1
|
Li C, Lanasa D, Park JH. Pathways and mechanisms of CD4 +CD8αα + intraepithelial T cell development. Trends Immunol 2024; 45:288-302. [PMID: 38514370 PMCID: PMC11015970 DOI: 10.1016/j.it.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
The mammalian small intestine epithelium harbors a peculiar population of CD4+CD8αα+ T cells that are derived from mature CD4+ T cells through reprogramming of lineage-specific transcription factors. CD4+CD8αα+ T cells occupy a unique niche in T cell biology because they exhibit mixed phenotypes and functional characteristics of both CD4+ helper and CD8+ cytotoxic T cells. The molecular pathways driving their generation are not fully mapped. However, recent studies demonstrate the unique role of the commensal gut microbiota as well as distinct cytokine and chemokine requirements in the differentiation and survival of these cells. We review the established and newly identified factors involved in the generation of CD4+CD8αα+ intraepithelial lymphocytes (IELs) and place them in the context of the molecular machinery that drives their phenotypic and functional differentiation.
Collapse
Affiliation(s)
- Can Li
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Lanasa
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung-Hyun Park
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
2
|
Nakandakari-Higa S, Walker S, Canesso MCC, van der Heide V, Chudnovskiy A, Kim DY, Jacobsen JT, Parsa R, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Kamphorst AO, Pritykin Y, Victora GD. Universal recording of immune cell interactions in vivo. Nature 2024; 627:399-406. [PMID: 38448581 PMCID: PMC11078586 DOI: 10.1038/s41586-024-07134-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Immune cells rely on transient physical interactions with other immune and non-immune populations to regulate their function1. To study these 'kiss-and-run' interactions directly in vivo, we previously developed LIPSTIC (labelling immune partnerships by SorTagging intercellular contacts)2, an approach that uses enzymatic transfer of a labelled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ T helper cells and antigen-presenting cells, however. Here we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the steady-state cellular partners of regulatory T cells and identify germinal centre-resident T follicular helper cells on the basis of their ability to interact cognately with germinal centre B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalogue of the immune populations that physically interact with intestinal epithelial cells at the steady state and profile the evolution of the interactome of lymphocytic choriomeningitis virus-specific CD8+ T cells in multiple organs following systemic infection. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
Collapse
Affiliation(s)
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Quantitative and Computational Biology, Princeton University, Princeton, NJ, USA
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Verena van der Heide
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Dong-Yoon Kim
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Institute for Immunology and Transfusion Medicine, Rikshospitalet, University of Oslo, Oslo, Norway
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Laboratory of Synthetic Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Alice O Kamphorst
- Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
3
|
Lutter L, Ter Linde JJM, Brand EC, Hoytema van Konijnenburg DP, Roosenboom B, Horjus Talabur-Horje C, Oldenburg B, van Wijk F. Compartment-driven imprinting of intestinal CD4 T cells in inflammatory bowel disease and homeostasis. Clin Exp Immunol 2023; 214:235-248. [PMID: 37565620 PMCID: PMC10719222 DOI: 10.1093/cei/uxad095] [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: 03/19/2023] [Revised: 07/16/2023] [Accepted: 08/09/2023] [Indexed: 08/12/2023] Open
Abstract
The mucosal immune system is implicated in the etiology and progression of inflammatory bowel diseases. The lamina propria and epithelium of the gut mucosa constitute two separate compartments, containing distinct T-cell populations. Human CD4 T-cell programming and regulation of lamina propria and epithelium CD4 T cells, especially during inflammation, remain incompletely understood. We performed flow cytometry, bulk, and single-cell RNA-sequencing to profile ileal lamina propria and intraepithelial CD4 T cells (CD4CD8αα, regulatory T cells (Tregs), CD69- and CD69high Trm T cells) in controls and Crohn's disease (CD) patients (paired non-inflamed and inflamed). Inflammation results in alterations of the CD4 T-cell population with a pronounced increase in Tregs and migrating/infiltrating cells. On a transcriptional level, inflammation within the epithelium induced T-cell activation, increased IFNγ responses, and an effector Treg profile. Conversely, few transcriptional changes within the lamina propria were observed. Key regulators including the chromatin remodelers ARID4B and SATB1 were found to drive compartment-specific transcriptional programming of CD4 T(reg) cells. In summary, inflammation in CD patients primarily induces changes within the epithelium and not the lamina propria. Additionally, there is compartment-specific CD4 T-cell imprinting, driven by shared regulators, between the lamina propria and the epithelium. The main consequence of intraepithelial adaptation, irrespective of inflammation, seems to be an overall dampening of broad (pro-inflammatory) responses and tight regulation of lifespan. These data suggest differential regulation of the lamina propria and epithelium, with a specific regulatory role in the inflamed epithelium.
Collapse
Affiliation(s)
- Lisanne Lutter
- Centre for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - José J M Ter Linde
- Centre for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Eelco C Brand
- Centre for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - David P Hoytema van Konijnenburg
- Centre for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Division of Immunology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Britt Roosenboom
- Department of Gastroenterology and Hepatology, Rijnstate Hospital, Arnhem, The Netherlands
| | | | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Femke van Wijk
- Centre for Translational Immunology, University Medical Centre Utrecht, Utrecht, The Netherlands
| |
Collapse
|
4
|
Ramanan D, Pratama A, Zhu Y, Venezia O, Sassone-Corsi M, Chowdhary K, Galván-Peña S, Sefik E, Brown C, Gélineau A, Mathis D, Benoist C. Regulatory T cells in the face of the intestinal microbiota. Nat Rev Immunol 2023; 23:749-762. [PMID: 37316560 DOI: 10.1038/s41577-023-00890-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
Regulatory T cells (Treg cells) are key players in ensuring a peaceful coexistence with microorganisms and food antigens at intestinal borders. Startling new information has appeared in recent years on their diversity, the importance of the transcription factor FOXP3, how T cell receptors influence their fate and the unexpected and varied cellular partners that influence Treg cell homeostatic setpoints. We also revisit some tenets, maintained by the echo chambers of Reviews, that rest on uncertain foundations or are a subject of debate.
Collapse
Affiliation(s)
| | - Alvin Pratama
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Yangyang Zhu
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Olivia Venezia
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Esen Sefik
- Department of Immunology, Yale University, New Haven, CT, USA
| | - Chrysothemis Brown
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Paediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | | |
Collapse
|
5
|
Hada A, Li L, Kandel A, Jin Y, Xiao Z. Characterization of Bovine Intraepithelial T Lymphocytes in the Gut. Pathogens 2023; 12:1173. [PMID: 37764981 PMCID: PMC10535955 DOI: 10.3390/pathogens12091173] [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: 08/23/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Intraepithelial T lymphocytes (T-IELs), which constitute over 50% of the total T lymphocytes in the animal, patrol the mucosal epithelial lining to defend against pathogen invasion while maintaining gut homeostasis. In addition to expressing T cell markers such as CD4 and CD8, T-IELs display T cell receptors (TCR), including either TCRαβ or TCRγδ. Both humans and mice share similar T-IEL subsets: TCRγδ+, TCRαβ+CD8αα+, TCRαβ+CD4+, and TCRαβ+CD8αβ+. Among these subsets, human T-IELs are predominantly TCRαβ+ (over 80%), whereas those in mice are mostly TCRγδ+ (~60%). Of note, the majority of the TCRγδ+ subset expresses CD8αα in both species. Although T-IELs have been extensively studied in humans and mice, their profiles in cattle have not been well examined. Our study is the first to characterize bovine T-IELs using flow cytometry, where we identified several distinct features. The percentage of TCRγδ+ was comparable to that of TCRαβ+ T-IELs (both ~50% of CD3+), and the majority of bovine TCRγδ+ T-IELs did not express CD8 (CD8-) (above 60%). Furthermore, about 20% of TCRαβ+ T-IELs were CD4+CD8αβ+, and the remaining TCRαβ+ T-IELs were evenly distributed between CD4+ and CD8αβ+ (~40% of TCRαβ+ T-IELs each) with no TCRαβ+CD8αα+ identified. Despite these unique properties, bovine T-IELs, similar to those in humans and mice, expressed a high level of CD69, an activation and tissue-retention marker, and a low level of CD62L, a lymphoid adhesion marker. Moreover, bovine T-IELs produced low levels of inflammatory cytokines such as IFNγ and IL17A, and secreted small amounts of the immune regulatory cytokine TGFβ1. Hence, bovine T-IELs' composition largely differs from that of human and mouse, with the dominance of the CD8- population among TCRγδ+ T-IELs, the substantial presence of TCRαβ+CD4+CD8αβ+ cells, and the absence of TCRαβ+CD8αα+ T-IELs. These results provide the groundwork for conducting future studies to examine how bovine T-IELs respond to intestinal pathogens and maintain the integrity of the gut epithelial barrier in animals.
Collapse
Affiliation(s)
| | | | | | | | - Zhengguo Xiao
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.H.); (L.L.); (A.K.); (Y.J.)
| |
Collapse
|
6
|
Ono K, Sujino T, Miyamoto K, Harada Y, Kojo S, Yoshimatsu Y, Tanemoto S, Koda Y, Zheng J, Sayama K, Koide T, Teratani T, Mikami Y, Takabayashi K, Nakamoto N, Hosoe N, London M, Ogata H, Mucida D, Taniuchi I, Kanai T. Downregulation of chemokine receptor 9 facilitates CD4 +CD8αα + intraepithelial lymphocyte development. Nat Commun 2023; 14:5152. [PMID: 37620389 PMCID: PMC10449822 DOI: 10.1038/s41467-023-40950-2] [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: 06/23/2022] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
Intestinal intraepithelial lymphocytes (IELs) reside in the gut epithelial layer, where they help in maintaining intestinal homeostasis. Peripheral CD4+ T cells can develop into CD4+CD8αα+ IELs upon arrival at the gut epithelium via the lamina propria (LP). Although this specific differentiation of T cells is well established, the mechanisms preventing it from occurring in the LP remain unclear. Here, we show that chemokine receptor 9 (CCR9) expression is low in epithelial CD4+CD8αα+ IELs, but CCR9 deficiency results in CD4+CD8αα+ over-differentiation in both the epithelium and the LP. Single-cell RNA sequencing shows an enriched precursor cell cluster for CD4+CD8αα+ IELs in Ccr9-/- mice. CD4+ T cells isolated from the epithelium of Ccr9-/- mice also display increased expression of Cbfβ2, and the genomic occupancy modification of Cbfβ2 expression reveals its important function in CD4+CD8αα+ differentiation. These results implicate a link between CCR9 downregulation and Cbfb2 splicing upregulation to enhance CD4+CD8αα+ IEL differentiation.
Collapse
Affiliation(s)
- Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan.
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
- Research Laboratory, Miyarisan Pharmaceutical Co., Tokyo, Japan
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Kojo
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Division of Immunology and Stem Cell Biology, Institute of Medical, Pharmaceutical and Health Science, Kanazawa University, Kanazawa, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shun Tanemoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yuzo Koda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
- Mitsubishi Tanabe Pharma Corporation, Kanagawa, Japan
| | - Jiawen Zheng
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazutoshi Sayama
- Applied Life Science Course, College of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Mariya London
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, 10065, USA
| | - Haruhiko Ogata
- Center for Diagnostic and Therapeutic Endoscopy, Keio University School of Medicine, Tokyo, Japan
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, 10065, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, 10065, USA
| | - Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| |
Collapse
|
7
|
Venkatesh H, Tracy SI, Farrar MA. Cytotoxic CD4 T cells in the mucosa and in cancer. Front Immunol 2023; 14:1233261. [PMID: 37654482 PMCID: PMC10466411 DOI: 10.3389/fimmu.2023.1233261] [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: 06/01/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023] Open
Abstract
CD4 T cells were initially described as helper cells that promote either the cellular immune response (Th1 cells) or the humoral immune response (Th2 cells). Since then, a plethora of functionally distinct helper and regulatory CD4 T cell subsets have been described. CD4 T cells with cytotoxic function were first described in the setting of viral infections and autoimmunity, and more recently in cancer and gut dysbiosis. Regulatory CD4 T cell subsets such as Tregs and T-regulatory type 1 (Tr1) cells have also been shown to have cytotoxic potential. Indeed, Tr1 cells have been shown to be important for maintenance of stem cell niches in the bone marrow and the gut. This review will provide an overview of cytotoxic CD4 T cell development, and discuss the role of inflammatory and Tr1-like cytotoxic CD4 T cells in maintenance of intestinal stem cells and in anti-cancer immune responses.
Collapse
Affiliation(s)
- Hrishi Venkatesh
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- University of Minnesota, Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
| | - Sean I. Tracy
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Michael A. Farrar
- Center for Immunology, Masonic Cancer Center, Minneapolis, MN, United States
- University of Minnesota, Department of Laboratory Medicine and Pathology, Minneapolis, MN, United States
| |
Collapse
|
8
|
Lockhart A, Reed A, Rezende de Castro T, Herman C, Campos Canesso MC, Mucida D. Dietary protein shapes the profile and repertoire of intestinal CD4+ T cells. J Exp Med 2023; 220:214115. [PMID: 37191720 DOI: 10.1084/jem.20221816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 04/11/2023] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
The intestinal immune system must tolerate food antigens to avoid allergy, a process requiring CD4+ T cells. Combining antigenically defined diets with gnotobiotic models, we show that food and microbiota distinctly influence the profile and T cell receptor repertoire of intestinal CD4+ T cells. Independent of the microbiota, dietary proteins contributed to accumulation and clonal selection of antigen-experienced CD4+ T cells at the intestinal epithelium, imprinting a tissue-specialized transcriptional program including cytotoxic genes on both conventional and regulatory CD4+ T cells (Tregs). This steady state CD4+ T cell response to food was disrupted by inflammatory challenge, and protection against food allergy in this context was associated with Treg clonal expansion and decreased proinflammatory gene expression. Finally, we identified both steady-state epithelium-adapted CD4+ T cells and tolerance-induced Tregs that recognize dietary antigens, suggesting that both cell types may be critical for preventing inappropriate immune responses to food.
Collapse
Affiliation(s)
- Ainsley Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | - Aubrey Reed
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | | | - Calvin Herman
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
| | | | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University , New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University , New York, NY, USA
| |
Collapse
|
9
|
Nguyen QP, Takehara KK, Deng TZ, O’Shea S, Heeg M, Omilusik KD, Milner JJ, Quon S, Pipkin ME, Choi J, Crotty S, Goldrath AW. Transcriptional programming of CD4 + T RM differentiation in viral infection balances effector- and memory-associated gene expression. Sci Immunol 2023; 8:eabq7486. [PMID: 37172104 PMCID: PMC10350289 DOI: 10.1126/sciimmunol.abq7486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 04/19/2023] [Indexed: 05/14/2023]
Abstract
After resolution of infection, T cells differentiate into long-lived memory cells that recirculate through secondary lymphoid organs or establish residence in tissues. In contrast to CD8+ tissue-resident memory T cells (TRM), the developmental origins and transcriptional regulation of CD4+ TRM remain largely undefined. Here, we investigated the phenotypic, functional, and transcriptional profiles of CD4+ TRM in the small intestine (SI) responding to acute viral infection, revealing a shared gene expression program and chromatin accessibility profile with circulating TH1 and the progressive acquisition of a mature TRM program. Single-cell RNA sequencing identified heterogeneity among established CD4+ TRM, which were predominantly located in the lamina propria, and revealed a population of cells that coexpressed both effector- and memory-associated genes, including the transcriptional regulators Blimp1, Id2, and Bcl6. TH1-associated Blimp1 and Id2 and TFH-associated Bcl6 were required for early TRM formation and development of a mature TRM population in the SI. These results demonstrate a developmental relationship between TH1 effector cells and the establishment of early TRM, as well as highlighted differences in CD4+ versus CD8+ TRM populations, providing insights into the mechanisms underlying the origins, differentiation, and persistence of CD4+ TRM in response to viral infection.
Collapse
Affiliation(s)
- Quynh P Nguyen
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kennidy K Takehara
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Tianda Z Deng
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Shannon O’Shea
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Maximilian Heeg
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Kyla D Omilusik
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - J Justin Milner
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Sara Quon
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| | - Matthew E Pipkin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida
| | - Jinyong Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA
| | - Ananda W Goldrath
- School of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA
| |
Collapse
|
10
|
Nakandakari-Higa S, Canesso MCC, Walker S, Chudnovskiy A, Jacobsen JT, Bilanovic J, Parigi SM, Fiedorczuk K, Fuchs E, Bilate AM, Pasqual G, Mucida D, Pritykin Y, Victora GD. Universal recording of cell-cell contacts in vivo for interaction-based transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533003. [PMID: 36993443 PMCID: PMC10055214 DOI: 10.1101/2023.03.16.533003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cellular interactions are essential for tissue organization and functionality. In particular, immune cells rely on direct and usually transient interactions with other immune and non-immune populations to specify and regulate their function. To study these "kiss-and-run" interactions directly in vivo, we previously developed LIPSTIC (Labeling Immune Partnerships by SorTagging Intercellular Contacts), an approach that uses enzymatic transfer of a labeled substrate between the molecular partners CD40L and CD40 to label interacting cells. Reliance on this pathway limited the use of LIPSTIC to measuring interactions between CD4+ helper T cells and antigen presenting cells, however. Here, we report the development of a universal version of LIPSTIC (uLIPSTIC), which can record physical interactions both among immune cells and between immune and non-immune populations irrespective of the receptors and ligands involved. We show that uLIPSTIC can be used, among other things, to monitor the priming of CD8+ T cells by dendritic cells, reveal the cellular partners of regulatory T cells in steady state, and identify germinal center (GC)-resident T follicular helper (Tfh) cells based on their ability to interact cognately with GC B cells. By coupling uLIPSTIC with single-cell transcriptomics, we build a catalog of the immune populations that physically interact with intestinal epithelial cells (IECs) and find evidence of stepwise acquisition of the ability to interact with IECs as CD4+ T cells adapt to residence in the intestinal tissue. Thus, uLIPSTIC provides a broadly useful technology for measuring and understanding cell-cell interactions across multiple biological systems.
Collapse
Affiliation(s)
| | - Maria C C Canesso
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Sarah Walker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Quantitative and Computational Biology Graduate Program, Princeton University, Princeton, NJ, USA
| | - Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Jana Bilanovic
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - S Martina Parigi
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Karol Fiedorczuk
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Elaine Fuchs
- Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Angelina M Bilate
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Giulia Pasqual
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Yuri Pritykin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| |
Collapse
|
11
|
Lockhart A, Reed A, de Castro TR, Herman C, Canesso MCC, Mucida D. Dietary protein shapes the profile and repertoire of intestinal CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536475. [PMID: 37090529 PMCID: PMC10120666 DOI: 10.1101/2023.04.11.536475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The intestinal immune system must tolerate food antigens to avoid allergy, a process requiring CD4 + T cells. Combining antigenically defined diets with gnotobiotic models, we show that food and microbiota distinctly influence the profile and T cell receptor repertoire of intestinal CD4 + T cells. Independent of the microbiota, dietary proteins contributed to accumulation and clonal selection of antigen-experienced CD4 + T cells at the intestinal epithelium, imprinting a tissue specialized transcriptional program including cytotoxic genes on both conventional and regulatory CD4 + T cells (Tregs). This steady state CD4 + T cell response to food was disrupted by inflammatory challenge, and protection against food allergy in this context was associated with Treg clonal expansion and decreased pro-inflammatory gene expression. Finally, we identified both steady state epithelium-adapted CD4 + T cells and tolerance-induced Tregs that recognize dietary antigens, suggesting that both cell types may be critical for preventing inappropriate immune responses to food.
Collapse
|
12
|
Bhuyan ZA, Rahman MA, Maradana MR, Mehdi AM, Bergot AS, Simone D, El-Kurdi M, Garrido-Mesa J, Cai CBB, Cameron AJ, Hanson AL, Nel HJ, Kenna T, Leo P, Rehaume L, Brown MA, Ciccia F, Thomas R. Genetically encoded Runx3 and CD4 + intestinal epithelial lymphocyte deficiencies link SKG mouse and human predisposition to spondyloarthropathy. Clin Immunol 2023; 247:109220. [PMID: 36596403 DOI: 10.1016/j.clim.2022.109220] [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: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/02/2023]
Abstract
Disturbances in immune regulation, intestinal dysbiosis and inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. In small intestine, Foxp3+ regulatory T cells (Treg) and CD4+CD8αα+TCRαβ+ intraepithelial lymphocytes (CD4-IEL) control inflammation. TGF-β and retinoic acid (RA)-producing dendritic cells and MHC-class II+ intestinal epithelial cells (IEC) are required for Treg and CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We show in SKG mouse ileum, that ZAP70W163C or ZAP70 inhibition prevented CD4-IEL but not Treg differentiation, dysregulating Runx3 and ThPOK. TGF-β/RA-mediated CD4-IEL development, T-cell IFN-γ production, MHC class-II+ IEC, tissue-resident memory T-cell and Runx3-regulated genes were reduced. In AS intestine, CD4-IEL were decreased, while in AS blood CD4+CD8+ T cells were reduced and Treg increased. Thus, genetically-encoded TCR signaling dysfunction links intestinal T-cell immunodeficiency in mouse and human spondyloarthropathy.
Collapse
Affiliation(s)
- Zaied Ahmed Bhuyan
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - M Arifur Rahman
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Muralidhara Rao Maradana
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Anne-Sophie Bergot
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Davide Simone
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marya El-Kurdi
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheng Bang Benjamin Cai
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Amy J Cameron
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Aimee L Hanson
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Hendrik J Nel
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Tony Kenna
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Paul Leo
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Linda Rehaume
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Genomics England Ltd, Charterhouse Square, London, United Kingdom
| | - Francesco Ciccia
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Ranjeny Thomas
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
| |
Collapse
|
13
|
Harada Y, Miyamoto K, Chida A, Okuzawa AT, Yoshimatsu Y, Kudo Y, Sujino T. Localization and movement of Tregs in gastrointestinal tract: a systematic review. Inflamm Regen 2022; 42:47. [PMID: 36329556 PMCID: PMC9632047 DOI: 10.1186/s41232-022-00232-8] [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: 08/04/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The intestine is rich in food-derived and microbe-derived antigens. Regulatory T cells (Tregs) are an essential T-cell population that prevents systemic autoimmune diseases and inhibits inflammation by encountering antigens. Previously, it was reported that the functional loss of Tregs induces systemic inflammation, including inflammatory bowel disease and graft-versus-host disease in human and murine models. However, there is a dearth of information about how Tregs localize in different tissues and suppress effector cells. MAIN BODY The development of Tregs and their molecular mechanism in the digestive tract have been elucidated earlier using murine genetic models, infectious models, and human samples. Tregs suppress immune and other nonimmune cells through direct effect and cytokine production. The recent development of in vivo imaging technology allows us to visualize how Tregs localize and move in the settings of inflammation and homeostasis. This is important because, according to a recent report, Treg characterization and function are regulated by their location. Tregs located in the proximal intestine and its draining lymph nodes induce tolerance against food antigens, and those located in the distal intestine suppress the inflammation induced by microbial antigens. Taken together, various Tregs are induced in a location-specific manner in the gastrointestinal tract and influence the homeostasis of the gut. CONCLUSION In this review, we summarize how Tregs are induced in the digestive tract and the application of in vivo Treg imaging to elucidate immune homeostasis in the digestive tract.
Collapse
Affiliation(s)
- Yosuke Harada
- Department of Gastroenterology and Hepatology, School of Medicine, Keio University, Tokyo, Japan
| | - Kentaro Miyamoto
- Department of Gastroenterology and Hepatology, School of Medicine, Keio University, Tokyo, Japan.,Miyarisan Pharm. Co. Ltd, Tokyo, Japan
| | - Akihiko Chida
- Department of Gastroenterology and Hepatology, School of Medicine, Keio University, Tokyo, Japan
| | - Anna Tojo Okuzawa
- Department of Gastroenterology and Hepatology, School of Medicine, Keio University, Tokyo, Japan
| | - Yusuke Yoshimatsu
- Department of Gastroenterology and Hepatology, School of Medicine, Keio University, Tokyo, Japan
| | - Yumi Kudo
- Department of Pediatric Surgery, School of Medicine, Keio University, Tokyo, Japan
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan.
| |
Collapse
|
14
|
Cervantes-Barragan L, Colonna M. A microbiota-derived antigen drives CD4 + intraepithelial lymphocyte (CD4IEL) development. Trends Immunol 2022; 43:858-860. [PMID: 36243620 DOI: 10.1016/j.it.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 01/12/2023]
Abstract
CD4+ intraepithelial lymphocytes (CD4IEL) are tissue-resident T cells with cytotoxic and regulatory properties; together with peripheral regulatory T cells, they control intestinal inflammation. Recently, Bousbaine and colleagues identified a microbiota-derived conserved antigen that induces CD4IEL differentiation and promotes their regulatory function, attenuating the severity of murine colitis.
Collapse
Affiliation(s)
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|
15
|
Tanemoto S, Sujino T, Miyamoto K, Moody J, Yoshimatsu Y, Ando Y, Koya I, Harada Y, Tojo AO, Ono K, Hayashi Y, Takabayashi K, Okabayashi K, Teratani T, Mikami Y, Nakamoto N, Hosoe N, Ogata H, Hon CC, Shin JW, Kanai T. Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4 +CD8A + T cells related to mouse CD4 cytotoxic T cells. Front Immunol 2022; 13:977117. [PMID: 36353619 PMCID: PMC9639511 DOI: 10.3389/fimmu.2022.977117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/07/2022] [Indexed: 08/21/2023] Open
Abstract
Cytotoxic CD4+ T cells (CD4-CTLs) show the presence of cytolytic granules, which include the enzymes granzyme and perforin. The cells have a pathogenic and protective role in various diseases, including cancer, viral infection, and autoimmune disease. In mice, cytotoxic CD4+ T cells express CD8αα+ and reside in the intestine (mouse CD4+CTLs; mCD4-CTLs). The population of cytotoxic CD4+ T cells in the human intestine is currently unknown. Moreover, it is unclear how cytotoxic CD4 T cells change in patients with inflammatory bowel disease (IBD). Here, we aimed to identify cytotoxic CD4+ T cells in the human intestine and analyze the characteristics of the population in patients with IBD using single-cell RNA-seq (scRNA-seq). In CD4+ T cells, granzyme and perforin expression was high in humanMAIT (hMAIT) cells and hCD4+CD8A+ T cell cluster. Both CD4 and CD8A were expressed in hTreg, hMAIT, and hCD4+CD8A+ T cell clusters. Next we performed fast gene set enrichment analysis to identify cell populations that showed homology to mCD4CTLs. The analysis identified the hCD4+CD8A+ T cell cluster (hCTL-like population; hCD4-CTL) similar to mouse CTLs. The percentage of CD4+CD8A+ T cells among the total CD4+ T cells in the inflamed intestine of the patients with Crohn's disease was significantly reduced compared with that in the noninflamed intestine of the patients. In summary, we identified cytotoxic CD4+CD8+ T cells in the small intestine of humans. The integration of the mouse and human sc-RNA-seq data analysis highlight an approach to identify human cell populations related to mouse cell populations, which may help determine the functional properties of several human cell populations in mice.
Collapse
Affiliation(s)
- Shun Tanemoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tomohisa Sujino
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
- Research Laboratory, Miyarisan Pharmaceutical Co., Ltd., Tokyo, Japan
| | - Jonathan Moody
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Yusuke Yoshimatsu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Ikuko Koya
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Yosuke Harada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Anna Okuzawa Tojo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keiko Ono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukie Hayashi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kaoru Takabayashi
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Koji Okabayashi
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Naoki Hosoe
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Haruhiko Ogata
- Center for Diagnostic and Therapeutic Endoscopy , Keio University School of Medicine, Tokyo, Japan
| | - Chung-Chau Hon
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Laboratory for Genomic Information Analysis, Yokohama, Japan
- Laboratory of Regulatory Genomics, Genome Institute of Singapore, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| |
Collapse
|
16
|
Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM. A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. Science 2022; 377:660-666. [PMID: 35926021 PMCID: PMC9766740 DOI: 10.1126/science.abg5645] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4+ T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4+ T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase-specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa.
Collapse
Affiliation(s)
- Djenet Bousbaine
- Microbiology Graduate Program, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Laura I Fisch
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Mariya London
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Preksha Bhagchandani
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Tiago B Rezende de Castro
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA.,Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Mark Mimee
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Synthetic Biology Center, MIT, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Scott Olesen
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - David VanInsberghe
- Microbiology Graduate Program, Massachussetts Institute of Technology (MIT), Cambridge, MA, USA.,Department of Civil and Environmental Engineering, MIT, Cambridge, MA, USA
| | - Juliana Bortolatto
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Mathilde Poyet
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jingjing Ling
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Aaron Gupta
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Timothy K Lu
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Synthetic Biology Center, MIT, Cambridge, MA, USA.,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA.,Department of Medicine, University of California, San Diego, CA, USA
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases and Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York NY, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA
| | - Angelina M Bilate
- Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| |
Collapse
|
17
|
Innate riddle of CD4 + T cells and the control of enteric infections. Immunity 2022; 55:1145-1147. [PMID: 35830821 DOI: 10.1016/j.immuni.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Intra-epithelial T cells make up a significant proportion of immune cells in the body, yet their development and function remain an enigma. In this issue of Immunity, Parsa et al. (2022) describe the differentiation and cross-protective function of CD4+ intra-epithelial T cells against enteric viruses.
Collapse
|
18
|
Yang K. Regulation of Treg Cell Metabolism and Function in Non-Lymphoid Tissues. Front Immunol 2022; 13:909705. [PMID: 35720275 PMCID: PMC9200993 DOI: 10.3389/fimmu.2022.909705] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022] Open
Abstract
Regulator T cells (Tregs) play pivotal roles in maintaining immune tolerance and regulating immune responses against pathogens and tumors. Reprogramming of cellular metabolism has been determined as a crucial process that connects microenvironmental cues and signaling networks to influence homeostasis and function of tissue Tregs. In adaptation to a variety of non-lymphoid tissues, Tregs coordinate local immune signals and signaling networks to rewire cellular metabolic programs to sustain their suppressive function. Altered Treg metabolism in turn shapes Treg activation and function. In light of the advanced understanding of immunometabolism, manipulation of systemic metabolites has been emerging as an attractive strategy aiming to modulate metabolism and function of tissue Tregs and improve the treatment of immune-related diseases. In this review, we summarize key immune signals and metabolic programs involved in the regulation of tissue Tregs, review the mechanisms underlying the differentiation and function of Tregs in various non-lymphoid tissues, and discuss therapeutic intervention of metabolic modulators of tissue Tregs for the treatment of autoimmune diseases and cancer.
Collapse
Affiliation(s)
- Kai Yang
- Department of Pediatrics and the Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| |
Collapse
|
19
|
Lockhart A, Mucida D, Parsa R. Immunity to enteric viruses. Immunity 2022; 55:800-818. [PMID: 35545029 PMCID: PMC9257994 DOI: 10.1016/j.immuni.2022.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 12/15/2022]
Abstract
Pathogenic enteric viruses are a major cause of morbidity and mortality, particularly among children in developing countries. The host response to enteric viruses occurs primarily within the mucosa, where the intestinal immune system must balance protection against pathogens with tissue protection and tolerance to harmless commensal bacteria and food. Here, we summarize current knowledge in natural immunity to enteric viruses, highlighting specialized features of the intestinal immune system. We further discuss how knowledge of intestinal anti-viral mechanisms can be translated into vaccine development with particular focus on immunization in the oral route. Research reveals that the intestine is a complex interface between enteric viruses and the host where environmental factors influence susceptibility and immunity to infection, while viral infections can have lasting implications for host health. A deeper mechanistic understanding of enteric anti-viral immunity with this broader context can ultimately lead to better vaccines for existing and emerging viruses.
Collapse
Affiliation(s)
- Ainsley Lockhart
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Roham Parsa
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
20
|
Aryl hydrocarbon receptor signals in epithelial cells govern the recruitment and location of Helios + Tregs in the gut. Cell Rep 2022; 39:110773. [PMID: 35545035 DOI: 10.1016/j.celrep.2022.110773] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 12/30/2021] [Accepted: 04/12/2022] [Indexed: 01/21/2023] Open
Abstract
CD4+Foxp3+ regulatory T cells (Tregs) are essential for homeostasis in the colon, but the mechanism by which local environmental cues determine the localization of colonic Tregs is unclear. Here, we administer indigo naturalis (IN), a nontoxic phytochemical aryl hydrocarbon receptor (AhR) agonist used for treating patients with ulcerative colitis (UC) in Asia, and we show that IN increases Helios+ Tregs and MHC class II+ epithelial cells (ECs) in the colon. Interactions between Tregs and MHC class II+ ECs occur mainly near the crypt bottom in the steady state, whereas Tregs dramatically increase and shift toward the crypt top following IN treatment. Moreover, the number of CD25+ T cells is increased near the surface of ECs in IN-treated UC patients compared with that in patients treated with other therapies. We also highlight additional AhR-signaling mechanisms in intestinal ECs that determine the accumulation and localization of Helios+ Tregs in the colon.
Collapse
|
21
|
Parsa R, London M, Rezende de Castro TB, Reis B, Buissant des Amorie J, Smith JG, Mucida D. Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection. Immunity 2022; 55:1234-1249.e6. [DOI: 10.1016/j.immuni.2022.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/07/2022] [Accepted: 05/03/2022] [Indexed: 12/31/2022]
|
22
|
Oja AE, van Lier RAW, Hombrink P. Two sides of the same coin: Protective versus pathogenic CD4 + resident memory T cells. Sci Immunol 2022; 7:eabf9393. [PMID: 35394815 DOI: 10.1126/sciimmunol.abf9393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The ability of the adaptive immune system to form memory is key to providing protection against secondary infections. Resident memory T cells (TRM) are specialized T cell populations that reside within tissue sites where they await reencounter with their cognate antigen. TRM are distinct from circulating memory cells, including central and effector memory T cells, both functionally and transcriptionally. Since the discovery of TRM, most research has focused on CD8+ TRM, despite that CD4+ TRM are also abundant in most tissues. In the past few years, more evidence has emerged that CD4+ TRM can contribute both protective and pathogenic roles in disease. A complexity inherent to the CD4+ TRM field is the ability of CD4+ T cells to polarize into a multitude of distinct subsets and recognize not only viruses and intracellular bacteria but also extracellular bacteria, fungi, and parasites. In this review, we outline the key features of CD4+ TRM in health and disease, including their contributions to protection against SARS-CoV-2 and potential contributions to immunopathology associated with COVID-19.
Collapse
Affiliation(s)
- Anna E Oja
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - René A W van Lier
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Pleun Hombrink
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
23
|
Lee SE, Rudd BD, Smith NL. Fate-mapping mice: new tools and technology for immune discovery. Trends Immunol 2022; 43:195-209. [PMID: 35094945 PMCID: PMC8882138 DOI: 10.1016/j.it.2022.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022]
Abstract
The fate-mapping mouse has become an essential tool in the immunologist's toolbox. Although traditionally used by developmental biologists to trace the origins of cells, immunologists are turning to fate-mapping to better understand the development and function of immune cells. Thus, an expansion in the variety of fate-mapping mouse models has occurred to answer fundamental questions about the immune system. These models are also being combined with new genetic tools to study cancer, infection, and autoimmunity. In this review, we summarize different types of fate-mapping mice and describe emerging technologies that might allow immunologists to leverage this valuable tool and expand our functional knowledge of the immune system.
Collapse
Affiliation(s)
- Scarlett E Lee
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14850, USA.
| |
Collapse
|
24
|
Zhang H, Weyand CM, Goronzy JJ, Gustafson CE. Understanding T cell aging to improve anti-viral immunity. Curr Opin Virol 2021; 51:127-133. [PMID: 34688983 DOI: 10.1016/j.coviro.2021.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022]
Abstract
T cells are a critical component of the immune system and required for protection against viral and bacterial infections. However, the capacity of these cells to provide sufficient protection declines with age, leading to an increased susceptibility to and mortality from infection in older individuals. In many cases, it also contributes to poor vaccine-induced immunity. Understanding the basic biology behind T cell aging is key to unraveling these defects and, in turn, designing more effective vaccines and therapeutics for the older population. Here, we will discuss recent studies that have provided significant insight into the features of T cell aging, how these features may contribute to poor immune responses with advancing age and newer avenues of research that may further enhance anti-viral immunity in older individuals.
Collapse
Affiliation(s)
- Huimin Zhang
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA; Department of Medicine, Veterans Administration Healthcare System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA; Department of Medicine, Veterans Administration Healthcare System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA; Department of Medicine, Veterans Administration Healthcare System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - Claire E Gustafson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, USA.
| |
Collapse
|
25
|
Abstract
Naïve T cells are critical for protection against emerging viral and bacterial infections. However, the ability of these cells to elicit effective long-term immune responses declines with age and contributes to increased disease susceptibility in older individuals. This decline has been linked with the breakdown of cellular quiescence that causes partial differentiation of naïve T cells with age, but the underlying mediators of this breakdown are unclear. Comparisons to stem cell quiescence in mice and man offer insight into naïve T cells and aging. However, the utilization of single cell technologies in combination with advances in the biology of human tissue aging is needed to provide further understanding of naïve T cell complexity and quiescence breakdown with age.
Collapse
|