1
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Loh L, Carcy S, Krovi HS, Domenico J, Spengler A, Lin Y, Torres J, Prabakar RK, Palmer W, Norman PJ, Stone M, Brunetti T, Meyer HV, Gapin L. Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models. Cell Rep 2024; 43:114705. [PMID: 39264810 DOI: 10.1016/j.celrep.2024.114705] [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: 05/13/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 09/14/2024] Open
Abstract
The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity. We explore the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single-cell RNA sequencing (scRNA-seq) and flow cytometry. In human blood, the majority of Tinn cells share an effector program driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type 1/type 17 effector potential. Cross-species analysis uncovers species-specific distinctions, including the absence of type 2 Tinn cells in humans, which implies distinct immune regulatory mechanisms across species.
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Affiliation(s)
- Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Salomé Carcy
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Joanne Domenico
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea Spengler
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yong Lin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshua Torres
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rishvanth K Prabakar
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - William Palmer
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paul J Norman
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hannah V Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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2
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Rautenstrauch P, Ohler U. Liam tackles complex multimodal single-cell data integration challenges. Nucleic Acids Res 2024; 52:e52. [PMID: 38842910 PMCID: PMC11229356 DOI: 10.1093/nar/gkae409] [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: 08/21/2023] [Revised: 03/08/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Multi-omics characterization of single cells holds outstanding potential for profiling the dynamics and relations of gene regulatory states of thousands of cells. How to integrate multimodal data is an open problem, especially when aiming to combine data from multiple sources or conditions containing both biological and technical variation. We introduce liam, a flexible model for the simultaneous horizontal and vertical integration of paired single-cell multimodal data and mosaic integration of paired with unimodal data. Liam learns a joint low-dimensional representation of the measured modalities, which proves beneficial when the information content or quality of the modalities differ. Its integration accounts for complex batch effects using a tunable combination of conditional and adversarial training, which can be optimized using replicate information while retaining selected biological variation. We demonstrate liam's superior performance on multiple paired multimodal data types, including Multiome and CITE-seq data, and in mosaic integration scenarios. Our detailed benchmarking experiments illustrate the complexities and challenges remaining for integration and the meaningful assessment of its success.
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Affiliation(s)
- Pia Rautenstrauch
- Humboldt-Universität zu Berlin, Department of Computer Science, 10099 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Uwe Ohler
- Humboldt-Universität zu Berlin, Department of Computer Science, 10099 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Humboldt-Universität zu Berlin, Department of Biology, 10099 Berlin, Germany
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3
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Sato K, Hara-Chikuma M, Yasui M, Inoue J, Kim YG. Sufficient water intake maintains the gut microbiota and immune homeostasis and promotes pathogen elimination. iScience 2024; 27:109903. [PMID: 38799550 PMCID: PMC11126815 DOI: 10.1016/j.isci.2024.109903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/16/2024] [Accepted: 05/01/2024] [Indexed: 05/29/2024] Open
Abstract
Water is the most abundant substance in the human body and plays a pivotal role in various bodily functions. While underhydration is associated with the incidence of certain diseases, the specific role of water in gut function remains largely unexplored. Here, we show that water restriction disrupts gut homeostasis, which is accompanied by a bloom of gut microbes and decreased numbers of immune cells, especially Th17 cells, within the colon. These microbial and immunological changes in the gut are associated with an impaired ability to eliminate the enteric pathogen Citrobacter rodentium. Moreover, aquaporin 3, a water channel protein, is required for the maintenance of Th17 cell function and differentiation. Taken together, adequate water intake is critical for maintaining bacterial and immunological homeostasis in the gut, thereby enhancing host defenses against enteric pathogens.
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Affiliation(s)
- Kensuke Sato
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Mariko Hara-Chikuma
- Department of Pharmacology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masato Yasui
- Department of Pharmacology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Joe Inoue
- Division of Biochemistry, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
| | - Yun-Gi Kim
- Department of Microbiology, School of Pharmacy, Kitasato University, Tokyo 108-8641, Japan
- Research Center for Drug Discovery, Faculty of Pharmacy and Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-8512, Japan
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4
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Singh P, Száraz-Széles M, Baráth S, Hevessy Z. A Comprehensive Investigation of Stimulatory Agents on MAIT and Vα7.2+/CD161- T Cell Response and Effects of Immunomodulatory Drugs. Int J Mol Sci 2024; 25:5895. [PMID: 38892082 PMCID: PMC11172258 DOI: 10.3390/ijms25115895] [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: 04/30/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Mucosal-associated invariant T (MAIT) cells, a subset of Vα7.2+ T cells, are a crucial link between innate and adaptive immunity, responding to various stimuli through TCR-dependent and independent pathways. We investigated the responses of MAIT cells and Vα7.2+/CD161- T cells to different stimuli and evaluated the effects of Cyclosporin A (CsA) and Vitamin D3 (VitD). Peripheral blood mononuclear cells (PBMCs) from healthy donors were stimulated with various agents (PMA/Ionomycin, 5-OP-RU, 5-OP-RU/IL-12/IL-33) with or without CsA and VitD. Flow cytometric analysis assessed surface markers and intracellular cytokine production. Under steady-state conditions, MAIT cells displayed elevated expression of CCR6 and IL-13. They showed upregulated activation and exhaustion markers after activation, producing IFNγ, TNFα, and TNFα/GzB. CsA significantly inhibited MAIT cell activation and cytokine production. Conversely, Vα7.2+/CD161- T cells exhibited distinct responses, showing negligible responses to 5-OP-RU ligand but increased cytokine production upon PMA stimulation. Our study underscores the distinct nature of MAIT cells compared to Vα7.2+/CD161- T cells, which resemble conventional T cells. CsA emerges as a potent immunosuppressive agent, inhibiting proinflammatory cytokine production in MAIT cells. At the same time, VitD supports MAIT cell activation and IL-13 production, shedding light on potential therapeutic avenues for immune modulation.
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5
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Gray EH, Srenathan U, Durham LE, Lalnunhlimi S, Steel KJA, Catrina A, Kirkham BW, Taams LS. Human in vitro-induced IL-17A+ CD8+ T-cells exert pro-inflammatory effects on synovial fibroblasts. Clin Exp Immunol 2023; 214:103-119. [PMID: 37367825 PMCID: PMC10711358 DOI: 10.1093/cei/uxad068] [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: 03/29/2023] [Revised: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 06/28/2023] Open
Abstract
IL-17A+ CD8+ T-cells, termed Tc17 cells, have been identified at sites of inflammation in several immune-mediated inflammatory diseases. However, the biological function of human IL-17A+ CD8+ T-cells is not well characterized, likely due in part to the relative scarcity of these cells. Here, we expanded IL-17A+ CD8+ T-cells from healthy donor PBMC or bulk CD8+ T-cell populations using an in vitro polarization protocol. We show that T-cell activation in the presence of IL-1β and IL-23 significantly increased the frequencies of IL-17A+ CD8+ T-cells, which was not further enhanced by IL-6, IL-2, or anti-IFNγ mAb addition. In vitro-generated IL-17A+ CD8+ T-cells displayed a distinct type-17 profile compared with IL-17A- CD8+ T-cells, as defined by transcriptional signature (IL17A, IL17F, RORC, RORA, MAF, IL23R, CCR6), high surface expression of CCR6 and CD161, and polyfunctional production of IL-17A, IL-17F, IL-22, IFNγ, TNFα, and GM-CSF. A significant proportion of in vitro-induced IL-17A+ CD8+ T-cells expressed TCRVα7.2 and bound MR1 tetramers indicative of MAIT cells, indicating that our protocol expanded both conventional and unconventional IL-17A+ CD8+ T-cells. Using an IL-17A secretion assay, we sorted the in vitro-generated IL-17A+ CD8+ T-cells for functional analysis. Both conventional and unconventional IL-17A+ CD8+ T-cells were able to induce pro-inflammatory IL-6 and IL-8 production by synovial fibroblasts from patients with psoriatic arthritis, which was reduced upon addition of anti-TNFα and anti-IL-17A neutralizing antibodies. Collectively, these data demonstrate that human in vitro-generated IL-17A+ CD8+ T-cells are biologically functional and that their pro-inflammatory function can be targeted, at least in vitro, using existing immunotherapy.
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Affiliation(s)
- Elizabeth H Gray
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Ushani Srenathan
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Lucy E Durham
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Sylvine Lalnunhlimi
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Kathryn J A Steel
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Anca Catrina
- Rheumatology Unit, Department of Medicine (Solna), Karolinska Institute, Stockholm, Sweden
| | - Bruce W Kirkham
- Department of Rheumatology, Guy's Hospital, Guy's and St. Thomas' NHS Foundation Trust Hospital, London, UK
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
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6
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Loh L, Carcy S, Krovi HS, Domenico J, Spengler A, Lin Y, Torres J, Palmer W, Norman PJ, Stone M, Brunetti T, Meyer HV, Gapin L. Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570707. [PMID: 38105962 PMCID: PMC10723458 DOI: 10.1101/2023.12.07.570707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity, having the ability to mount rapid responses following activation. In mice, this ability is acquired during thymic development. We explored the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single cell RNA sequencing and flow cytometry. We reveal that in human blood, the majority of Tinn cells, including iNKT, MAIT, and Vδ2+Vγ9+ T cells, share an effector program characterized by the expression of unique chemokine and cytokine receptors, and cytotoxic molecules. This program is driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type I/type III effector potential. To conduct a comprehensive cross-species analysis, we constructed a murine Tinn developmental atlas and uncovered additional species-specific distinctions, including the absence of type II Tinn cells in humans, which implies distinct immune regulatory mechanisms across species. The study provides insights into the development and functionality of Tinn cells, emphasizing their role in immune responses and their potential as targets for therapeutic interventions.
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Affiliation(s)
- Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Salomé Carcy
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Yong Lin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshua Torres
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - William Palmer
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Paul J. Norman
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Hannah V. Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, USA
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7
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Wang R, Song S, Qin J, Yoshimura K, Peng F, Chu Y, Li Y, Fan Y, Jin J, Dang M, Dai E, Pei G, Han G, Hao D, Li Y, Chatterjee D, Harada K, Pizzi MP, Scott AW, Tatlonghari G, Yan X, Xu Z, Hu C, Mo S, Shanbhag N, Lu Y, Sewastjanow-Silva M, Fouad Abdelhakeem AA, Peng G, Hanash SM, Calin GA, Yee C, Mazur P, Marsden AN, Futreal A, Wang Z, Cheng X, Ajani JA, Wang L. Evolution of immune and stromal cell states and ecotypes during gastric adenocarcinoma progression. Cancer Cell 2023; 41:1407-1426.e9. [PMID: 37419119 PMCID: PMC10528152 DOI: 10.1016/j.ccell.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
Understanding tumor microenvironment (TME) reprogramming in gastric adenocarcinoma (GAC) progression may uncover novel therapeutic targets. Here, we performed single-cell profiling of precancerous lesions, localized and metastatic GACs, identifying alterations in TME cell states and compositions as GAC progresses. Abundant IgA+ plasma cells exist in the premalignant microenvironment, whereas immunosuppressive myeloid and stromal subsets dominate late-stage GACs. We identified six TME ecotypes (EC1-6). EC1 is exclusive to blood, while EC4, EC5, and EC2 are highly enriched in uninvolved tissues, premalignant lesions, and metastases, respectively. EC3 and EC6, two distinct ecotypes in primary GACs, associate with histopathological and genomic characteristics, and survival outcomes. Extensive stromal remodeling occurs in GAC progression. High SDC2 expression in cancer-associated fibroblasts (CAFs) is linked to aggressive phenotypes and poor survival, and SDC2 overexpression in CAFs contributes to tumor growth. Our study provides a high-resolution GAC TME atlas and underscores potential targets for further investigation.
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Affiliation(s)
- Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiangjiang Qin
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Katsuhiro Yoshimura
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yuan Li
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, Shenyang 110001, China
| | - Yibo Fan
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiankang Jin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yating Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Deyali Chatterjee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kazuto Harada
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melissa Pool Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ailing W Scott
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ghia Tatlonghari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhiyuan Xu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Can Hu
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Shaowei Mo
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China
| | - Namita Shanbhag
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matheus Sewastjanow-Silva
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ahmed Adel Fouad Abdelhakeem
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pawel Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Autumn N Marsden
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenning Wang
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, Shenyang 110001, China
| | - Xiangdong Cheng
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX 77030, USA.
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8
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Chasman DA, Welch Schwartz R, Vazquez J, Chavarria M, Jenkins ET, Lopez GE, Tyler CT, Stanic AK, Ong IM. Proteogenomic and V(D)J Analysis of Human Decidual T Cells Highlights Unique Transcriptional Programming and Clonal Distribution. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:154-162. [PMID: 37195197 PMCID: PMC10330249 DOI: 10.4049/jimmunol.2200061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/25/2023] [Indexed: 05/18/2023]
Abstract
Immunological tolerance toward the semiallogeneic fetus is one of many maternal adaptations required for a successful pregnancy. T cells are major players of the adaptive immune system and balance tolerance and protection at the maternal-fetal interface; however, their repertoire and subset programming are still poorly understood. Using emerging single-cell RNA sequencing technologies, we simultaneously obtained transcript, limited protein, and receptor repertoire at the single-cell level, from decidual and matched maternal peripheral human T cells. The decidua maintains a tissue-specific distribution of T cell subsets compared with the periphery. We find that decidual T cells maintain a unique transcriptome programming, characterized by restraint of inflammatory pathways by overexpression of negative regulators (DUSP, TNFAIP3, ZFP36) and expression of PD-1, CTLA-4, TIGIT, and LAG3 in some CD8 clusters. Finally, analyzing TCR clonotypes demonstrated decreased diversity in specific decidual T cell populations. Overall, our data demonstrate the power of multiomics analysis in revealing regulation of fetal-maternal immune coexistence.
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Affiliation(s)
- Deborah A. Chasman
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Rene Welch Schwartz
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI
| | - Jessica Vazquez
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Melina Chavarria
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Eryne T. Jenkins
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Gladys E. Lopez
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Chanel T. Tyler
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Aleksandar K. Stanic
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| | - Irene M. Ong
- Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
- Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI
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9
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Yang R, He Q, Zhang J, Yan Y, Shi J, Zhou P. The redirected killing of PD-L1 positive tumor cells by the expanded mucosa-associated invariant T (MAIT) cells is mediated with a bispecific antibody targeting TCR Vα7.2 and PD-L1. Biochem Biophys Res Commun 2023; 644:1-7. [PMID: 36621147 DOI: 10.1016/j.bbrc.2023.01.006] [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: 12/13/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Pan-T cell targeting by CD3-based T cell engagers has brought program-shift treatment and management of blood tumors. However, these modalities have been shown to provoke all types of T cells leading to cytokine storm syndrome, and activate Treg cells. Thus, modulating and potentiating the antitumor responses of a specific T cell subset was encouraged. We initially found that high purity of mucosa-associated invariant T (MAIT) cells could be expanded by the combination of plate-immobilized Vα7.2 mAb (Clone 3C10) and IL2 plus IL15. Then, we generated a novel anti-Vα7.2 TCR bsAb, Vα7.2 x PD-L1, to invoke the anti-tumor potency of these expanded MAIT cells. Furthermore, our data have demonstrated that Vα7.2 x PD-L1 could mediate the cell-to-cell conjunction between MAIT cell and tumor cell line, selectively elicit the activation, cytokine production, degranulation, and cytotoxicity of the expanded MAIT cells in the presence of target cell only. Collectively, this proof-of-concept study provides a new tool to explore the clinical potential of MAIT cells in fighting against PD-L1 positive solid tumors and suggests additional encouragement in designing novel T cell engagers targeting TCR alpha chain specific innate-like T cells subsets, other than pan CD3+ T cells.
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Affiliation(s)
- Rui Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China; Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China.
| | - Qing He
- Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China
| | - Jing Zhang
- Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China
| | - Yongxiang Yan
- Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China
| | - Jian Shi
- Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China
| | - Pengfei Zhou
- Department of Early Discovery and Research, Wuhan YZY Biopharma Co. Ltd, Wuhan, China.
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10
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Jakob J, Kröger A, Klawonn F, Bruder D, Jänsch L. Translatome analyses by bio-orthogonal non-canonical amino acid labeling reveal that MR1-activated MAIT cells induce an M1 phenotype and antiviral programming in antigen-presenting monocytes. Front Immunol 2023; 14:1091837. [PMID: 36875139 PMCID: PMC9977998 DOI: 10.3389/fimmu.2023.1091837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
MAIT cells are multifunctional innate-like effector cells recognizing bacterial-derived vitamin B metabolites presented by the non-polymorphic MHC class I related protein 1 (MR1). However, our understanding of MR1-mediated responses of MAIT cells upon their interaction with other immune cells is still incomplete. Here, we performed the first translatome study of primary human MAIT cells interacting with THP-1 monocytes in a bicellular system. We analyzed the interaction between MAIT and THP-1 cells in the presence of the activating 5-OP-RU or the inhibitory Ac-6-FP MR1-ligand. Using bio-orthogonal non-canonical amino acid tagging (BONCAT) we were able to enrich selectively those proteins that were newly translated during MR1-dependent cellular interaction. Subsequently, newly translated proteins were measured cell-type-specifically by ultrasensitive proteomics to decipher the coinciding immune responses in both cell types. This strategy identified over 2,000 MAIT and 3,000 THP-1 active protein translations following MR1 ligand stimulations. Translation in both cell types was found to be increased by 5-OP-RU, which correlated with their conjugation frequency and CD3 polarization at MAIT cell immunological synapses in the presence of 5-OP-RU. In contrast, Ac-6-FP only regulated a few protein translations, including GSK3B, indicating an anergic phenotype. In addition to known effector responses, 5-OP-RU-induced protein translations uncovered type I and type II Interferon-driven protein expression profiles in both MAIT and THP-1 cells. Interestingly, the translatome of THP-1 cells suggested that activated MAIT cells can impact M1/M2 polarization in these cells. Indeed, gene and surface expression of CXCL10, IL-1β, CD80, and CD206 confirmed an M1-like phenotype of macrophages being induced in the presence of 5-OP-RU-activated MAIT cells. Furthermore, we validated that the Interferon-driven translatome was accompanied by the induction of an antiviral phenotype in THP-1 cells, which were found able to suppress viral replication following conjugation with MR1-activated MAIT cells. In conclusion, BONCAT translatomics extended our knowledge of MAIT cell immune responses at the protein level and discovered that MR1-activated MAIT cells are sufficient to induce M1 polarization and an anti-viral program of macrophages.
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Affiliation(s)
- Josefine Jakob
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andrea Kröger
- Innate Immunity and Infection, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.,Institute of Medical Microbiology and Hospital Hygiene, Molecular Microbiology, Health Campus Immunology, Infectiology and Inflammation, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Frank Klawonn
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology and Hospital Hygiene, Infection Immunology, Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.,Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, Braunschweig, Germany
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11
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Rosati E, Rios Martini G, Pogorelyy MV, Minervina AA, Degenhardt F, Wendorff M, Sari S, Mayr G, Fazio A, Dowds CM, Hauser C, Tran F, von Schönfels W, Pochhammer J, Salnikova MA, Jaeckel C, Gigla JB, Sabet SS, Hübenthal M, Schiminsky E, Schreiber S, Rosenstiel PC, Scheffold A, Thomas PG, Lieb W, Bokemeyer B, Witte M, Aden K, Hendricks A, Schafmayer C, Egberts JH, Mamedov IZ, Bacher P, Franke A. A novel unconventional T cell population enriched in Crohn's disease. Gut 2022; 71:2194-2204. [PMID: 35264446 PMCID: PMC9554086 DOI: 10.1136/gutjnl-2021-325373] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls. DESIGN We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq. RESULTS We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs. CONCLUSIONS We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriela Rios Martini
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anastasia A Minervina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Soner Sari
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Christel Marie Dowds
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Charlotte Hauser
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Julius Pochhammer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Maria A Salnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Charlot Jaeckel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Johannes Boy Gigla
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernd Bokemeyer
- Interdisciplinary Crohn Colitis Centre Minden, Minden, Germany
| | - Maria Witte
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jan-Hendrick Egberts
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- CEITEC, Masaryk University, Brno, Czech Republic
- Dmitry Rogachev National Research Center of Pediatric Hematology, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russian Federation
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
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12
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Soler-Ferran D, Louis F, Woo SB, Greenberg SA. Infiltration of Mature KLRG1 Expressing Cytotoxic T Cells in Oral Lichen Planus. Head Neck Pathol 2022; 16:1124-1129. [PMID: 35904747 PMCID: PMC9729675 DOI: 10.1007/s12105-022-01472-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Oral lichen planus (OLP) is a chronic inflammatory disease affecting oral mucosa. Its pathogenesis includes T cell infiltration. T cells may be naïve or in response to antigen stimulation, progress through differentiation stages. The differentiated states of T cells in OLP mucosa have not previously been reported. METHODS Available OLP microarray gene expression data from Gene Expression Omnibus were analyzed for markers of T cell cytotoxicity. Immunohistochemical studies of T cell subset markers CD4 and CD8 and the T cell differentiation marker killer cell lectin-like receptor G1 (KLRG1) were performed on paraffin embedded formalin fixed oral mucosa biopsy samples from 10 patients with OLP. RESULTS Gene expression analysis of OLP oral mucosa samples disclosed increased transcript expression of KLRG1, CD8A, and granzyme K (GZMK). By immunohistochemistry, prominent CD4 + and CD8 + T cell infiltration was seen in all patient samples. KLRG1 + T cells were abundant, constituting a mean of 51% (range 40-65%) of the number of CD8 + T cells. KLRG1 + T cells localized at the epithelium and lamina propria junction, infiltrating both basal and intraepithelial regions and adjacent to both basal and intraepithelial keratinocytes. CONCLUSIONS OLP oral mucosa T cell infiltration includes KLRG1 + highly differentiated cytotoxic T cells, suggesting continued antigen exposure driving T cells to a highly differentiated phenotype. The known phenotype of these cells, together with microarray detected increases in cytotoxic molecules, suggests that highly differentiated cytotoxic T cells contribute to oral mucosa injury in OLP.
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Affiliation(s)
| | | | - Sook-Bin Woo
- Center for Oral Pathology, StrataDx, Lexington, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Steven A Greenberg
- Department of Neurology, Division of Neuromuscular Disease, Brigham and Women's Hospital, and Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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13
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Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, Bader GD. Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. Nat Protoc 2021; 16:2749-2764. [PMID: 34031612 DOI: 10.1038/s41596-021-00534-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/12/2021] [Indexed: 11/09/2022]
Abstract
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard experimental protocols and analysis workflows have been developed to create single-cell transcriptomic maps from tissues. This tutorial focuses on how to interpret these data to identify cell types, states and other biologically relevant patterns with the objective of creating an annotated map of cells. We recommend a three-step workflow including automatic cell annotation (wherever possible), manual cell annotation and verification. Frequently encountered challenges are discussed, as well as strategies to address them. Guiding principles and specific recommendations for software tools and resources that can be used for each step are covered, and an R notebook is included to help run the recommended workflow. Basic familiarity with computer software is assumed, and basic knowledge of programming (e.g., in the R language) is recommended.
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Affiliation(s)
- Zoe A Clarke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Tallulah S Andrews
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jawairia Atif
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Brendan T Innes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Sonya A MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, Ontario, Canada. .,Department of Immunology, University of Toronto, Toronto, Ontario, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. .,Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada.
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14
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Milenkovic U, Boeckx B, Lambrechts D, Janky R, Hatzichristodoulou G, van Renterghem K, Gevaert T, Cellek S, Bivalacqua TJ, De Ridder D, Albersen M. Single-cell Transcriptomics Uncover a Novel Role of Myeloid Cells and T-lymphocytes in the Fibrotic Microenvironment in Peyronie's Disease. Eur Urol Focus 2021; 8:814-828. [PMID: 33962884 DOI: 10.1016/j.euf.2021.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 04/04/2021] [Accepted: 04/15/2021] [Indexed: 01/23/2023]
Abstract
BACKGROUND Peyronie's disease (PD) is an acquired fibrotic disease affecting the penile tunica albuginea that can lead to curvature and deformities, shortening, and erectile dysfunction. Although immunological mechanisms have been suggested for the pathophysiology of PD, these have not been investigated using single-cell transcriptomics. OBJECTIVE To investigate the immunological signature of plaques from PD patients using immunohistochemistry (IHC) and single-cell RNA sequencing (scRNA-Seq). DESIGN, SETTING, AND PARTICIPANTS Tunica albuginea biopsy was performed in patients undergoing penile surgery for either PD (n = 12) or plication or penile cancer (control, n = 6). The inclusion criteria for PD patients were stable chronic disease (≥12 mo in duration) and no previous penile surgery or intralesional injection therapy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS IHC was performed on surgical samples from ten patients with PD and five control subjects. An additional two PD and one control sample were used for scRNA-Seq (droplet-based; 10X Genomics). Cell clusters were visualised using heatmaps and t-distributed stochastic neighbour embedding plots (BioTuring v2.7.5). RESULTS AND LIMITATIONS IHC revealed the presence of myeloid dendritic cells (DCs; CD68+, TLR4+, CD206+), cytotoxic T lymphocytes (CTLs; CD3+, CD8+), and B lymphocytes (CD20+) in PD plaques, which were absent in controls. scRNA-Seq yielded results for 3312 PD and 5658 control cells. Cell clusters contained fibroblasts (COL1A2+), myofibroblasts (COL1A2+, ACTA2+), smooth muscle cells (ACTA2+, DES+), endothelial cells (VWF+), myeloid cells (CD14+), T lymphocytes (CD3D+), and neutrophils (ALPL+). Myeloid cell subclustering showed infiltration of monocyte-derived cells; control tissue contained classical DCs and resident macrophages. Lymphocyte subclustering revealed mucosal-associated invariant T (MAIT) cells and CTLs in PD. Differential gene expression suggests an increase in inflammatory and immune responses in chronic PD. The study is limited by the small scRNA-seq sample size (n = 3) for IHC, mitigated by a larger cohort of historic paraffin-embedded samples (n = 15), which showed largely parallel findings. Owing to tissue stiffness and extracellular matrix adhesion, our single-cell yield was lower for PD than for the control sample. CONCLUSIONS Our data suggest that even in the chronic PD stage (painless and stable curvature) there is a sustained inflammatory reaction. While vascularisation and collagen production are elevated, the inflammation is driven by specialised monocyte-derived CTL and MAIT cells. These findings could uncover new avenues for medical treatment of PD. PATIENT SUMMARY We looked at the role of the immune system in patients suffering from Peyronie's disease, a condition causing shortening and curvature of the penis. We found that even in a stable, chronic stage of the disease, there is activation of the immune system. Our results suggest that there is potential for novel treatments for this condition.
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Affiliation(s)
- Uros Milenkovic
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Leuven, Belgium.
| | - Bram Boeckx
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium; VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | | | | | - Thomas Gevaert
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Selim Cellek
- Medical Technology Centre, Faculty of Health, Education, Medicine and Social Care, Anglia Ruskin University, Chelmsford, UK
| | - Trinity J Bivalacqua
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Dirk De Ridder
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Leuven, Belgium
| | - Maarten Albersen
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium; Department of Urology, University Hospitals Leuven, Leuven, Belgium
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15
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Khuzwayo S, Mthembu M, Meermeier EW, Prakadan SM, Kazer SW, Bassett T, Nyamande K, Khan DF, Maharaj P, Mitha M, Suleman M, Mhlane Z, Ramjit D, Karim F, Shalek AK, Lewinsohn DM, Ndung'u T, Wong EB. MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection. Front Immunol 2021; 12:631410. [PMID: 33897687 PMCID: PMC8062704 DOI: 10.3389/fimmu.2021.631410] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Mucosal associated invariant T (MAIT) cells are a class of innate-like T cells that utilize a semi-invariant αβ T cell receptor to recognize small molecule ligands produced by bacteria and fungi. Despite growing evidence that immune cells at mucosal surfaces are often phenotypically and functionally distinct from those in the peripheral circulation, knowledge about the characteristics of MAIT cells at the lung mucosal surface, the site of exposure to respiratory pathogens, is limited. HIV infection has been shown to have a profound effect on the number and function of MAIT cells in the peripheral blood, but its effect on lung mucosal MAIT cells is unknown. We examined the phenotypic, functional, and transcriptomic features of major histocompatibility complex (MHC) class I-related (MR1)-restricted MAIT cells from the peripheral blood and bronchoalveolar compartments of otherwise healthy individuals with latent Mycobacterium tuberculosis (Mtb) infection who were either HIV uninfected or HIV infected. Peripheral blood MAIT cells consistently co-expressed typical MAIT cell surface markers CD161 and CD26 in HIV-negative individuals, while paired bronchoalveolar MAIT cells displayed heterogenous expression of these markers. Bronchoalveolar MAIT cells produced lower levels of pro-inflammatory cytokine IFN-γ and expressed higher levels of co-inhibitory markers PD-1 and TIM-3 than peripheral MAIT cells. HIV infection resulted in decreased frequencies and pro-inflammatory function of peripheral blood MAIT cells, while in the bronchoalveolar compartment MAIT cell frequency was decreased but phenotype and function were not significantly altered. Single-cell transcriptomic analysis demonstrated greater heterogeneity among bronchoalveolar compared to peripheral blood MAIT cells and suggested a distinct subset in the bronchoalveolar compartment. The transcriptional features of this bronchoalveolar subset were associated with MAIT cell tissue repair functions. In summary, we found previously undescribed phenotypic and transcriptional heterogeneity of bronchoalveolar MAIT cells in HIV-negative people. In HIV infection, we found numeric depletion of MAIT cells in both anatomical compartments but preservation of the novel phenotypic and transcriptional features of bronchoalveolar MAIT cells.
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Affiliation(s)
- Sharon Khuzwayo
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Maphe Mthembu
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Erin W Meermeier
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States
| | - Sanjay M Prakadan
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Samuel W Kazer
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thierry Bassett
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Kennedy Nyamande
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Dilshaad Fakey Khan
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Priya Maharaj
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Mohammed Mitha
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa
| | - Moosa Suleman
- Department of Pulmonology, Inkosi Albert Luthuli Hospital, Durban, South Africa.,Department of Pulmonology and Critical Care, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Zoey Mhlane
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Dirhona Ramjit
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Alex K Shalek
- The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,Institute for Medical Engineering & Science (IMES), Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - David M Lewinsohn
- Department of Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States.,Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States.,Department of Research, VA Portland Health Care Center, Portland, OR, United States
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT, and Harvard University, Cambridge, MA, United States.,HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.,Max Planck Institute for Infection Biology, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Emily B Wong
- Africa Health Research Institute (AHRI), Durban, South Africa.,Division of Infection and Immunity, University College London, London, United Kingdom.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States.,Division of Infectious Diseases, University of Alabama Birmingham, Birmingham, AL, United States
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16
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Lawlor N, Nehar-Belaid D, Grassmann JD, Stoeckius M, Smibert P, Stitzel ML, Pascual V, Banchereau J, Williams A, Ucar D. Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28. Front Immunol 2021; 12:636720. [PMID: 33815388 PMCID: PMC8010670 DOI: 10.3389/fimmu.2021.636720] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/).
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | | | | | - Michael L. Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
| | - Virginia Pascual
- Ronay Menschel Professor of Pediatrics, Drukier Institute, Weill Cornell Medicine, New York, NY, United States
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Adam Williams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
- Institute of Systems Genomics, University of Connecticut, Farmington, CT, United States
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, United States
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17
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Amini A, Pang D, Hackstein CP, Klenerman P. MAIT Cells in Barrier Tissues: Lessons from Immediate Neighbors. Front Immunol 2020; 11:584521. [PMID: 33329559 PMCID: PMC7734211 DOI: 10.3389/fimmu.2020.584521] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells present at considerable frequencies in human blood and barrier tissues, armed with an expanding array of effector functions in response to homeostatic perturbations. Analogous to other barrier immune cells, their phenotype and function is driven by crosstalk with host and dynamic environmental factors, most pertinently the microbiome. Given their distribution, they must function in diverse extracellular milieus. Tissue-specific and adapted functions of barrier immune cells are shaped by transcriptional programs and regulated through a blend of local cellular, inflammatory, physiological, and metabolic mediators unique to each microenvironment. This review compares the phenotype and function of MAIT cells with other barrier immune cells, highlighting potential areas for future exploration. Appreciation of MAIT cell biology within tissues is crucial to understanding their niche in health and disease.
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Affiliation(s)
- Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Declan Pang
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Carl-Philipp Hackstein
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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18
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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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19
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Parrot T, Gorin JB, Ponzetta A, Maleki KT, Kammann T, Emgård J, Perez-Potti A, Sekine T, Rivera-Ballesteros O, Gredmark-Russ S, Rooyackers O, Folkesson E, Eriksson LI, Norrby-Teglund A, Ljunggren HG, Björkström NK, Aleman S, Buggert M, Klingström J, Strålin K, Sandberg JK. MAIT cell activation and dynamics associated with COVID-19 disease severity. Sci Immunol 2020; 5:eabe1670. [PMID: 32989174 PMCID: PMC7857393 DOI: 10.1126/sciimmunol.abe1670] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Severe COVID-19 is characterized by excessive inflammation of the lower airways. The balance of protective versus pathological immune responses in COVID-19 is incompletely understood. Mucosa-associated invariant T (MAIT) cells are antimicrobial T cells that recognize bacterial metabolites, and can also function as innate-like sensors and mediators of antiviral responses. Here, we investigated the MAIT cell compartment in COVID-19 patients with moderate and severe disease, as well as in convalescence. We show profound and preferential decline in MAIT cells in the circulation of patients with active disease paired with strong activation. Furthermore, transcriptomic analyses indicated significant MAIT cell enrichment and pro-inflammatory IL-17A bias in the airways. Unsupervised analysis identified MAIT cell CD69high and CXCR3low immunotypes associated with poor clinical outcome. MAIT cell levels normalized in the convalescent phase, consistent with dynamic recruitment to the tissues and later release back into the circulation when disease is resolved. These findings indicate that MAIT cells are engaged in the immune response against SARS-CoV-2 and suggest their possible involvement in COVID-19 immunopathogenesis.
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Affiliation(s)
- Tiphaine Parrot
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jean-Baptiste Gorin
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Ponzetta
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kimia T Maleki
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Tobias Kammann
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Emgård
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - André Perez-Potti
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Takuya Sekine
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olga Rivera-Ballesteros
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Gredmark-Russ
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Rooyackers
- Department of Clinical Interventions and Technology, Karolinska Institutet, Stockholm, Sweden
- Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
| | - Elin Folkesson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lars I Eriksson
- Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Norrby-Teglund
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kristoffer Strålin
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Division of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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20
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Yao T, Shooshtari P, Haeryfar SMM. Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies. Front Immunol 2020; 11:1691. [PMID: 32849590 PMCID: PMC7413026 DOI: 10.3389/fimmu.2020.01691] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Mucosa-associated invariant T (MAIT) cells are unconventional, innate-like T lymphocytes that recognize vitamin B metabolites of microbial origin among other antigens displayed by the monomorphic molecule MHC class I-related protein 1 (MR1). Abundant in human tissues, reactive to local inflammatory cues, and endowed with immunomodulatory and cytolytic functions, MAIT cells are likely to play key roles in human malignancies. They accumulate in various tumor microenvironments (TMEs) where they often lose some of their functional capacities. However, the potential roles of MAIT cells in anticancer immunity or cancer progression and their significance in shaping clinical outcomes remain largely unknown. In this study, we analyzed publicly available bulk and single-cell tumor transcriptomic datasets to investigate the tissue distribution, phenotype, and prognostic significance of MAIT cells across several human cancers. We found that expanded MAIT cell clonotypes were often shared between the blood, tumor tissue and adjacent healthy tissue of patients with colorectal, hepatocellular, and non-small cell lung carcinomas. Gene expression comparisons between tumor-infiltrating and healthy tissue MAIT cells revealed the presence of activation and/or exhaustion programs within the TMEs of primary hepatocellular and colorectal carcinomas. Interestingly, in basal and squamous cell carcinomas of the skin, programmed cell death-1 (PD-1) blockade upregulated the expression of several effector genes in tumor-infiltrating MAIT cells. We derived a signature comprising stable and specific MAIT cell gene markers across several tissue compartments and cancer types. By applying this signature to estimate MAIT cell abundance in pan-cancer gene expression data, we demonstrate that a heavier intratumoral MAIT cell presence is positively correlated with a favorable prognosis in esophageal carcinoma but predicts poor overall survival in colorectal and squamous cell lung carcinomas. Finally, in colorectal carcinoma and four other cancer types, we found a positive correlation between MR1 expression and estimated MAIT cell abundance. Collectively, our findings indicate that MAIT cells serve important but diverse roles in human cancers. Our work provides useful models and resources that employ gene expression data platforms to enable future studies in the realm of MAIT cell biology.
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Affiliation(s)
- Tony Yao
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Parisa Shooshtari
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.,Lawson Health Research Institute, London Health Sciences Centre, London, ON, Canada
| | - S M Mansour Haeryfar
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Lawson Health Research Institute, London Health Sciences Centre, London, ON, Canada.,Division of Clinical Immunology and Allergy, Department of Medicine, Western University, London, ON, Canada.,Division of General Surgery, Department of Surgery, Western University, London, ON, Canada.,Centre for Human Immunology, Western University, London, ON, Canada
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21
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Rudak PT, Yao T, Richardson CD, Haeryfar SMM. Measles Virus Infects and Programs MAIT Cells for Apoptosis. J Infect Dis 2020; 223:667-672. [PMID: 32623457 DOI: 10.1093/infdis/jiaa407] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/02/2020] [Indexed: 01/07/2023] Open
Abstract
Measles virus (MeV) binds, infects, and kills CD150+ memory T cells, leading to immune amnesia. Whether MeV targets innate, memory-like T cells is unknown. We demonstrate that human peripheral blood and hepatic mucosa-associated invariant T (MAIT) cells and invariant natural killer T cells express surprisingly high levels of CD150, more than other lymphocyte subsets. Furthermore, exposing MAIT cells to MeV results in their efficient infection and rapid apoptosis. This constitutes the first report of direct MAIT cell infection by a viral pathogen. Given MAIT cells' antimicrobial properties, their elimination by MeV may contribute to measles-induced immunosuppression and heightened vulnerability to unrelated infections.
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Affiliation(s)
- Patrick T Rudak
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Tony Yao
- Department of Microbiology and Immunology, Western University, London, Canada
| | | | - S M Mansour Haeryfar
- Department of Microbiology and Immunology, Western University, London, Canada.,Department of Medicine, Western University, London, Canada.,Department of Surgery, Western University, London, Canada
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22
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Meggyes M, Nagy DU, Szigeti B, Csiszar B, Sandor B, Tamas P, Szereday L. Investigation of mucosal-associated invariant T (MAIT) cells expressing immune checkpoint receptors (TIGIT and CD226) in early-onset preeclampsia. Eur J Obstet Gynecol Reprod Biol 2020; 252:373-381. [PMID: 32682212 DOI: 10.1016/j.ejogrb.2020.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE During our work, we examined the possible contribution of MAIT cells in the pathogenesis of the clinical phase of early-onset preeclampsia and how this could be influenced by TIGIT and CD226 immune checkpoint molecules. STUDY DESIGN 37 pregnant women diagnosed with early-onset preeclampsia and 36 healthy, age-matched control women were involved in this study. Peripheral blood mononuclear cells were isolated by density gradient and frozen. After thawing, cells were stained with monoclonal antibodies to characterize MAIT, MAIT-like, and non-MAIT cells. Flow cytometric analyses were used to measure TIGIT, CD226, intracellular perforin, and granzyme B expression. RESULTS MAIT (CD3+ CD8+ Vα7.2+ CD161++), MAIT-like (CD3+ CD8+ Vα7.2+ CD161+) and non-MAIT (CD3+ CD8+ Vα7.2+ CD161-) cell population were identified based on their CD161 receptor positivity. MAIT cells markedly differed in proportion, TIGIT expression, granzyme B, and perforin content compared to MAIT-like and non-MAIT cells. A significant difference was determined in TIGIT expression by non-MAIT cells and in CD8/CD226 positive relationship between the preeclamptic and healthy condition. CONCLUSIONS Considering that we did not detect a notable difference between early-onset preeclampsia and healthy pregnancy, we suppose that peripheral MAIT cells expressing TIGIT and CD226 immune checkpoint molecules have a marginal role in the pathogenesis of early-onset preeclampsia.
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Affiliation(s)
- Matyas Meggyes
- University of Pecs, Medical School, Department of Medical Microbiology and Immunology, 7624, Pecs, 12 Szigeti Street, Hungary; Janos Szentagothai Research Centre, 7624 Pecs, 20 Ifjusag Street, Hungary.
| | - David U Nagy
- University of Pécs, Department of Genetics and Molecular Biology, 7624 Pecs, 6 Ifjusag Street, Hungary.
| | - Brigitta Szigeti
- University of Pecs, Medical School, Department of Medical Microbiology and Immunology, 7624, Pecs, 12 Szigeti Street, Hungary.
| | - Beata Csiszar
- University of Pecs, Medical School, 1st Department of Medicine, 7624 Pecs, 13 Ifjusag Street, Hungary.
| | - Barbara Sandor
- University of Pecs, Medical School, 1st Department of Medicine, 7624 Pecs, 13 Ifjusag Street, Hungary.
| | - Peter Tamas
- University of Pecs, Medical School, Department of Obstetrics and Gynaecology, 7624 Pecs, 17 Edesanyak Street, Hungary.
| | - Laszlo Szereday
- University of Pecs, Medical School, Department of Medical Microbiology and Immunology, 7624, Pecs, 12 Szigeti Street, Hungary; Janos Szentagothai Research Centre, 7624 Pecs, 20 Ifjusag Street, Hungary.
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23
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Pomaznoy M, Kuan R, Lindvall M, Burel JG, Seumois G, Vijayanand P, Taplitz R, Gilman RH, Saito M, Lewinsohn DM, Sette A, Peters B, Lindestam Arlehamn CS. Quantitative and Qualitative Perturbations of CD8 + MAITs in Healthy Mycobacterium tuberculosis-Infected Individuals. Immunohorizons 2020; 4:292-307. [PMID: 32499216 PMCID: PMC7543048 DOI: 10.4049/immunohorizons.2000031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
CD8 T cells are considered important contributors to the immune response against Mycobacterium tuberculosis, yet limited information is currently known regarding their specific immune signature and phenotype. In this study, we applied a cell population transcriptomics strategy to define immune signatures of human latent tuberculosis infection (LTBI) in memory CD8 T cells. We found a 41-gene signature that discriminates between memory CD8 T cells from healthy LTBI subjects and uninfected controls. The gene signature was dominated by genes associated with mucosal-associated invariant T cells (MAITs) and reflected the lower frequency of MAITs observed in individuals with LTBI. There was no evidence for a conventional CD8 T cell–specific signature between the two cohorts. We, therefore, investigated MAITs in more detail based on Vα7.2 and CD161 expression and staining with an MHC-related protein 1 (MR1) tetramer. This revealed two distinct populations of CD8+Vα7.2+CD161+ MAITs: MR1 tetramer+ and MR1 tetramer−, which both had distinct gene expression compared with memory CD8 T cells. Transcriptomic analysis of LTBI versus noninfected individuals did not reveal significant differences for MR1 tetramer+ MAITs. However, gene expression of MR1 tetramer− MAITs showed large interindividual diversity and a tuberculosis-specific signature. This was further strengthened by a more diverse TCR-α and -β repertoire of MR1 tetramer− cells as compared with MR1 tetramer+. Thus, circulating memory CD8 T cells in subjects with latent tuberculosis have a reduced number of conventional MR1 tetramer+ MAITs as well as a difference in phenotype in the rare population of MR1 tetramer− MAITs compared with uninfected controls.
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Affiliation(s)
- Mikhail Pomaznoy
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Rebecca Kuan
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Mikaela Lindvall
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Julie G Burel
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Grégory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | | | - Randy Taplitz
- Division of Infectious Diseases, University of California San Diego, La Jolla, CA 92093
| | - Robert H Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Universidad Peruana Caytano Hereida, Lima 15102, Peru
| | - Mayuko Saito
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205.,Department of Virology, Tohuku University Graduate School of Medicine, Sendai 9808575, Japan
| | - David M Lewinsohn
- Department of Medicine, VA Portland Health Care System, Portland, OR 97239.,Pulmonary and Critical Care Medicine, Department of Medicine, Oregon Health & Science University, Portland, OR 97239; and
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.,Department of Medicine, University of California San Diego, La Jolla, CA 92093
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24
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Koay HF, Su S, Amann-Zalcenstein D, Daley SR, Comerford I, Miosge L, Whyte CE, Konstantinov IE, d'Udekem Y, Baldwin T, Hickey PF, Berzins SP, Mak JYW, Sontani Y, Roots CM, Sidwell T, Kallies A, Chen Z, Nüssing S, Kedzierska K, Mackay LK, McColl SR, Deenick EK, Fairlie DP, McCluskey J, Goodnow CC, Ritchie ME, Belz GT, Naik SH, Pellicci DG, Godfrey DI. A divergent transcriptional landscape underpins the development and functional branching of MAIT cells. Sci Immunol 2019; 4:eaay6039. [PMID: 31757835 PMCID: PMC10627559 DOI: 10.1126/sciimmunol.aay6039] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/15/2019] [Indexed: 12/11/2022]
Abstract
MR1-restricted mucosal-associated invariant T (MAIT) cells play a unique role in the immune system. These cells develop intrathymically through a three-stage process, but the events that regulate this are largely unknown. Here, using bulk and single-cell RNA sequencing-based transcriptomic analysis in mice and humans, we studied the changing transcriptional landscape that accompanies transition through each stage. Many transcripts were sharply modulated during MAIT cell development, including SLAM (signaling lymphocytic activation molecule) family members, chemokine receptors, and transcription factors. We also demonstrate that stage 3 "mature" MAIT cells comprise distinct subpopulations including newly arrived transitional stage 3 cells, interferon-γ-producing MAIT1 cells and interleukin-17-producing MAIT17 cells. Moreover, the validity and importance of several transcripts detected in this study are directly demonstrated using specific mutant mice. For example, MAIT cell intrathymic maturation was found to be halted in SLAM-associated protein (SAP)-deficient and CXCR6-deficient mouse models, providing clear evidence for their role in modulating MAIT cell development. These data underpin a model that maps the changing transcriptional landscape and identifies key factors that regulate the process of MAIT cell differentiation, with many parallels between mice and humans.
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Affiliation(s)
- H-F Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S Su
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - D Amann-Zalcenstein
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - S R Daley
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - I Comerford
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - L Miosge
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - C E Whyte
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - I E Konstantinov
- Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
- Melbourne Children's Centre for Cardiovascular Genomics and Regenerative Medicine, Murdoch Children's Research Institute, Victoria 3052, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - Y d'Udekem
- Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia
- Melbourne Children's Centre for Cardiovascular Genomics and Regenerative Medicine, Murdoch Children's Research Institute, Victoria 3052, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - T Baldwin
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
- Blood Cells and Blood Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - P F Hickey
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - S P Berzins
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Federation University Australia, Ballarat, Victoria 3350, Australia
- Fiona Elsey Cancer Research Institute, Ballarat, Victoria 3350, Australia
| | - J Y W Mak
- Division of Chemistry and Structural Biology, and Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Y Sontani
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - C M Roots
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - T Sidwell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - A Kallies
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Z Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S Nüssing
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - K Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - L K Mackay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - S R McColl
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - E K Deenick
- Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Sydney, Australia
| | - D P Fairlie
- Division of Chemistry and Structural Biology, and Centre for Inflammation and Disease Research, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland 4072, Australia
| | - J McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - C C Goodnow
- Garvan Institute of Medical Research, Sydney, Australia
- UNSW Cellular Genomics Futures Institute, UNSW, Sydney, Australia
| | - M E Ritchie
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - G T Belz
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - S H Naik
- Single Cell Open Research Endeavour (SCORE), Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - D G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
- Murdoch Children's Research Institute, Victoria 3052, Australia
| | - D I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria 3000, Australia.
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria 3000, Australia
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