1
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Schattgen SA, Turner JS, Ghonim MA, Crawford JC, Schmitz AJ, Kim H, Zhou JQ, Awad W, Mettelman RC, Kim W, McIntire KM, Haile A, Klebert MK, Suessen T, Middleton WD, Teefey SA, Presti RM, Ellebedy AH, Thomas PG. Influenza vaccination stimulates maturation of the human T follicular helper cell response. Nat Immunol 2024:10.1038/s41590-024-01926-6. [PMID: 39164477 DOI: 10.1038/s41590-024-01926-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/11/2024] [Indexed: 08/22/2024]
Abstract
The differentiation and specificity of human CD4+ T follicular helper cells (TFH cells) after influenza vaccination have been poorly defined. Here we profiled blood and draining lymph node (LN) samples from human volunteers for over 2 years after two influenza vaccines were administered 1 year apart to define the evolution of the CD4+ TFH cell response. The first vaccination induced an increase in the frequency of circulating TFH (cTFH) and LN TFH cells at week 1 postvaccination. This increase was transient for cTFH cells, whereas the LN TFH cells further expanded during week 2 and remained elevated in frequency for at least 3 months. We observed several distinct subsets of TFH cells in the LN, including pre-TFH cells, memory TFH cells, germinal center (GC) TFH cells and interleukin-10+ TFH cell subsets beginning at baseline and at all time points postvaccination. The shift toward a GC TFH cell phenotype occurred with faster kinetics after the second vaccine compared to the first vaccine. We identified several influenza-specific TFH cell clonal lineages, including multiple responses targeting internal influenza virus proteins, and found that each TFH cell state was attainable within a clonal lineage. Thus, human TFH cells form a durable and dynamic multitissue network.
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Affiliation(s)
- Stefan A Schattgen
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Mohamed A Ghonim
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeremy Chase Crawford
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Aaron J Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyunjin Kim
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Julian Q Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Walid Awad
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert C Mettelman
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Microbiology, Korea University College of Medicine, Seoul, Korea
| | - Katherine M McIntire
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alem Haile
- Clinical Trials Unit, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael K Klebert
- Clinical Trials Unit, Washington University School of Medicine, St. Louis, MO, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - William D Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharlene A Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel M Presti
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA.
| | - Paul G Thomas
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Williams CG, Moreira ML, Asatsuma T, Lee HJ, Li S, Barrera I, Murray E, Soon MSF, Engel JA, Khoury DS, Le S, Wanrooy BJ, Schienstock D, Alexandre YO, Skinner OP, Joseph R, Beattie L, Mueller SN, Chen F, Haque A. Plasmodium infection induces phenotypic, clonal, and spatial diversity among differentiating CD4 + T cells. Cell Rep 2024; 43:114317. [PMID: 38848213 DOI: 10.1016/j.celrep.2024.114317] [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: 12/10/2023] [Revised: 04/21/2024] [Accepted: 05/20/2024] [Indexed: 06/09/2024] Open
Abstract
Naive CD4+ T cells must differentiate in order to orchestrate immunity to Plasmodium, yet understanding of their emerging phenotypes, clonality, spatial distributions, and cellular interactions remains incomplete. Here, we observe that splenic polyclonal CD4+ T cells differentiate toward T helper 1 (Th1) and T follicular helper (Tfh)-like states and exhibit rarer phenotypes not elicited among T cell receptor (TCR) transgenic counterparts. TCR clones present at higher frequencies exhibit Th1 skewing, suggesting that variation in major histocompatibility complex class II (MHC-II) interaction influences proliferation and Th1 differentiation. To characterize CD4+ T cell interactions, we map splenic microarchitecture, cellular locations, and molecular interactions using spatial transcriptomics at near single-cell resolution. Tfh-like cells co-locate with stromal cells in B cell follicles, while Th1 cells in red pulp co-locate with activated monocytes expressing multiple chemokines and MHC-II. Spatial mapping of individual transcriptomes suggests that proximity to chemokine-expressing monocytes correlates with stronger effector phenotypes in Th1 cells. Finally, CRISPR-Cas9 gene disruption reveals a role for CCR5 in promoting clonal expansion and Th1 differentiation. A database of cellular locations and interactions is presented: https://haquelab.mdhs.unimelb.edu.au/spatial_gui/.
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Affiliation(s)
- Cameron G Williams
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Marcela L Moreira
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Takahiro Asatsuma
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Hyun Jae Lee
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Irving Barrera
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Jessica A Engel
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - David S Khoury
- Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
| | - Shirley Le
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Brooke J Wanrooy
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Dominick Schienstock
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Yannick O Alexandre
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Oliver P Skinner
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Rainon Joseph
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Lynette Beattie
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ashraful Haque
- Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia.
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3
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Nguyen C, Kudek M, Zander R, Niu H, Shen J, Bauer A, Alson D, Khatun A, Chen Y, Sun J, Drobyski W, Edelson BT, Cui W. Bhlhe40 Promotes CD4+ T Helper 1 Cell and Suppresses T Follicular Helper Cell Differentiation during Viral Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1829-1842. [PMID: 38619295 DOI: 10.4049/jimmunol.2300355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/18/2024] [Indexed: 04/16/2024]
Abstract
In response to acute infection, naive CD4+ T cells primarily differentiate into T helper 1 (Th1) or T follicular helper (Tfh) cells that play critical roles in orchestrating cellular or humoral arms of immunity, respectively. However, despite the well established role of T-bet and BCL-6 in driving Th1 and Tfh cell lineage commitment, respectively, whether additional transcriptional circuits also underlie the fate bifurcation of Th1 and Tfh cell subsets is not fully understood. In this article, we study how the transcriptional regulator Bhlhe40 dictates the Th1/Tfh differentiation axis in mice. CD4+ T cell-specific deletion of Bhlhe40 abrogates Th1 but augments Tfh differentiation. We also assessed an increase in germinal center B cells and Ab production, suggesting that deletion of Bhlhe40 in CD4+ T cells not only alters Tfh differentiation but also their capacity to provide help to B cells. To identify molecular mechanisms by which Bhlhe40 regulates Th1 versus Tfh lineage choice, we first performed epigenetic profiling in the virus specific Th1 and Tfh cells following LCMV infection, which revealed distinct promoter and enhancer activities between the two helper cell lineages. Furthermore, we identified that Bhlhe40 directly binds to cis-regulatory elements of Th1-related genes such as Tbx21 and Cxcr6 to activate their expression while simultaneously binding to regions of Tfh-related genes such as Bcl6 and Cxcr5 to repress their expression. Collectively, our data suggest that Bhlhe40 functions as a transcription activator to promote Th1 cell differentiation and a transcription repressor to suppress Tfh cell differentiation.
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Affiliation(s)
- Christine Nguyen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Matthew Kudek
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Ryan Zander
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA
| | - Hongshen Niu
- Department of Pathology, Northwestern University, Chicago, IL
| | - Jian Shen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Pathology, Northwestern University, Chicago, IL
| | - Ashley Bauer
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Pathology, Northwestern University, Chicago, IL
| | - Donia Alson
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Sun
- University of Virginia School of Medicine, Charlottesville, VA
| | - William Drobyski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Brian T Edelson
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Versiti Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
- Department of Pathology, Northwestern University, Chicago, IL
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4
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Jin Y, He Y, Liu B, Zhang X, Song C, Wu Y, Hu W, Yan Y, Chen N, Ding Y, Ou Y, Wu Y, Zhang M, Xing S. Single-cell RNA sequencing reveals the dynamics and heterogeneity of lymph node immune cells during acute and chronic viral infections. Front Immunol 2024; 15:1341985. [PMID: 38352870 PMCID: PMC10863051 DOI: 10.3389/fimmu.2024.1341985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction The host immune response determines the differential outcome of acute or chronic viral infections. The comprehensive comparison of lymphoid tissue immune cells at the single-cell level between acute and chronic viral infections is largely insufficient. Methods To explore the landscape of immune responses to acute and chronic viral infections, single-cell RNA sequencing(scRNA-seq), scTCR-seq and scBCR-seq were utilized to evaluate the longitudinal dynamics and heterogeneity of lymph node CD45+ immune cells in mouse models of acute (LCMV Armstrong) and chronic (LCMV clone 13) viral infections. Results In contrast with acute viral infection, chronic viral infection distinctly induced more robust NK cells and plasma cells at the early stage (Day 4 post-infection) and acute stage (Day 8 post-infection), respectively. Moreover, chronic viral infection exerted decreased but aberrantly activated plasmacytoid dendritic cells (pDCs) at the acute phase. Simultaneously, there were significantly increased IgA+ plasma cells (MALT B cells) but differential usage of B-cell receptors in chronic infection. In terms of T-cell responses, Gzma-high effector-like CD8+ T cells were significantly induced at the early stage in chronic infection, which showed temporally reversed gene expression throughout viral infection and the differential usage of the most dominant TCR clonotype. Chronic infection also induced more robust CD4+ T cell responses, including follicular helper T cells (Tfh) and regulatory T cells (Treg). In addition, chronic infection compromised the TCR diversity in both CD8+ and CD4+ T cells. Discussion In conclusion, gene expression and TCR/BCR immune repertoire profiling at the single-cell level in this study provide new insights into the dynamic and differential immune responses to acute and chronic viral infections.
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Affiliation(s)
- Yubei Jin
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Yudan He
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Xiaohui Zhang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Caimei Song
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Yunchen Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Wenjing Hu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Yiwen Yan
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Nuo Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Yingying Ding
- Department of Life Sciences, Bengbu Medical College, Bengbu, Anhui, China
| | - Yuanyuan Ou
- Department of Life Sciences, Bengbu Medical College, Bengbu, Anhui, China
| | - Yixiu Wu
- Department of Life Sciences, Bengbu Medical College, Bengbu, Anhui, China
| | - Mingxia Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong, China
| | - Shaojun Xing
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
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5
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Textor J, Buytenhuijs F, Rogers D, Gauthier ÈM, Sultan S, Wortel IMN, Kalies K, Fähnrich A, Pagel R, Melichar HJ, Westermann J, Mandl JN. Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity. Cell Syst 2023; 14:1059-1073.e5. [PMID: 38061355 DOI: 10.1016/j.cels.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The T cell receptor (TCR) determines specificity and affinity for both foreign and self-peptides presented by the major histocompatibility complex (MHC). Although the strength of TCR interactions with self-pMHC impacts T cell function, it has been challenging to identify TCR sequence features that predict T cell fate. To discern patterns distinguishing TCRs from naive CD4+ T cells with low versus high self-reactivity, we used data from 42 mice to train a machine learning (ML) algorithm that identifies population-level differences between TCRβ sequence sets. This approach revealed that weakly self-reactive T cell populations were enriched for longer CDR3β regions and acidic amino acids. We tested our ML predictions of self-reactivity using retrogenic mice with fixed TCRβ sequences. Extrapolating our analyses to independent datasets, we predicted high self-reactivity for regulatory T cells and slightly reduced self-reactivity for T cells responding to chronic infections. Our analyses suggest a potential trade-off between TCR repertoire diversity and self-reactivity. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Johannes Textor
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands.
| | - Franka Buytenhuijs
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Ève Mallet Gauthier
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Shabaz Sultan
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Inge M N Wortel
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Kathrin Kalies
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Anke Fähnrich
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - René Pagel
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Medicine, Université de Montréal, Montréal, QC H1T 2M4, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | | | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada.
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6
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Kasmani MY, Topchyan P, Brown AK, Brown RJ, Wu X, Chen Y, Khatun A, Alson D, Wu Y, Burns R, Lin CW, Kudek MR, Sun J, Cui W. A spatial sequencing atlas of age-induced changes in the lung during influenza infection. Nat Commun 2023; 14:6597. [PMID: 37852965 PMCID: PMC10584893 DOI: 10.1038/s41467-023-42021-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/26/2023] [Indexed: 10/20/2023] Open
Abstract
Influenza virus infection causes increased morbidity and mortality in the elderly. Aging impairs the immune response to influenza, both intrinsically and because of altered interactions with endothelial and pulmonary epithelial cells. To characterize these changes, we performed single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk RNA sequencing (bulk RNA-seq) on lung tissue from young and aged female mice at days 0, 3, and 9 post-influenza infection. Our analyses identified dozens of key genes differentially expressed in kinetic, age-dependent, and cell type-specific manners. Aged immune cells exhibited altered inflammatory, memory, and chemotactic profiles. Aged endothelial cells demonstrated characteristics of reduced vascular wound healing and a prothrombotic state. Spatial transcriptomics identified novel profibrotic and antifibrotic markers expressed by epithelial and non-epithelial cells, highlighting the complex networks that promote fibrosis in aged lungs. Bulk RNA-seq generated a timeline of global transcriptional activity, showing increased expression of genes involved in inflammation and coagulation in aged lungs. Our work provides an atlas of high-throughput sequencing methodologies that can be used to investigate age-related changes in the response to influenza virus, identify novel cell-cell interactions for further study, and ultimately uncover potential therapeutic targets to improve health outcomes in the elderly following influenza infection.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Paytsar Topchyan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Ryan J Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Xiaopeng Wu
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Donia Alson
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yue Wu
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
| | - Chien-Wei Lin
- Department of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Matthew R Kudek
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, 53226, USA.
- Department of Pathology, Northwestern University, Chicago, IL, 60611, USA.
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7
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Guo M, Abd-Rabbo D, Bertol BC, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic, and functional CD4 T cell paralysis in the lymph node impedes tumor control. Cell Rep 2023; 42:113047. [PMID: 37651234 PMCID: PMC10578141 DOI: 10.1016/j.celrep.2023.113047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
CD4 T cells are central effectors of anti-cancer immunity and immunotherapy, yet the regulation of CD4 tumor-specific T (TTS) cells is unclear. We demonstrate that CD4 TTS cells are quickly primed and begin to divide following tumor initiation. However, unlike CD8 TTS cells or exhaustion programming, CD4 TTS cell proliferation is rapidly frozen in place by a functional interplay of regulatory T cells and CTLA4. Together these mechanisms paralyze CD4 TTS cell differentiation, redirecting metabolic circuits, and reducing their accumulation in the tumor. The paralyzed state is actively maintained throughout cancer progression and CD4 TTS cells rapidly resume proliferation and functional differentiation when the suppressive constraints are alleviated. Overcoming their paralysis established long-term tumor control, demonstrating the importance of rapidly crippling CD4 TTS cells for tumor progression and their potential restoration as therapeutic targets.
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Affiliation(s)
- Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Diala Abd-Rabbo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bruna C Bertol
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Madeleine Carew
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sabelo Lukhele
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Laura M Snell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Microbiology and Immunology and Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Giselle M Boukhaled
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Heidi Elsaesser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marie Jo Halaby
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Tracy L McGaha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
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8
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Cotet TS, Agrafiotis A, Kreiner V, Kuhn R, Shlesinger D, Manero-Carranza M, Khodaverdi K, Kladis E, Desideri Perea A, Maassen-Veeters D, Glänzer W, Massery S, Guerci L, Hong KL, Han J, Stiklioraitis K, D’Arcy VM, Dizerens R, Kilchenmann S, Stalder L, Nissen L, Vogelsanger B, Anzböck S, Laslo D, Bakker S, Kondorosy M, Venerito M, Sanz García A, Feller I, Oxenius A, Reddy ST, Yermanos A. ePlatypus: an ecosystem for computational analysis of immunogenomics data. Bioinformatics 2023; 39:btad553. [PMID: 37682115 PMCID: PMC10518073 DOI: 10.1093/bioinformatics/btad553] [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: 11/11/2022] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023] Open
Abstract
MOTIVATION The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. RESULTS Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is an open-source web-based platform and provides programming tutorials and an integrative database that helps elucidate signatures of B and T cell clonal selection. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand-receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics, and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science. AVAILABILITY AND IMPLEMENTATION Platypus code used in this manuscript can be found at github.com/alexyermanos/Platypus.
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Affiliation(s)
- Tudor-Stefan Cotet
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, Zurich 8093, Switzerland
| | - Victor Kreiner
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Danielle Shlesinger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Marcos Manero-Carranza
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Keywan Khodaverdi
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Evgenios Kladis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Aurora Desideri Perea
- Center for Translational Immunology, University Medical Center Utrecht, Lundlaan 6, Utrecht 3584 EA, The Netherlands
| | - Dylan Maassen-Veeters
- Center for Translational Immunology, University Medical Center Utrecht, Lundlaan 6, Utrecht 3584 EA, The Netherlands
| | - Wiona Glänzer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Solène Massery
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Lorenzo Guerci
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Kostas Stiklioraitis
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | | | - Raphael Dizerens
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Samuel Kilchenmann
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Lucas Stalder
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Leon Nissen
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Basil Vogelsanger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Stine Anzböck
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Daria Laslo
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Sophie Bakker
- Center for Translational Immunology, University Medical Center Utrecht, Lundlaan 6, Utrecht 3584 EA, The Netherlands
| | - Melinda Kondorosy
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Marco Venerito
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Alejandro Sanz García
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Isabelle Feller
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, Zurich 8093, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, Zurich 8093, Switzerland
- Center for Translational Immunology, University Medical Center Utrecht, Lundlaan 6, Utrecht 3584 EA, The Netherlands
- Department of Pathology and Immunology, University of Geneva, 24 rue du Général-Dufour, Geneva 1211, Switzerland
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9
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Xie J, Jeon H, Xin G, Ma Q, Chung D. LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity. PLoS Comput Biol 2023; 19:e1011300. [PMID: 37428794 PMCID: PMC10358952 DOI: 10.1371/journal.pcbi.1011300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) data has been widely used for cell trajectory inference, with the assumption that cells with similar expression profiles share the same differentiation state. However, the inferred trajectory may not reveal clonal differentiation heterogeneity among T cell clones. Single-cell T cell receptor sequencing (scTCR-seq) data provides invaluable insights into the clonal relationship among cells, yet it lacks functional characteristics. Therefore, scRNA-seq and scTCR-seq data complement each other in improving trajectory inference, where a reliable computational tool is still missing. We developed LRT, a computational framework for the integrative analysis of scTCR-seq and scRNA-seq data to explore clonal differentiation trajectory heterogeneity. Specifically, LRT uses the transcriptomics information from scRNA-seq data to construct overall cell trajectories and then utilizes both the TCR sequence information and phenotype information to identify clonotype clusters with distinct differentiation biasedness. LRT provides a comprehensive analysis workflow, including preprocessing, cell trajectory inference, clonotype clustering, trajectory biasedness evaluation, and clonotype cluster characterization. We illustrated its utility using scRNA-seq and scTCR-seq data of CD8+ T cells and CD4+ T cells with acute lymphocytic choriomeningitis virus infection. These analyses identified several clonotype clusters with distinct skewed distribution along the differentiation path, which cannot be revealed solely based on scRNA-seq data. Clones from different clonotype clusters exhibited diverse expansion capability, V-J gene usage pattern and CDR3 motifs. The LRT framework was implemented as an R package 'LRT', and it is now publicly accessible at https://github.com/JuanXie19/LRT. In addition, it provides two Shiny apps 'shinyClone' and 'shinyClust' that allow users to interactively explore distributions of clonotypes, conduct repertoire analysis, implement clustering of clonotypes, trajectory biasedness evaluation, and clonotype cluster characterization.
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Affiliation(s)
- Juan Xie
- The Interdisciplinary Program in Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Hyeongseon Jeon
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Gang Xin
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Dongjun Chung
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America
- Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
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10
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Morita R, Kubota-Koketsu R, Lu X, Sasaki T, Nakayama EE, Liu YC, Okuzaki D, Motooka D, Wing JB, Fujikawa Y, Ichida Y, Amo K, Goto T, Hara J, Shirano M, Yamasaki S, Shioda T. COVID-19 relapse associated with SARS-CoV-2 evasion from CD4 + T-cell recognition in an agammaglobulinemia patient. iScience 2023; 26:106685. [PMID: 37124420 PMCID: PMC10116114 DOI: 10.1016/j.isci.2023.106685] [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: 06/30/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023] Open
Abstract
A 25-year-old patient with a primary immunodeficiency lacking immunoglobulin production experienced a relapse after a 239-day period of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral genetic sequencing demonstrated that SARS-CoV-2 had evolved during the infection period, with at least five mutations associated with host cellular immune recognition. Among them, the T32I mutation in ORF3a was found to evade recognition by CD4+ T cells. The virus found after relapse showed an increased proliferative capacity in vitro. SARS-CoV-2 may have evolved to evade recognition by CD4+ T cells and increased in its proliferative capacity during the persistent infection, likely leading to relapse. These mutations may further affect viral clearance in hosts with similar types of human leukocyte antigens. The early elimination of SARS-CoV-2 in immunocompromised patients is therefore important not only to improve the condition of patients but also to prevent the emergence of mutants that threaten public health.
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Affiliation(s)
- Ryo Morita
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Ritsuko Kubota-Koketsu
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Xiuyuan Lu
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tadahiro Sasaki
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - James Badger Wing
- Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Yasunori Fujikawa
- Department of Medical Laboratory, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Yuji Ichida
- Department of Pharmacy, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Kiyoko Amo
- Department of Pediatric Emergency Medicine, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Tetsushi Goto
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Junichi Hara
- Department of Pediatric Hematology and Oncology, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Michinori Shirano
- Department of Infectious Diseases, Osaka City General Hospital, Osaka 534-0021, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
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11
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Straub A, Grassmann S, Jarosch S, Richter L, Hilgendorf P, Hammel M, Wagner KI, Buchholz VR, Schober K, Busch DH. Recruitment of epitope-specific T cell clones with a low-avidity threshold supports efficacy against mutational escape upon re-infection. Immunity 2023:S1074-7613(23)00179-6. [PMID: 37164014 DOI: 10.1016/j.immuni.2023.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/01/2023] [Accepted: 04/13/2023] [Indexed: 05/12/2023]
Abstract
Repetitive pathogen exposure leads to the dominant outgrowth of T cell clones with high T cell receptor (TCR) affinity to the relevant pathogen-associated antigens. However, low-affinity clones are also known to expand and form immunological memory. While these low-affinity clones contribute less immunity to the original pathogen, their role in protection against pathogens harboring immune escape mutations remains unclear. Based on identification of the TCR repertoire and functionality landscape of naive epitope-specific CD8+ T cells, we reconstructed defined repertoires that could be followed as polyclonal populations during immune responses in vivo. We found that selective clonal expansion is governed by clear TCR avidity thresholds. Simultaneously, initial recruitment of broad TCR repertoires provided a polyclonal niche from which flexible secondary responses to mutant epitopes could be recalled. Elucidating how T cell responses develop "from scratch" is informative for the development of enhanced immunotherapies and vaccines.
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Affiliation(s)
- Adrian Straub
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Simon Grassmann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; The Joseph Sun Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Lena Richter
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Philipp Hilgendorf
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Monika Hammel
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Karolin I Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Veit R Buchholz
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany; Partner site Munich, German Center for Infection Research (DZIF), Munich, Germany.
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12
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Tang J, Jia X, Li J, Dong J, Wang J, Li W, Zhu Y, Hu Y, Hou B, Lin C, Cong Y, Ren T, Yan C, Yang H, Lai Q, Zheng H, Bao Y, Gautam N, Wang HR, Xu B, Chen XL, Li Q, Gascoigne NRJ, Fu G. Themis suppresses the effector function of CD8 + T cells in acute viral infection. Cell Mol Immunol 2023; 20:512-524. [PMID: 36977779 PMCID: PMC10203318 DOI: 10.1038/s41423-023-00997-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
CD8+ T cells play a central role in antiviral immune responses. Upon infection, naive CD8+ T cells differentiate into effector cells to eliminate virus-infected cells, and some of these effector cells further differentiate into memory cells to provide long-term protection after infection is resolved. Although extensively investigated, the underlying mechanisms of CD8+ T-cell differentiation remain incompletely understood. Themis is a T-cell-specific protein that plays critical roles in T-cell development. Recent studies using Themis T-cell conditional knockout mice also demonstrated that Themis is required to promote mature CD8+ T-cell homeostasis, cytokine responsiveness, and antibacterial responses. In this study, we used LCMV Armstrong infection as a probe to explore the role of Themis in viral infection. We found that preexisting CD8+ T-cell homeostasis defects and cytokine hyporesponsiveness do not impair viral clearance in Themis T-cell conditional knockout mice. Further analyses showed that in the primary immune response, Themis deficiency promoted the differentiation of CD8+ effector cells and increased their TNF and IFNγ production. Moreover, Themis deficiency impaired memory precursor cell (MPEC) differentiation but promoted short-lived effector cell (SLEC) differentiation. Themis deficiency also enhanced effector cytokine production in memory CD8+ T cells while impairing central memory CD8+ T-cell formation. Mechanistically, we found that Themis mediates PD-1 expression and its signaling in effector CD8+ T cells, which explains the elevated cytokine production in these cells when Themis is disrupted.
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Affiliation(s)
- Jian Tang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Xian Jia
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Junchen Dong
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayu Wang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wanyun Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhen Zhu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanyan Hu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Bowen Hou
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Chunjie Lin
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Yu Cong
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Tong Ren
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Changsheng Yan
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Hongying Yang
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Qian Lai
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Haiping Zheng
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Yuzhou Bao
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Namrata Gautam
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Hong-Rui Wang
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Bing Xu
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China
| | - Xiao Lei Chen
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Qing Li
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
| | - Nicholas R J Gascoigne
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
- Department of Hematology, The First Affiliated Hospital and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.
- Cancer Research Center of Xiamen University, Xiamen, China.
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13
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Guo M, Abd-Rabbo D, Bertol B, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic and functional CD4 T cell paralysis impedes tumor control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.15.536946. [PMID: 37131587 PMCID: PMC10153152 DOI: 10.1101/2023.04.15.536946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
CD4 T cells are important effectors of anti-tumor immunity, yet the regulation of CD4 tumor-specific T (T TS ) cells during cancer development is still unclear. We demonstrate that CD4 T TS cells are initially primed in the tumor draining lymph node and begin to divide following tumor initiation. Distinct from CD8 T TS cells and previously defined exhaustion programs, CD4 T TS cell proliferation is rapidly frozen in place and differentiation stunted by a functional interplay of T regulatory cells and both intrinsic and extrinsic CTLA4 signaling. Together these mechanisms paralyze CD4 T TS cell differentiation, redirecting metabolic and cytokine production circuits, and reducing CD4 T TS cell accumulation in the tumor. Paralysis is actively maintained throughout cancer progression and CD4 T TS cells rapidly resume proliferation and functional differentiation when both suppressive reactions are alleviated. Strikingly, Treg depletion alone reciprocally induced CD4 T TS cells to themselves become tumor-specific Tregs, whereas CTLA4 blockade alone failed to promote T helper differentiation. Overcoming their paralysis established long-term tumor control, demonstrating a novel immune evasion mechanism that specifically cripples CD4 T TS cells to favor tumor progression.
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14
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Osum KC, Jenkins MK. Toward a general model of CD4 + T cell subset specification and memory cell formation. Immunity 2023; 56:475-484. [PMID: 36921574 PMCID: PMC10084496 DOI: 10.1016/j.immuni.2023.02.010] [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: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 03/17/2023]
Abstract
In the past few decades, a number of transformative discoveries have been made regarding memory CD8+ T cell biology; meanwhile, the CD4+ T cell field has lagged behind this progress. This perspective focuses on CD4+ helper T (Th) cell subset specification and memory cell formation. Here, we argue that the sheer number of Th effector and memory cell subsets and a focus on their differences have been a barrier to a general model of CD4+ memory T cell formation that applies to all immune responses. We highlight a bifurcation model that relies on an IL-2 signal-dependent switch as an explanation for the balanced production of diverse Th memory cells that participate in cell-mediated or humoral immunity in most contexts.
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Affiliation(s)
- Kevin C Osum
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Marc K Jenkins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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15
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Shanmuganad S, Ferguson A, Paranjpe A, Cianciolo EE, Katz JD, Herold MJ, Hildeman DA. Subset-specific and temporal control of effector and memory CD4+ T cell survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.01.530323. [PMID: 36909576 PMCID: PMC10002744 DOI: 10.1101/2023.03.01.530323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Following their proliferative expansion and differentiation into effector cells like Th1, Tfh, and T central memory precursors (Tcmp), most effector CD4+ T cells die, while some survive and become memory cells. Here, we explored how Bcl-2 family members controlled the survival of CD4+ T cells during distinct phases of mouse acute LCMV infection. During expansion, we found that Th1 cells dominated the response, downregulated expression of Bcl-2, and did not require Bcl-2 for survival. Instead, they relied on the anti-apoptotic protein, A1 for survival. Similarly, Th17 cells in an EAE model also depended on A1 for survival. However, after the peak of the response, CD4+ effector T cells required Bcl-2 to counteract Bim to aid their transition into memory. This Bcl-2 dependence persisted in established memory CD4+ T cells. Combined, these data show a temporal switch in Bcl-2 family-mediated survival of CD4+ T cells over the course of an immune response. This knowledge can help improve T cell survival to boost immunity and conversely, target pathogenic T cells.
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16
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Hsiung S, Egawa T. Population dynamics and gene regulation of T cells in response to chronic antigen stimulation. Int Immunol 2023; 35:67-77. [PMID: 36334059 DOI: 10.1093/intimm/dxac050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/04/2022] [Indexed: 11/07/2022] Open
Abstract
T cells are activated by antigen and co-stimulatory receptor signaling and undergo robust proliferation and differentiation into effector cells with protective function. Such quantitatively and qualitatively amplified T cell responses are effective in controlling acute infection and are followed by contraction of the effector population and the formation of resting memory T cells for enhanced protection against previously experienced antigens. However, in the face of persistent antigen during chronic viral infection, in autoimmunity, or in the tumor microenvironment, T cells exhibit distinct responses relative to those in acute insult in several aspects, including reduced clonal expansion and impaired effector function associated with inhibitory receptor expression, a state known as exhaustion. Nevertheless, their responses to chronic infection and tumors are sustained through the establishment of hierarchical heterogeneity, which preserves the duration of the response by generating newly differentiated effector cells. In this review, we highlight recent findings on distinct dynamics of T cell responses under "exhausting" conditions and the roles of the transcription factors that support attenuated yet long-lasting T cell responses as well as the establishment of dysfunctional states.
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Affiliation(s)
- Sunnie Hsiung
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA
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17
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Kasmani MY, Zander R, Chung HK, Chen Y, Khatun A, Damo M, Topchyan P, Johnson KE, Levashova D, Burns R, Lorenz UM, Tarakanova VL, Joshi NS, Kaech SM, Cui W. Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection. J Exp Med 2023; 220:e20220679. [PMID: 36315049 PMCID: PMC9623343 DOI: 10.1084/jem.20220679] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/17/2022] [Accepted: 08/08/2022] [Indexed: 11/05/2022] Open
Abstract
Although recent evidence demonstrates heterogeneity among CD8+ T cells during chronic infection, developmental relationships and mechanisms underlying their fate decisions remain incompletely understood. Using single-cell RNA and TCR sequencing, we traced the clonal expansion and differentiation of CD8+ T cells during chronic LCMV infection. We identified immense clonal and phenotypic diversity, including a subset termed intermediate cells. Trajectory analyses and infection models showed intermediate cells arise from progenitor cells before bifurcating into terminal effector and exhausted subsets. Genetic ablation experiments identified that type I IFN drives exhaustion through an IRF7-dependent mechanism, possibly through an IFN-stimulated subset bridging progenitor and exhausted cells. Conversely, Zeb2 was critical for generating effector cells. Intriguingly, some T cell clones exhibited lineage bias. Mechanistically, we identified that TCR avidity correlates with an exhausted fate, whereas SHP-1 selectively restricts low-avidity effector cell accumulation. Thus, our work elucidates novel mechanisms underlying CD8+ T cell fate determination during persistent infection and suggests two potential pathways leading to exhaustion.
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Affiliation(s)
- Moujtaba Y. Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Ryan Zander
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - H. Kay Chung
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
| | - Yao Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Achia Khatun
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Martina Damo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Paytsar Topchyan
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Kaitlin E. Johnson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Darya Levashova
- Department of Microbiology, Immunology, and Cancer Biology, and Carter Immunology Center, University of Virginia, Charlottesville, VA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
| | - Ulrike M. Lorenz
- Department of Microbiology, Immunology, and Cancer Biology, and Carter Immunology Center, University of Virginia, Charlottesville, VA
| | - Vera L. Tarakanova
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Nikhil S. Joshi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI
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18
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Zander R, Khatun A, Kasmani MY, Chen Y, Cui W. Delineating the transcriptional landscape and clonal diversity of virus-specific CD4 + T cells during chronic viral infection. eLife 2022; 11:e80079. [PMID: 36255051 PMCID: PMC9629829 DOI: 10.7554/elife.80079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
Although recent evidence indicates that CD4+ T cells responding to chronic viral infection are functionally heterogenous, our understanding of the developmental relationships between these subsets, and a determination of how their transcriptional landscape compares to their acute infection counterparts remains unclear. Additionally, whether cell-intrinsic factors such as TCR usage influence CD4+ T cell fate commitment during persistent infection has not previously been studied. Herein, we perform single-cell RNA sequencing (scRNA-seq) combined with single-cell T cell receptor sequencing (scTCR-seq) on virus-specific CD4+ T cells isolated from mice infected with chronic lymphocytic choriomeningitis virus (LCMV) infection. We identify several transcriptionally distinct states among the Th1, Tfh, and memory-like T cell subsets that form at the peak of infection, including the presence of a previously unrecognized Slamf7+ subset with cytolytic features. We further show that the relative distribution of these populations differs substantially between acute and persistent LCMV infection. Moreover, while the progeny of most T cell clones displays membership within each of these transcriptionally unique populations, overall supporting a one cell-multiple fate model, a small fraction of clones display a biased cell fate decision, suggesting that TCR usage may impact CD4+ T cell development during chronic infection. Importantly, comparative analyses further reveal both subset-specific and core gene expression programs that are differentially regulated between CD4+ T cells responding to acute and chronic LCMV infection. Together, these data may serve as a useful framework and allow for a detailed interrogation into the clonal distribution and transcriptional circuits underlying CD4+ T cell differentiation during chronic viral infection.
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Affiliation(s)
- Ryan Zander
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
| | - Achia Khatun
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Moujtaba Y Kasmani
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Yao Chen
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
| | - Weiguo Cui
- Blood Research Institute, Versiti WisconsinMilwaukeeUnited States
- Department of Microbiology and Immunology, Medical College of WisconsinMilwaukeeUnited States
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19
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Robinson AM, Higgins BW, Shuparski AG, Miller KB, McHeyzer-Williams LJ, McHeyzer-Williams MG. Evolution of antigen-specific follicular helper T cell transcription from effector function to memory. Sci Immunol 2022; 7:eabm2084. [PMID: 36206356 PMCID: PMC9881730 DOI: 10.1126/sciimmunol.abm2084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Understanding how follicular helper T cells (TFH) regulate the specialization, maturation, and differentiation of adaptive B cell immunity is crucial for developing durable high-affinity immune protection. Using indexed single-cell molecular strategies, we reveal a skewed intraclonal assortment of higher-affinity T cell receptors and the distinct molecular programming of the localized TFH compartment compared with emigrant conventional effector TH cells. We find a temporal shift in B cell receptor class switch, which permits identification of inflammatory and anti-inflammatory modules of transcriptional programming that subspecialize TFH function before and during the germinal center (GC) reaction. Late collapse of this local primary GC reaction reveals a persistent post-GC TFH population that discloses a putative memory TFH program. These studies define subspecialized antigen-specific TFH transcriptional programs that progressively change with antibody class-specific evolution of high-affinity B cell immunity and a memory TFH transcriptional program that emerges upon local GC resolution.
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20
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Kasmani MY, Ciecko AE, Brown AK, Petrova G, Gorski J, Chen YG, Cui W. Autoreactive CD8 T cells in NOD mice exhibit phenotypic heterogeneity but restricted TCR gene usage. Life Sci Alliance 2022; 5:5/10/e202201503. [PMID: 35667687 PMCID: PMC9170949 DOI: 10.26508/lsa.202201503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/27/2022] Open
Abstract
Paired scRNA-seq and scTCR-seq reveals that diabetogenic CD8 T cells in the islets and spleens of NOD mice exhibit phenotypic and clonal heterogeneity despite restricted TCR gene usage. Expression of certain TCR genes correlates with clonal proliferation and effector phenotype. Type 1 diabetes (T1D) is an autoimmune disorder defined by CD8 T cell–mediated destruction of pancreatic β cells. We have previously shown that diabetogenic CD8 T cells in the islets of non-obese diabetic mice are phenotypically heterogeneous, but clonal heterogeneity remains relatively unexplored. Here, we use paired single-cell RNA and T-cell receptor sequencing (scRNA-seq and scTCR-seq) to characterize autoreactive CD8 T cells from the islets and spleens of non-obese diabetic mice. scTCR-seq demonstrates that CD8 T cells targeting the immunodominant β-cell epitope IGRP206-214 exhibit restricted TCR gene usage. scRNA-seq identifies six clusters of autoreactive CD8 T cells in the islets and six in the spleen, including memory and exhausted cells. Clonal overlap between IGRP206-214–reactive CD8 T cells in the islets and spleen suggests these cells may circulate between the islets and periphery. Finally, we identify correlations between TCR genes and T-cell clonal expansion and effector fate. Collectively, our work demonstrates that IGRP206-214–specific CD8 T cells are phenotypically heterogeneous but clonally restricted, raising the possibility of selectively targeting these TCR structures for therapeutic benefit.
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Affiliation(s)
- Moujtaba Y Kasmani
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Ashley E Ciecko
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ashley K Brown
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Galina Petrova
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jack Gorski
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
| | - Yi-Guang Chen
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA.,Max McGee National Research Center for Juvenile Diabetes, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Weiguo Cui
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA .,Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, USA
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21
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Petrova GV, Naumov YN, Naumova EN, Gorski J. Role of cross-reactivity in cellular immune targeting of influenza A M1 58-66 variant peptide epitopes. Front Immunol 2022; 13:956103. [PMID: 36211433 PMCID: PMC9539824 DOI: 10.3389/fimmu.2022.956103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022] Open
Abstract
The immunologic significance of cross-reactivity of TCR recognition of peptide:MHC complexes is still poorly understood. We have described TCR cross-reactivity in a system involving polyclonal CD8 T cell recognition of the well characterized influenza viral M158-66 epitope. While M158-66 is generally conserved between influenza A isolates, error-prone transcription generates stable variant RNA during infection which could act as novel epitopes. If packaged and viable, variant genomic RNA generates an influenza quasispecies. The stable RNA variants would generate a new transmissible epitope that can select a specific repertoire, which itself should have cross-reactive properties. We tested two candidate peptides in which Thr65 is changed to Ala (A65) or Ser (S65) using recall responses to identify responding T cell clonotypes. Both peptides generated large polyclonal T cell repertoires of their own with repertoire characteristics and cross-reactivity patterns like that observed for the M158-66 repertoire. Both substitutions could be present in viral genomes or mRNA at sufficient frequency during an infection to drive immunity. Peptides from the resulting protein would be a target for CD8 cells irrespective of virus viability or transmissibility. These data support the hypothesis that cross-reactivity is important for immunity against RNA virus infections.
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Affiliation(s)
- Galina V. Petrova
- The Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, United States
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | - Elena N. Naumova
- Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Jack Gorski
- The Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, United States
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22
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Han J, Masserey S, Shlesinger D, Kuhn R, Papadopoulou C, Agrafiotis A, Kreiner V, Dizerens R, Hong KL, Weber C, Greiff V, Oxenius A, Reddy ST, Yermanos A. Echidna: integrated simulations of single-cell immune receptor repertoires and transcriptomes. BIOINFORMATICS ADVANCES 2022; 2:vbac062. [PMID: 36699357 PMCID: PMC9710610 DOI: 10.1093/bioadv/vbac062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/31/2022] [Accepted: 08/26/2022] [Indexed: 02/01/2023]
Abstract
Motivation Single-cell sequencing now enables the recovery of full-length immune receptor repertoires [B cell receptor (BCR) and T cell receptor (TCR) repertoires], in addition to gene expression information. The feature-rich datasets produced from such experiments require extensive and diverse computational analyses, each of which can significantly influence the downstream immunological interpretations, such as clonal selection and expansion. Simulations produce validated standard datasets, where the underlying generative model can be precisely defined and furthermore perturbed to investigate specific questions of interest. Currently, there is no tool that can be used to simulate single-cell datasets incorporating immune receptor repertoires and gene expression. Results We developed Echidna, an R package that simulates immune receptors and transcriptomes at single-cell resolution with user-tunable parameters controlling a wide range of features such as clonal expansion, germline gene usage, somatic hypermutation, transcriptional phenotypes and spatial location. Echidna can additionally simulate time-resolved B cell evolution, producing mutational networks with complex selection histories incorporating class-switching and B cell subtype information. We demonstrated the benchmarking potential of Echidna by simulating clonal lineages and comparing the known simulated networks with those inferred from only the BCR sequences as input. Finally, we simulated immune repertoire information onto existing spatial transcriptomic experiments, thereby generating novel datasets that could be used to develop and integrate methods to profile clonal selection in a spatially resolved manner. Together, Echidna provides a framework that can incorporate experimental data to simulate single-cell immune repertoires to aid software development and bioinformatic benchmarking of clonotyping, phylogenetics, transcriptomics and machine learning strategies. Availability and implementation The R package and code used in this manuscript can be found at github.com/alexyermanos/echidna and also in the R package Platypus (Yermanos et al., 2021). Installation instructions and the vignette for Echidna is described in the Platypus Computational Ecosystem (https://alexyermanos.github.io/Platypus/index.html). Publicly available data and corresponding sample accession numbers can be found in Supplementary Tables S2 and S3. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Solène Masserey
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Danielle Shlesinger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Chrysa Papadopoulou
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Kreiner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Raphael Dizerens
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Cédric Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo 0450, Norway
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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23
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Single-cell immune repertoire sequencing of B and T cells in murine models of infection and autoimmunity. Genes Immun 2022; 23:183-195. [PMID: 36028771 PMCID: PMC9519453 DOI: 10.1038/s41435-022-00180-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Adaptive immune repertoires are composed by the ensemble of B and T-cell receptors within an individual, reflecting both past and current immune responses. Recent advances in single-cell sequencing enable recovery of the complete adaptive immune receptor sequences in addition to transcriptional information. Here, we recovered transcriptome and immune repertoire information for polyclonal T follicular helper cells following lymphocytic choriomeningitis virus (LCMV) infection, CD8+ T cells with binding specificity restricted to two distinct LCMV peptides, and B and T cells isolated from the nervous system in the context of experimental autoimmune encephalomyelitis. We could relate clonal expansion, germline gene usage, and clonal convergence to cell phenotypes spanning activation, memory, naive, antibody secretion, T-cell inflation, and regulation. Together, this dataset provides a resource for immunologists that can be integrated with future single-cell immune repertoire and transcriptome sequencing datasets.
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24
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Richard AC. Divide and Conquer: Phenotypic and Temporal Heterogeneity Within CD8+ T Cell Responses. Front Immunol 2022; 13:949423. [PMID: 35911755 PMCID: PMC9334874 DOI: 10.3389/fimmu.2022.949423] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
The advent of technologies that can characterize the phenotypes, functions and fates of individual cells has revealed extensive and often unexpected levels of diversity between cells that are nominally of the same subset. CD8+ T cells, also known as cytotoxic T lymphocytes (CTLs), are no exception. Investigations of individual CD8+ T cells both in vitro and in vivo have highlighted the heterogeneity of cellular responses at the levels of activation, differentiation and function. This review takes a broad perspective on the topic of heterogeneity, outlining different forms of variation that arise during a CD8+ T cell response. Specific attention is paid to the impact of T cell receptor (TCR) stimulation strength on heterogeneity. In particular, this review endeavors to highlight connections between variation at different cellular stages, presenting known mechanisms and key open questions about how variation between cells can arise and propagate.
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25
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Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4 + T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. eLife 2022; 11:e76339. [PMID: 35829695 PMCID: PMC9323004 DOI: 10.7554/elife.76339] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells are critical orchestrators of immune responses against a large variety of pathogens, including viruses. While multiple CD4+ T cell subtypes and their key transcriptional regulators have been identified, there is a lack of consistent definition for CD4+ T cell transcriptional states. In addition, the progressive changes affecting CD4+ T cell subtypes during and after immune responses remain poorly defined. Using single-cell transcriptomics, we characterized the diversity of CD4+ T cells responding to self-resolving and chronic viral infections in mice. We built a comprehensive map of virus-specific CD4+ T cells and their evolution over time, and identified six major cell states consistently observed in acute and chronic infections. During the course of acute infections, T cell composition progressively changed from effector to memory states, with subtype-specific gene modules and kinetics. Conversely, in persistent infections T cells acquired distinct, chronicity-associated programs. By single-cell T cell receptor (TCR) analysis, we characterized the clonal structure of virus-specific CD4+ T cells across individuals. Virus-specific CD4+ T cell responses were essentially private across individuals and most T cells differentiated into both Tfh and Th1 subtypes irrespective of their TCR. Finally, we showed that our CD4+ T cell map can be used as a reference to accurately interpret cell states in external single-cell datasets across tissues and disease models. Overall, this study describes a previously unappreciated level of adaptation of the transcriptional states of CD4+ T cells responding to viruses and provides a new computational resource for CD4+ T cell analysis.
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Affiliation(s)
- Massimo Andreatta
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Ariel Tjitropranoto
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Zachary Sherman
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
| | - Michael C Kelly
- Single Cell Analysis Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research IncFrederickUnited States
| | - Thomas Ciucci
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of RochesterRochesterUnited States
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Santiago J Carmona
- Department of Oncology, UNIL CHUV and Ludwig Institute for Cancer Research Lausanne, University of LausanneLausanneSwitzerland
- Agora Cancer Research CenterLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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26
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Zhang Q, Xiong D, Pan J, Wang Y, Hardy M, Kalyanaraman B, You M. Chemoprevention of Lung Cancer with a Combination of Mitochondria-Targeted Compounds. Cancers (Basel) 2022; 14:cancers14102538. [PMID: 35626143 PMCID: PMC9140024 DOI: 10.3390/cancers14102538] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Previous reports showed that mitochondria-targeted honokiol and mitochondria-targeted lonidamine potently inhibit complex-I- and complexes-I/II-induced respiration and cancer cell proliferation. In this study, we investigated the efficacy of combining mitochondria-targeted honokiol and mitochondria-targeted lonidamine treatments for lung cancer prevention. We found that their combination exhibited striking tumor inhibition in the benzo[a]pyrene-induced murine lung tumor model without causing detectable side effects. Using single-cell RNA sequencing, we found combined treatment has a clear advantage in that it can significantly inhibit two oncogenic pathways—STAT3 signaling and AKT/mTOR/p70S6K signaling. Such dual inhibition may contribute to the greater efficacy of the combined drug treatment. Therefore, the combination provides a novel option for lung cancer chemoprevention. Abstract Combined treatment targeting mitochondria may improve the efficacy of lung cancer chemoprevention. Here, mitochondria-targeted honokiol (Mito-HNK), an inhibitor of mitochondrial complex I and STAT3 phosphorylation, and mitochondria-targeted lonidamine (Mito-LND), an inhibitor of mitochondrial complexes I/II and AKT/mTOR/p70S6K signaling, were evaluated for their combinational chemopreventive efficacy on mouse lung carcinogenesis. All chemopreventive treatments began one-week post-carcinogen treatment and continued daily for 24 weeks. No evidence of toxicity (including liver toxicity) was detected by monitoring serum levels of alanine aminotransferase and aspartate aminotransferase enzymes. Mito-HNK or Mito-LND treatment alone reduced tumor load by 56% and 48%, respectively, whereas the combination of Mito-HNK and Mito-LND reduced tumor load by 83%. To understand the potential mechanism(s) of action for the observed combinatorial effects, single-cell RNA sequencing was performed using mouse tumors treated with Mito-HNK, Mito-LND, and their combination. In lung tumor cells, Mito-HNK treatment blocked the expression of genes involved in mitochondrial complex ǀ, oxidative phosphorylation, glycolysis, and STAT3 signaling. Mito-LND inhibited the expression of genes for mitochondrial complexes I/II, oxidative phosphorylation, and AKT/mTOR/p70S6K signaling in lung tumor cells. In addition to these changes, a combination of Mito-HNK with Mito-LND decreased arginine and proline metabolism, N-glycan biosynthesis, and tryptophan metabolism in lung tumor cells. Our results demonstrate that Mito-LND enhanced the antitumor efficacy of Mito-HNK, where both compounds inhibited common targets (oxidative phosphorylation) as well as unique targets for each agent (STAT3 and mTOR signaling). Therefore, the combination of Mito-HNK with Mito-LND may present an effective strategy for lung cancer chemoprevention.
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Affiliation(s)
- Qi Zhang
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX 77030, USA; (Q.Z.); (D.X.); (J.P.); (Y.W.)
| | - Donghai Xiong
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX 77030, USA; (Q.Z.); (D.X.); (J.P.); (Y.W.)
| | - Jing Pan
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX 77030, USA; (Q.Z.); (D.X.); (J.P.); (Y.W.)
| | - Yian Wang
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX 77030, USA; (Q.Z.); (D.X.); (J.P.); (Y.W.)
| | - Micael Hardy
- Aix-Marseille University, CNRS, ICR, UMR 7273, 13013 Marseille, France;
| | - Balaraman Kalyanaraman
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA;
- Center for Disease Prevention Research, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX 77030, USA; (Q.Z.); (D.X.); (J.P.); (Y.W.)
- Correspondence:
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27
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Parsa R, London M, Rezende de Castro TB, Reis B, Buissant des Amorie J, Smith JG, Mucida D. Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection. Immunity 2022; 55:1234-1249.e6. [DOI: 10.1016/j.immuni.2022.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 02/07/2022] [Accepted: 05/03/2022] [Indexed: 12/31/2022]
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Kuhn R, Sandu I, Agrafiotis A, Hong KL, Shlesinger D, Neimeier D, Merkler D, Oxenius A, Reddy ST, Yermanos A. Clonally Expanded Virus-Specific CD8 T Cells Acquire Diverse Transcriptional Phenotypes During Acute, Chronic, and Latent Infections. Front Immunol 2022; 13:782441. [PMID: 35185882 PMCID: PMC8847396 DOI: 10.3389/fimmu.2022.782441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
CD8+ T cells play a crucial role in the control and resolution of viral infections and can adopt a wide range of phenotypes and effector functions depending on the inflammatory context and the duration and extent of antigen exposure. Similarly, viral infections can exert diverse selective pressures on populations of clonally related T cells. Technical limitations have nevertheless made it challenging to investigate the relationship between clonal selection and transcriptional phenotypes of virus-specific T cells. We therefore performed single-cell T cell receptor (TCR) repertoire and transcriptome sequencing of virus-specific CD8 T cells in murine models of acute, chronic and latent infection. We observed clear infection-specific populations corresponding to memory, effector, exhausted, and inflationary phenotypes. We further uncovered a mouse-specific and polyclonal T cell response, despite all T cells sharing specificity to a single viral epitope, which was accompanied by stereotypic TCR germline gene usage in all three infection types. Persistent antigen exposure during chronic and latent viral infections resulted in a higher proportion of clonally expanded T cells relative to acute infection. We furthermore observed a relationship between transcriptional heterogeneity and clonal expansion for all three infections, with highly expanded clones having distinct transcriptional phenotypes relative to less expanded clones. Together our work relates clonal selection to gene expression in the context of viral infection and further provides a dataset and accompanying software for the immunological community.
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Affiliation(s)
- Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ioana Sandu
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Danielle Shlesinger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel Neimeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.,Division of Clinical Pathology, Geneva University Hospital, Geneva, Switzerland
| | | | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland.,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
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29
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Zander R, Kasmani MY, Chen Y, Topchyan P, Shen J, Zheng S, Burns R, Ingram J, Cui C, Joshi N, Craft J, Zajac A, Cui W. Tfh-cell-derived interleukin 21 sustains effector CD8 + T cell responses during chronic viral infection. Immunity 2022; 55:475-493.e5. [PMID: 35216666 PMCID: PMC8916994 DOI: 10.1016/j.immuni.2022.01.018] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 10/14/2021] [Accepted: 01/27/2022] [Indexed: 02/03/2023]
Abstract
CD4+ T cell-derived interleukin 21 (IL-21) sustains CD8+ T cell responses during chronic viral infection, but the helper subset that confers this protection remains unclear. Here, we applied scRNA and ATAC-seq approaches to determine the heterogeneity of IL-21+CD4+ T cells during LCMV clone 13 infection. CD4+ T cells were comprised of three transcriptionally and epigenetically distinct populations: Cxcr6+ Th1 cells, Cxcr5+ Tfh cells, and a previously unrecognized Slamf6+ memory-like (Tml) subset. T cell differentiation was specifically redirected toward the Tml subset during chronic, but not acute, LCMV infection. Although this subset displayed an enhanced capacity to accumulate and some developmental plasticity, it remained largely quiescent, which may hinder its helper potential. Conversely, mixed bone marrow chimera experiments revealed that Tfh cell-derived IL-21 was critical to sustain CD8+ T cell responses and viral control. Thus, strategies that bolster IL-21+Tfh cell responses may prove effective in enhancing CD8+ T cell-mediated immunity.
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Affiliation(s)
- Ryan Zander
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA
| | - Moujtaba Y Kasmani
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yao Chen
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Paytsar Topchyan
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jian Shen
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shikan Zheng
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA
| | - Robert Burns
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer Ingram
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Can Cui
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nikhil Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Joseph Craft
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Allan Zajac
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Weiguo Cui
- Blood Research Institute, Versiti Wisconsin, Milwaukee, WI 53226, USA; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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30
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Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA). Nat Biotechnol 2022; 40:54-63. [PMID: 34426704 PMCID: PMC8832949 DOI: 10.1038/s41587-021-00989-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
Links between T cell clonotypes, as defined by T cell receptor (TCR) sequences, and phenotype, as reflected in gene expression (GEX) profiles, surface protein expression and peptide:major histocompatibility complex binding, can reveal functional relationships beyond the features shared by clonally related cells. Here we present clonotype neighbor graph analysis (CoNGA), a graph theoretic approach that identifies correlations between GEX profile and TCR sequence through statistical analysis of GEX and TCR similarity graphs. Using CoNGA, we uncovered associations between TCR sequence and GEX profiles that include a previously undescribed 'natural lymphocyte' population of human circulating CD8+ T cells and a set of TCR sequence determinants of differentiation in thymocytes. These examples show that CoNGA might help elucidate complex relationships between TCR sequence and T cell phenotype in large, heterogeneous, single-cell datasets.
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31
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Rogers D, Sood A, Wang H, van Beek JJP, Rademaker TJ, Artusa P, Schneider C, Shen C, Wong DC, Bhagrath A, Lebel MÈ, Condotta SA, Richer MJ, Martins AJ, Tsang JS, Barreiro LB, François P, Langlais D, Melichar HJ, Textor J, Mandl JN. Pre-existing chromatin accessibility and gene expression differences among naive CD4 + T cells influence effector potential. Cell Rep 2021; 37:110064. [PMID: 34852223 DOI: 10.1016/j.celrep.2021.110064] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/26/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
CD4+ T cells have a remarkable potential to differentiate into diverse effector lineages following activation. Here, we probe the heterogeneity present among naive CD4+ T cells before encountering their cognate antigen to ask whether their effector potential is modulated by pre-existing transcriptional and chromatin landscape differences. Single-cell RNA sequencing shows that key drivers of variability are genes involved in T cell receptor (TCR) signaling. Using CD5 expression as a readout of the strength of tonic TCR interactions with self-peptide MHC, and sorting on the ends of this self-reactivity spectrum, we find that pre-existing transcriptional differences among naive CD4+ T cells impact follicular helper T (TFH) cell versus non-TFH effector lineage choice. Moreover, our data implicate TCR signal strength during thymic development in establishing differences in naive CD4+ T cell chromatin landscapes that ultimately shape their effector potential.
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Affiliation(s)
- Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Aditi Sood
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Microbiology, Immunology, and Infectious Disease, Université de Montréal, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Jasper J P van Beek
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | | | - Patricio Artusa
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Caitlin Schneider
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Connie Shen
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Dylan C Wong
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Aanya Bhagrath
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada
| | - Marie-Ève Lebel
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada
| | - Stephanie A Condotta
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Martin J Richer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luis B Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, IL, USA
| | - Paul François
- Department of Physics, McGill University, Montreal, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill University Genome Centre, Montreal, QC, Canada
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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32
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Muschaweck M, Kopplin L, Ticconi F, Schippers A, Iljazovic A, Gálvez EJC, Abdallah AT, Wagner N, Costa IG, Strowig T, Pabst O. Cognate recognition of microbial antigens defines constricted CD4 + T cell receptor repertoires in the inflamed colon. Immunity 2021; 54:2565-2577.e6. [PMID: 34582747 DOI: 10.1016/j.immuni.2021.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 05/27/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Key aspects of intestinal T cells, including their antigen specificity and their selection by the microbiota and other intestinal antigens, as well as the contribution of individual T cell clones to regulatory and effector functions, remain unresolved. Here we tracked adoptively transferred T cell populations to specify the interrelation of T cell receptor repertoire and the gut antigenic environment. We show that dominant TCRα clonotypes were shared between interferon-γ- and interleukin-17-producing but not regulatory Foxp3+ T cells. Identical TCRα clonotypes accumulated in the colon of different individuals, whereas antibiotics or defined colonization correlated with the expansion of distinct expanded T cell clonotypes. Our results demonstrate key aspects of intestinal CD4+ T cell activation and suggest that few microbial species exert a dominant effect on the intestinal T cell repertoire during colitis. We speculate that dominant proinflammatory T cell clones might provide a therapeutic target in human inflammatory bowel disease.
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Affiliation(s)
- Moritz Muschaweck
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany; Department of Pediatrics, RWTH Aachen University, Aachen, Germany.
| | - Lydia Kopplin
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Fabio Ticconi
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany; Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Angela Schippers
- Department of Pediatrics, RWTH Aachen University, Aachen, Germany
| | - Aida Iljazovic
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research (IZKF), RWTH Aachen University, Aachen, Germany
| | - Norbert Wagner
- Department of Pediatrics, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Hannover Medical School, Hannover, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH Aachen University, Aachen, Germany.
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33
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Huang W, Wang D, Yao YF. Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing. MICROBIAL CELL 2021; 8:208-222. [PMID: 34527720 PMCID: PMC8404151 DOI: 10.15698/mic2021.09.759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022]
Abstract
Infections are highly orchestrated and dynamic processes, which involve both pathogen and host. Transcriptional profiling at the single-cell level enables the analysis of cell diversity, heterogeneity of the immune response, and detailed molecular mechanisms underlying infectious diseases caused by bacteria, viruses, fungi, and parasites. Herein, we highlight recent remarkable advances in single-cell RNA sequencing (scRNA-seq) technologies and their applications in the investigation of host-pathogen interactions, current challenges and potential prospects for disease treatment are discussed as well. We propose that with the aid of scRNA-seq, the mechanism of infectious diseases will be further revealed thus inspiring the development of novel interventions and therapies.
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Affiliation(s)
- Wanqiu Huang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
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34
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Mendoza A, Yewdell WT, Hoyos B, Schizas M, Bou-Puerto R, Michaels AJ, Brown CC, Chaudhuri J, Rudensky AY. Assembly of a spatial circuit of T-bet-expressing T and B lymphocytes is required for antiviral humoral immunity. Sci Immunol 2021; 6:6/60/eabi4710. [PMID: 34117110 PMCID: PMC8418793 DOI: 10.1126/sciimmunol.abi4710] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022]
Abstract
Effective antiviral immunity requires generation of T and B lymphocytes expressing the transcription factor T-bet, a regulator of type 1 inflammatory responses. Using T-bet expression as an endogenous marker for cells participating in a type 1 response, we report coordinated interactions of T-bet-expressing T and B lymphocytes on the basis of their dynamic colocalization at the T cell zone and B follicle boundary (T-B boundary) and germinal centers (GCs) during lung influenza infection. We demonstrate that the assembly of this circuit takes place in distinct anatomical niches within the draining lymph node, guided by CXCR3 that enables positioning of TH1 cells at the T-B boundary. The encounter of B and TH1 cells at the T-B boundary enables IFN-γ produced by the latter to induce IgG2c class switching. Within GCs, T-bet+ TFH cells represent a specialized stable sublineage required for GC growth but dispensable for IgG2c class switching. Our studies show that during respiratory viral infection, T-bet-expressing T and B lymphocytes form a circuit assembled in a spatiotemporally controlled manner that acts as a functional unit enabling a robust and coherent humoral response tailored for optimal antiviral immunity.
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Affiliation(s)
- Alejandra Mendoza
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - William T Yewdell
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Beatrice Hoyos
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michail Schizas
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Regina Bou-Puerto
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Anthony J Michaels
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Chrysothemis C Brown
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jayanta Chaudhuri
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA.,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
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35
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Brown IK, Dyjack N, Miller MM, Krovi H, Rios C, Woolaver R, Harmacek L, Tu TH, O’Connor BP, Danhorn T, Vestal B, Gapin L, Pinilla C, Seibold MA, Scott-Browne J, Santos RG, Reinhardt RL. Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire. PLoS Pathog 2021; 17:e1009602. [PMID: 34106992 PMCID: PMC8216541 DOI: 10.1371/journal.ppat.1009602] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 06/21/2021] [Accepted: 05/01/2021] [Indexed: 12/30/2022] Open
Abstract
The CD4+ T cell response is critical to host protection against helminth infection. How this response varies across different hosts and tissues remains an important gap in our understanding. Using IL-4-reporter mice to identify responding CD4+ T cells to Nippostrongylus brasiliensis infection, T cell receptor sequencing paired with novel clustering algorithms revealed a broadly reactive and clonally diverse CD4+ T cell response. While the most prevalent clones and clonotypes exhibited some tissue selectivity, most were observed to reside in both the lung and lung-draining lymph nodes. Antigen-reactivity of the broader repertoires was predicted to be shared across both tissues and individual mice. Transcriptome, trajectory, and chromatin accessibility analysis of lung and lymph-node repertoires revealed three unique but related populations of responding IL-4+ CD4+ T cells consistent with T follicular helper, T helper 2, and a transitional population sharing similarity with both populations. The shared antigen reactivity of lymph node and lung repertoires combined with the adoption of tissue-specific gene programs allows for the pairing of cellular and humoral responses critical to the orchestration of anti-helminth immunity. Using various “omic” approaches, the CD4+ T cell receptor (TCR) repertoire was explored after primary helminth infection. Infection generated a broadly reactive and clonally diverse CD4+ T cell response with the most prevalent clonotypes and predicted antigen specificities residing in both the lung and lung-draining lymph nodes. Tissue-specific programming of responding CD4+ T cells directed the establishment of committed Tfh and Th2 cells, both critical for driving distinct hallmarks of type-2 inflammation. These datasets help to explore the diverse yet tissue-specific nature of anti-helminth immunity.
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Affiliation(s)
- Ivy K. Brown
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Nathan Dyjack
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Mindy M. Miller
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Rachel Woolaver
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Laura Harmacek
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Ting-Hui Tu
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Brian P. O’Connor
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
| | - Thomas Danhorn
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Brian Vestal
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Clemencia Pinilla
- Florida International University, Port Saint Lucie, Florida, United States of America
| | - Max A. Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - James Scott-Browne
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
- Center for Genes, Environment, and Health, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Radleigh G. Santos
- Department of Mathematics, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - R. Lee Reinhardt
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- * E-mail:
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