory characteristics. We sought to define early TCR-dependent activation events that control T cell differentiation. A polyclonal panel of TCRs specific for the same viral antigen demonstrated substantial variability in TCR signal strength, expression of CD25, and activation of nuclear factor of activated T cells and nuclear factor κB. After viral infection, strong TCR signals corresponded to T helper cell (TH1) differentiation, whereas T follicular helper cell and memory T cell differentiation were most efficient when TCR signals were comparatively lower. We observed substantial heterogeneity in TCR-dependent CD25 expression in vivo, and the vast majority of CD4+ memory T cells were derived from CD25lo effector cells that displayed decreased TCR signaling in vivo. Nevertheless, memory T cells derived from either CD25lo or CD25hi effector cells responded vigorously to rechallenge, indicating that, although early clonal differences in CD25 expression predicted memory T cell numbers, they did not predict memory T cell function on a per cell basis. Gene transcription analysis demonstrated expression clustering based on CD25 expression and enrichment of transcripts associated with enhanced T follicular helper cell and memory development within CD25lo effector cells. Direct enhancement of TCR signaling via knockdown of Src homology region 2 domain-containing phosphatase 1, a tyrosine phosphatase that suppresses early TCR signaling events, favored the differentiation of TH1 effector and memory cells. We conclude that strong TCR signals during early T cell activation favor terminal TH1 differentiation over long-term TH1 and T follicular helper cell memory responses.
Collapse
Affiliation(s)
- Jeremy P Snook
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Chulwoo Kim
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew A Williams
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| |
Collapse
|
32
|
Schober K, Buchholz VR, Busch DH. TCR repertoire evolution during maintenance of CMV-specific T-cell populations. Immunol Rev 2019; 283:113-128. [PMID: 29664573 DOI: 10.1111/imr.12654] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During infections and cancer, the composition of the T-cell receptor (TCR) repertoire of antigen-specific CD8+ T cells changes over time. TCR avidity is thought to be a major driver of this process, thereby interacting with several additional regulators of T-cell responses to form a composite immune response architecture. Infections with latent viruses, such as cytomegalovirus (CMV), can lead to large T-cell responses characterized by an oligoclonal TCR repertoire. Here, we review the current status of experimental studies and theoretical models of TCR repertoire evolution during CMV infection. We will particularly discuss the degree to which this process may be determined through structural TCR avidity. As engineered TCR-redirected T cells have moved into the spotlight for providing more effective immunotherapies, it is essential to understand how the key features of a given TCR influence T-cell expansion and maintenance in settings of infection or malignancy. Deeper insights into these mechanisms will improve our basic understanding of T-cell immunology and help to identify optimal TCRs for immunotherapy.
Collapse
Affiliation(s)
- Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany.,Focus Group 'Clinical Cell Processing and Purification', Institute for Advanced Study, TUM, Munich, Germany.,National Centre for Infection Research (DZIF), Munich, Germany
| |
Collapse
|
33
|
Ciucci T, Vacchio MS, Gao Y, Tomassoni Ardori F, Candia J, Mehta M, Zhao Y, Tran B, Pepper M, Tessarollo L, McGavern DB, Bosselut R. The Emergence and Functional Fitness of Memory CD4 + T Cells Require the Transcription Factor Thpok. Immunity 2019; 50:91-105.e4. [PMID: 30638736 DOI: 10.1016/j.immuni.2018.12.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/19/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Memory CD4+ T cells mediate long-term immunity, and their generation is a key objective of vaccination strategies. However, the transcriptional circuitry controlling the emergence of memory cells from early CD4+ antigen-responders remains poorly understood. Here, using single-cell RNA-seq to study the transcriptome of virus-specific CD4+ T cells, we identified a gene signature that distinguishes potential memory precursors from effector cells. We found that both that signature and the emergence of memory CD4+ T cells required the transcription factor Thpok. We further demonstrated that Thpok cell-intrinsically protected memory cells from a dysfunctional, effector-like transcriptional program, similar to but distinct from the exhaustion pattern of cells responding to chronic infection. Mechanistically, Thpok- bound genes encoding the transcription factors Blimp1 and Runx3 and acted by antagonizing their expression. Thus, a Thpok-dependent circuitry promotes both memory CD4+ T cells' differentiation and functional fitness, two previously unconnected critical attributes of adaptive immunity.
Collapse
Affiliation(s)
- Thomas Ciucci
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yayi Gao
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Julian Candia
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD, USA
| | - Monika Mehta
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
34
|
Morel PA. Differential T-cell receptor signals for T helper cell programming. Immunology 2018; 155:63-71. [PMID: 29722021 DOI: 10.1111/imm.12945] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/29/2018] [Accepted: 04/17/2018] [Indexed: 12/24/2022] Open
Abstract
Upon encounter with their cognate antigen, naive CD4 T cells become activated and are induced to differentiate into several possible T helper (Th) cell subsets. This differentiation depends on a number of factors including antigen-presenting cells, cytokines and co-stimulatory molecules. The strength of the T-cell receptor (TCR) signal, related to the affinity of TCR for antigen and antigen dose, has emerged as a dominant factor in determining Th cell fate. Recent studies have revealed that TCR signals of high or low strength do not simply induce quantitatively different signals in the T cells, but rather qualitatively distinct pathways can be induced based on TCR signal strength. This review examines the recent literature in this area and highlights important new developments in our understanding of Th cell differentiation and TCR signal strength.
Collapse
Affiliation(s)
- Penelope A Morel
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
35
|
Fähnrich A, Klein S, Sergé A, Nyhoegen C, Kombrink S, Möller S, Keller K, Westermann J, Kalies K. CD154 Costimulation Shifts the Local T-Cell Receptor Repertoire Not Only During Thymic Selection but Also During Peripheral T-Dependent Humoral Immune Responses. Front Immunol 2018; 9:1019. [PMID: 29867987 PMCID: PMC5966529 DOI: 10.3389/fimmu.2018.01019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/24/2018] [Indexed: 12/20/2022] Open
Abstract
CD154 is a transmembrane cytokine expressed transiently on activated CD4 T cells upon T-cell receptor (TCR) stimulation that interacts with CD40 on antigen-presenting cells. The signaling via CD154:CD40 is essential for B-cell maturation and germinal center formation and also for the final differentiation of CD4 T cells during T-dependent humoral immune responses. Recent data demonstrate that CD154 is critically involved in the selection of T-cell clones during the negative selection process in the thymus. Whether CD154 signaling influences the TCR repertoire during peripheral T-dependent humoral immune responses has not yet been elucidated. To find out, we used CD154-deficient mice and assessed the global TCRβ repertoire in T-cell zones (TCZ) of spleens by high-throughput sequencing after induction of a Th2 response to the multiepitopic antigen sheep red blood cells. Qualitative and quantitative comparison of the splenic TCZ-specific TCRβ repertoires revealed that CD154 deficiency shifts the distribution of Vβ-Jβ genes after antigen exposure. This data led to the conclusion that costimulation via CD154:CD40 during the interaction of T cells with CD40-matured B cells contributes to the recruitment of T-cell clones into the immune response and thereby shapes the peripheral TCR repertoire.
Collapse
Affiliation(s)
- Anke Fähnrich
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
| | - Sebastian Klein
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
| | - Arnauld Sergé
- Centre de Recherche en Cancérologie de Marseille (CRCM) U1068 INSERM - UMR7258 CNRS - Institut Paoli Calmette, Aix-Marseille University, UM105, Marseille, France
| | | | - Sabrina Kombrink
- Institute of Mathematics, University of Luebeck, Luebeck, Germany
| | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock, Germany
| | - Karsten Keller
- Institute of Mathematics, University of Luebeck, Luebeck, Germany
| | | | - Kathrin Kalies
- Institute of Anatomy, University of Luebeck, Luebeck, Germany
| |
Collapse
|
36
|
Heinzel S, Marchingo JM, Horton MB, Hodgkin PD. The regulation of lymphocyte activation and proliferation. Curr Opin Immunol 2018; 51:32-38. [PMID: 29414529 DOI: 10.1016/j.coi.2018.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 01/10/2023]
Abstract
Activation induced proliferation and clonal expansion of antigen specific lymphocytes is a hallmark of the adaptive immune response to pathogens. Recent studies identify two distinct control phases. In the first T and B lymphocytes integrate antigen and additional costimuli to motivate a programmed proliferative burst that ceases with a return to cell quiescence and eventual death. This proliferative burst is autonomously timed, ensuring an appropriate response magnitude whilst preventing uncontrolled expansion. This initial response is subject to further modification and extension by a range of signals that modify, expand and direct the emergence of a rich array of new cell types. Thus, both robust clonal expansion of a small number of antigen specific T cells, and the concurrent emergence of extensive cellular diversity, confers immunity to a vast array of different pathogens. The in vivo response to a given pathogen is made up by the sum of all responding clones and is reproducible and pathogen specific. Thus, a precise description of the regulatory principles governing lymphocyte proliferation, differentiation and survival is essential to a unified understanding of the immune system.
Collapse
Affiliation(s)
- Susanne Heinzel
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Julia M Marchingo
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Miles B Horton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Philip D Hodgkin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
37
|
|