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Li R, Qu R, Parisi F, Strino F, Cheng X, Kluger Y. LMD: Multiscale Marker Identification in Single-cell RNA-seq Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.12.566780. [PMID: 38014159 PMCID: PMC10680591 DOI: 10.1101/2023.11.12.566780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Accurate cell marker identification in single-cell RNA-seq data is crucial for understanding cellular diversity and function. An ideal marker is highly specific in identifying cells that are similar in terms of function and state. Current marker identification methods, commonly based on clustering and differential expression, capture general cell-type markers but often miss markers for subtypes or functional cell subsets, with their performance largely dependent on clustering quality. Moreover, cluster-independent approaches tend to favor genes that lack the specificity required to characterize regions within the transcriptomic space at multiple scales. Here we introduce Localized Marker Detector (LMD), a novel tool to identify "localized genes" - genes with expression profiles specific to certain groups of highly similar cells - thereby characterizing cellular diversity in a multi-resolution and fine-grained manner. LMD's strategy involves building a cell-cell affinity graph, diffusing the gene expression value across the cell graph, and assigning a score to each gene based on its diffusion dynamics. We show that LMD exhibits superior accuracy in recovering known cell-type markers in the Tabula Muris bone marrow dataset relative to other methods for marker identification. Notably, markers favored by LMD exhibit localized expression, whereas markers prioritized by other clustering-free algorithms are often dispersed in the transcriptomic space. We further group the markers suggested by LMD into functional gene modules to improve the separation of cell types and subtypes in a more fine-grained manner. These modules also identify other sources of variation, such as cell cycle status. In conclusion, LMD is a novel algorithm that can identify fine-grained markers for cell subtypes or functional states without relying on clustering or differential expression analysis. LMD exploits the complex interactions among cells and reveals cellular diversity at high resolution.
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Souter MN, Awad W, Li S, Pediongco TJ, Meehan BS, Meehan LJ, Tian Z, Zhao Z, Wang H, Nelson A, Le Nours J, Khandokar Y, Praveena T, Wubben J, Lin J, Sullivan LC, Lovrecz GO, Mak JY, Liu L, Kostenko L, Kedzierska K, Corbett AJ, Fairlie DP, Brooks AG, Gherardin NA, Uldrich AP, Chen Z, Rossjohn J, Godfrey DI, McCluskey J, Pellicci DG, Eckle SB. CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells. J Exp Med 2022; 219:213423. [PMID: 36018322 PMCID: PMC9424912 DOI: 10.1084/jem.20210828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells detect microbial infection via recognition of riboflavin-based antigens presented by the major histocompatibility complex class I (MHC-I)-related protein 1 (MR1). Most MAIT cells in human peripheral blood express CD8αα or CD8αβ coreceptors, and the binding site for CD8 on MHC-I molecules is relatively conserved in MR1. Yet, there is no direct evidence of CD8 interacting with MR1 or the functional consequences thereof. Similarly, the role of CD8αα in lymphocyte function remains ill-defined. Here, using newly developed MR1 tetramers, mutated at the CD8 binding site, and by determining the crystal structure of MR1-CD8αα, we show that CD8 engaged MR1, analogous to how it engages MHC-I molecules. CD8αα and CD8αβ enhanced MR1 binding and cytokine production by MAIT cells. Moreover, the CD8-MR1 interaction was critical for the recognition of folate-derived antigens by other MR1-reactive T cells. Together, our findings suggest that both CD8αα and CD8αβ act as functional coreceptors for MAIT and other MR1-reactive T cells.
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Affiliation(s)
- Michael N.T. Souter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Troi J. Pediongco
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bronwyn S. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy J. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zehua Tian
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhe Zhao
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Adam Nelson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Yogesh Khandokar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - T. Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacinta Wubben
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy C. Sullivan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - George O. Lovrecz
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Jeffrey Y.W. Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Adam P. Uldrich
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Murdoch Children’s Research Institute, Parkville, Melbourne, Australia
| | - Sidonia B.G. Eckle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Goodall KJ, Nguyen A, Andrews DM, Sullivan LC. Ribosylation of the CD8αβ heterodimer permits binding of the nonclassical major histocompatibility molecule, H2-Q10. J Biol Chem 2021; 297:101141. [PMID: 34478713 PMCID: PMC8517849 DOI: 10.1016/j.jbc.2021.101141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
The CD8αβ heterodimer plays a crucial role in the stabilization between major histocompatibility complex class I molecules (MHC-I) and the T cell receptor (TCR). The interaction between CD8 and MHC-I can be regulated by posttranslational modifications, which are proposed to play an important role in the development of CD8 T cells. One modification that has been proposed to control CD8 coreceptor function is ribosylation. Utilizing NAD+, the ecto-enzyme adenosine diphosphate (ADP) ribosyl transferase 2.2 (ART2.2) catalyzes the addition of ADP-ribosyl groups onto arginine residues of CD8α or β chains and alters the interaction between the MHC and TCR complexes. To date, only interactions between modified CD8 and classical MHC-I (MHC-Ia), have been investigated and the interaction with non-classical MHC (MHC-Ib) has not been explored. Here, we show that ADP-ribosylation of CD8 facilitates the binding of the liver-restricted nonclassical MHC, H2-Q10, independent of the associated TCR or presented peptide, and propose that this highly regulated binding imposes an additional inhibitory leash on the activation of CD8-expressing cells in the presence of NAD+. These findings highlight additional important roles for nonclassical MHC-I in the regulation of immune responses.
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Affiliation(s)
- Katharine Jennifer Goodall
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Australia.
| | - Angela Nguyen
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Australia
| | - Daniel Mark Andrews
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Australia
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Papadogianni G, Ravens I, Dittrich-Breiholz O, Bernhardt G, Georgiev H. Impact of Aging on the Phenotype of Invariant Natural Killer T Cells in Mouse Thymus. Front Immunol 2020; 11:575764. [PMID: 33193368 PMCID: PMC7662090 DOI: 10.3389/fimmu.2020.575764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/12/2020] [Indexed: 11/16/2022] Open
Abstract
Invariant natural killer T (iNKT) cells represent a subclass of T cells possessing a restricted repertoire of T cell receptors enabling them to recognize lipid derived ligands. iNKT cells are continuously generated in thymus and differentiate into three main subpopulations: iNKT1, iNKT2, and iNKT17 cells. We investigated the transcriptomes of these subsets comparing cells isolated from young adult (6–10 weeks old) and aged BALB/c mice (25–30 weeks of age) in order to identify genes subject to an age-related regulation of expression. These time points were selected to take into consideration the consequences of thymic involution that radically alter the existing micro-milieu. Significant differences were detected in the expression of histone genes affecting all iNKT subsets. Also the proliferative capacity of iNKT cells decreased substantially upon aging. Several genes were identified as possible candidates causing significant age-dependent changes in iNKT cell generation and/or function such as genes coding for granzyme A, ZO-1, EZH2, SOX4, IGF1 receptor, FLT4, and CD25. Moreover, we provide evidence that IL2 differentially affects homeostasis of iNKT subsets with iNKT17 cells engaging a unique mechanism to respond to IL2 by initiating a slow rate of proliferation.
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Affiliation(s)
| | - Inga Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | | | - Günter Bernhardt
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Hristo Georgiev
- Institute of Immunology, Hannover Medical School, Hannover, Germany
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5
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Bartsch LM, Damasio MPS, Subudhi S, Drescher HK. Tissue-Resident Memory T Cells in the Liver-Unique Characteristics of Local Specialists. Cells 2020; 9:cells9112457. [PMID: 33187162 PMCID: PMC7696520 DOI: 10.3390/cells9112457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 12/23/2022] Open
Abstract
T cells play an important role to build up an effective immune response and are essential in the eradication of pathogens. To establish a long-lasting protection even after a re-challenge with the same pathogen, some T cells differentiate into memory T cells. Recently, a certain subpopulation of memory T cells at different tissue-sites of infection was detected-tissue-resident memory T cells (TRM cells). These cells can patrol in the tissue in order to encounter their cognate antigen to establish an effective protection against secondary infection. The liver as an immunogenic organ is exposed to a variety of pathogens entering the liver through the systemic blood circulation or via the portal vein from the gut. It could be shown that intrahepatic TRM cells can reside within the liver tissue for several years. Interestingly, hepatic TRM cell differentiation requires a distinct cytokine milieu. In addition, TRM cells express specific surface markers and transcription factors, which allow their identification delimited from their circulating counterparts. It could be demonstrated that liver TRM cells play a particular role in many liver diseases such as hepatitis B and C infection, non-alcoholic fatty liver disease and even play a role in the development of hepatocellular carcinoma and in building long-lasting immune responses after vaccination. A better understanding of intrahepatic TRM cells is critical to understand the pathophysiology of many liver diseases and to identify new potential drug targets for the development of novel treatment strategies.
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Affiliation(s)
- Lea M. Bartsch
- Correspondence: (L.M.B.); (H.K.D.); Tel.: +1-(617)-724-7515 (L.M.B. & H.K.D.)
| | | | | | - Hannah K. Drescher
- Correspondence: (L.M.B.); (H.K.D.); Tel.: +1-(617)-724-7515 (L.M.B. & H.K.D.)
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6
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La Flamme AC. Immunology & Cell Biology Publication of the Year Awards 2019. Immunol Cell Biol 2020; 98:796-797. [PMID: 33137214 DOI: 10.1111/imcb.12411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Anne C La Flamme
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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7
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Suzuki T, Hayman L, Kilbey A, Edwards J, Coffelt SB. Gut γδ T cells as guardians, disruptors, and instigators of cancer. Immunol Rev 2020; 298:198-217. [PMID: 32840001 DOI: 10.1111/imr.12916] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 08/17/2023]
Abstract
Colorectal cancer is the third most common cancer worldwide with nearly 2 million cases per year. Immune cells and inflammation are a critical component of colorectal cancer progression, and they are used as reliable prognostic indicators of patient outcome. With the growing appreciation for immunology in colorectal cancer, interest is growing on the role γδ T cells have to play, as they represent one of the most prominent immune cell populations in gut tissue. This group of cells consists of both resident populations-γδ intraepithelial lymphocytes (γδ IELs)-and transient populations that each has unique functions. The homeostatic role of these γδ T cell subsets is to maintain barrier integrity and prevent microorganisms from breaching the mucosal layer, which is accomplished through crosstalk with enterocytes and other immune cells. Recent years have seen a surge in discoveries regarding the regulation of γδ IELs in the intestine and the colon with particular new insights into the butyrophilin family. In this review, we discuss the development, specialities, and functions of γδ T cell subsets during cancer progression. We discuss how these cells may be used to predict patient outcome, as well as how to exploit their behavior for cancer immunotherapy.
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Affiliation(s)
- Toshiyasu Suzuki
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Liam Hayman
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Anna Kilbey
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Joanne Edwards
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Seth B Coffelt
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
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8
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Innate lymphocytes: pathogenesis and therapeutic targets of liver diseases and cancer. Cell Mol Immunol 2020; 18:57-72. [PMID: 33041339 DOI: 10.1038/s41423-020-00561-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
The liver is a lymphoid organ with unique immunological properties, particularly, its predominant innate immune system. The balance between immune tolerance and immune activity is critical to liver physiological functions and is responsible for the sensitivity of this organ to numerous diseases, including hepatotropic virus infection, alcoholic liver disease, nonalcoholic fatty liver disease, autoimmune liver disease, and liver cancer, which are major health problems globally. In the past decade, with the discovery of liver-resident natural killer cells, the importance of innate lymphocytes with tissue residency has gradually become the focus of research. In this review, we address the current knowledge regarding hepatic innate lymphocytes with unique characteristics, including NK cells, ILC1/2/3s, NKT cells, γδ T cells, and MAIT cells, and their potential roles in liver homeostasis maintenance and the progression of liver diseases and cancer. A better understanding of the immunopathogenesis of hepatic innate lymphocytes will be helpful for proposing effective treatments for liver diseases and cancer.
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Goodall KJ, Nguyen A, McKenzie C, Eckle SBG, Sullivan LC, Andrews DM. The murine CD94/NKG2 ligand, Qa-1 b, is a high-affinity, functional ligand for the CD8αα homodimer. J Biol Chem 2020; 295:3239-3246. [PMID: 31992596 PMCID: PMC7062157 DOI: 10.1074/jbc.ra119.010509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
The immune co-receptor CD8 molecule (CD8) has two subunits, CD8α and CD8β, which can assemble into homo or heterodimers. Nonclassical (class-Ib) major histocompatibility complex (MHC) molecules (MHC-Ibs) have recently been identified as ligands for the CD8αα homodimer. This was demonstrated by the observation that histocompatibility 2, Q region locus 10 (H2-Q10) is a high-affinity ligand for CD8αα which also binds the MHC-Ib molecule H2-TL. This suggests that MHC-Ib proteins may be an extended source of CD8αα ligands. Expression of H2-T3/TL and H2-Q10 is restricted to the small intestine and liver, respectively, yet CD8αα-containing lymphocytes are present more broadly. Therefore, here we sought to determine whether murine CD8αα binds only to tissue-specific MHC-Ib molecules or also to ubiquitously expressed MHC-Ib molecules. Using recombinant proteins and surface plasmon resonance-based binding assays, we show that the MHC-Ib family furnishes multiple binding partners for murine CD8αα, including H2-T22 and the CD94/NKG2-A/B-activating NK receptor (NKG2) ligand Qa-1b We also demonstrate a hierarchy among MHC-Ib proteins with respect to CD8αα binding, in which Qa-1b > H2-Q10 > TL. Finally, we provide evidence that Qa-1b is a functional ligand for CD8αα, distinguishing it from its human homologue MHC class I antigen E (HLA-E). These findings provide additional clues as to how CD8αα-expressing cells are controlled in different tissues. They also highlight an unexpected immunological divergence of Qa-1b/HLA-E function, indicating the need for more robust studies of murine MHC-Ib proteins as models for human disease.
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Affiliation(s)
- Katharine Jennifer Goodall
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia.
| | - Angela Nguyen
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Craig McKenzie
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Sidonia Barbara Guiomar Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Lucy Catherine Sullivan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, 3000, Australia
| | - Daniel Mark Andrews
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
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10
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La Flamme AC. Immunology & Cell Biology's Top 10 original research articles 2018-2019. Immunol Cell Biol 2020; 98:6-8. [PMID: 31923926 DOI: 10.1111/imcb.12307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Anne C La Flamme
- School of Biological Sciences, Victoria University of Wellington and Malaghan Institute of Medical Research, Wellington, New Zealand
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11
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Robinson MJ, Pitt C, Brodie EJ, Valk AM, O'Donnell K, Nitschke L, Jones S, Tarlinton DM. BAFF, IL-4 and IL-21 separably program germinal center-like phenotype acquisition, BCL6 expression, proliferation and survival of CD40L-activated B cells in vitro. Immunol Cell Biol 2019; 97:826-839. [PMID: 31276232 DOI: 10.1111/imcb.12283] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/05/2019] [Accepted: 07/03/2019] [Indexed: 11/28/2022]
Abstract
A B cell culture system using BAFF, IL-4 and IL-21 was recently developed that generates B cells with phenotypic and functional characteristics of in vivo-generated germinal center (GC) B cells. Here, we observe discrete influences of each exogenous signal on the expansion and differentiation of a CD40L-activated B cell pool. IL-4 was expressly necessary, but neither BAFF nor IL-21 was required for B cell acquisition of the GC B cell phenotypes of peanut agglutinin binding and loss of CD38 and IgD expression. Both IL-4 and IL-21 enhanced cell cycle entry upon initial activation dose-dependently, and did so additively. Importantly, while both cytokines acted in concert to increase overall BCL6 expression amounts, IL-21 exposure uniquely caused a small proportion of cells to attain a higher level of BCL6 expression, reminiscent of in vivo GC B cells. In contrast, BAFF supported survival of a fraction of memory-like B cells in extended cultures after removal of surrogate T cell-help signals. Thus, by separably programming proliferation, survival and GC phenotype acquisition, IL-4, BAFF and IL-21 drive distinct components of activated B cell fate.
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Affiliation(s)
- Marcus J Robinson
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
| | - Catherine Pitt
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
| | - Erica J Brodie
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
| | - Anika M Valk
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
| | - Kristy O'Donnell
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
| | - Lars Nitschke
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia.,Department of Biology, University of Erlangen, Staudtstr. 5, 91058, Erlangen, Germany
| | - Sarah Jones
- Centre for Inflammatory Diseases, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - David M Tarlinton
- Department of Immunology & Pathology, Alfred Research Alliance, Monash University, Melbourne, VIC, 3004, Australia
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12
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Wang Y, Zhang C. The Roles of Liver-Resident Lymphocytes in Liver Diseases. Front Immunol 2019; 10:1582. [PMID: 31379818 PMCID: PMC6648801 DOI: 10.3389/fimmu.2019.01582] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
Tissue-resident lymphocytes usually reside in barrier sites and are involved in innate and adaptive immunity. In recent years, many studies have shown that multiple types of lymphocytes are resident in the liver, including memory CD8+ T (TRM) cells; "unconventional" T cells, such as invariant natural killer T (iNKT) cells, mucosal associated invariant T (MAIT) cells, and γδT cells; innate lymphoid cells (ILCs) such as natural killer (NK) cells and other ILCs. Although diverse types of tissue-resident lymphocytes share similar phenotypes, functional properties, and transcriptional regulation, the unique microenvironment of the liver can reshape their phenotypic and functional characteristics. Liver-resident lymphocytes serve as sentinels and perform immunosurveillance in response to infection and non-infectious insults, and are involved in the maintenance of liver homeostasis. Under the pathological conditions, distinct liver-resident lymphocytes exert protective or pathological effects in the process of various liver diseases. In this review, we highlight the unique properties of liver-resident lymphocytes, and discuss their functional characteristics in different liver diseases.
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Affiliation(s)
- Yanan Wang
- Institute of Immunopharmacology and Immunotherapy, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Cai Zhang
- Institute of Immunopharmacology and Immunotherapy, School of Pharmaceutical Sciences, Shandong University, Jinan, China
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