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van de Wall S, Anthony SM, Hancox LS, Pewe LL, Langlois RA, Zehn D, Badovinac VP, Harty JT. Dynamic landscapes and protective immunity coordinated by influenza-specific lung-resident memory CD8 + T cells revealed by intravital imaging. Immunity 2024; 57:1878-1892.e5. [PMID: 39043185 DOI: 10.1016/j.immuni.2024.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/09/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Lung-tissue-resident memory (TRM) CD8+ T cells are critical for heterosubtypic immunity against influenza virus (IAV) reinfection. How TRM cells surveil the lung, respond to infection, and interact with other cells remains unresolved. Here, we used IAV infection of mice in combination with intravital and static imaging to define the spatiotemporal dynamics of lung TRM cells before and after recall infection. CD69+CD103+ TRM cells preferentially localized to lung sites of prior IAV infection, where they exhibited patrolling behavior. After rechallenge, lung TRM cells formed tight clusters in an antigen-dependent manner. Transcriptomic analysis of IAV-specific TRM cells revealed the expression of several factors that regulate myeloid cell biology. In vivo rechallenge experiments demonstrated that protection elicited by TRM cells is orchestrated in part by interferon (IFN)-γ-mediated recruitment of inflammatory monocytes into the lungs. Overall, these data illustrate the dynamic landscapes of CD103+ lung TRM cells that mediate early protective immunity against IAV infection.
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Affiliation(s)
- Stephanie van de Wall
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Scott M Anthony
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lisa S Hancox
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lecia L Pewe
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ryan A Langlois
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, MN, USA
| | - Dietmar Zehn
- TUM Center for Infection Prevention (ZIP) and Division of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Vladimir P Badovinac
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - John T Harty
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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2
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Kunes RZ, Walle T, Land M, Nawy T, Pe'er D. Supervised discovery of interpretable gene programs from single-cell data. Nat Biotechnol 2024; 42:1084-1095. [PMID: 37735262 PMCID: PMC10958532 DOI: 10.1038/s41587-023-01940-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 08/09/2023] [Indexed: 09/23/2023]
Abstract
Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene-gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
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Affiliation(s)
- Russell Z Kunes
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Statistics, Columbia University, New York, NY, USA
| | - Thomas Walle
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Cooperation Unit Virotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Max Land
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tal Nawy
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe'er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Maurice NJ, Dalzell TS, Jarjour NN, DePauw TA, Jameson SC. Steady-state, therapeutic, and helminth-induced IL-4 compromise protective CD8 T cell bystander activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598293. [PMID: 38915668 PMCID: PMC11195063 DOI: 10.1101/2024.06.10.598293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Memory CD8 T cells (Tmem) can be activated into innate-like killers by cytokines like IL-12, IL-15, and/or IL-18; but mechanisms regulating this phenomenon (termed bystander activation) are not fully resolved. We found strain-intrinsic deficiencies in bystander activation using specific pathogen-free mice, whereby basal IL-4 signals antagonize IL-18 sensing. We show that therapeutic and helminth-induced IL-4 impairs protective bystander-mediated responses against pathogens. However, this IL-4/IL-18 axis does not completely abolish bystander activation but rather tunes the expression of direct versus indirect mediators of cytotoxicity (granzymes and interferon-γ, respectively). We show that antigen-experience overrides strain-specific deficiencies in bystander activation, leading to uniform IL-18 receptor expression and enhanced capacity for bystander activation/cytotoxicity. Our data highlight that bystander activation is not a binary process but tuned/deregulated by other cytokines that are elevated by contemporaneous infections. Further, our findings underscore the importance of antigen-experienced Tmem to dissect the contributions of bystander Tmem in health and disease.
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Affiliation(s)
- Nicholas J Maurice
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Talia S Dalzell
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Nicholas N Jarjour
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Taylor A DePauw
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Stephen C Jameson
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
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4
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Heidarian M, Jensen IJ, Kannan SK, Pewe LL, Hassert M, Park S, Xue HH, Harty JT, Badovinac VP. Sublethal whole-body irradiation induces permanent loss and dysfunction in pathogen-specific circulating memory CD8 T cell populations. Proc Natl Acad Sci U S A 2023; 120:e2302785120. [PMID: 37364124 PMCID: PMC10318958 DOI: 10.1073/pnas.2302785120] [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: 02/17/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The increasing use of nuclear energy sources inevitably raises the risk of accidental or deliberate radiation exposure and associated immune dysfunction. However, the extent to which radiation exposure impacts memory CD8 T cells, potent mediators of immunity to recurring intracellular infections and malignancies, remains understudied. Using P14 CD8 T cell chimeric mice (P14 chimeras) with an lymphocytic choriomeningitis virus (LCMV) infection model, we observed that sublethal (5Gy) whole-body irradiation (WBI) induced a rapid decline in the number of naive (TN) and P14 circulating memory CD8 T cells (TCIRCM), with the former being more susceptible to radiation-induced numeric loss. While TN cell numbers rapidly recovered, as previously described, the number of P14 TCIRCM cells remained low at least 9 mo after radiation exposure. Additionally, the remaining P14 TCIRCM in irradiated hosts exhibited an inefficient transition to a central memory (CD62L+) phenotype compared to nonirradiated P14 chimeras. WBI also resulted in long-lasting T cell intrinsic deficits in memory CD8 T cells, including diminished cytokine and chemokine production along with impaired secondary expansion upon cognate Ag reencounter. Irradiated P14 chimeras displayed significantly higher bacterial burden after challenge with Listeria monocytogenes expressing the LCMV GP33-41 epitope relative to nonirradiated controls, likely due to radiation-induced numerical and functional impairments. Taken together, our findings suggest that sublethal radiation exposure caused a long-term numerical, impaired differentiation, and functional dysregulation in preexisting TCIRCM, rendering previously protected hosts susceptible to reinfection.
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Affiliation(s)
| | - Isaac J. Jensen
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY10032
| | - Shravan Kumar Kannan
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
| | - Lecia L. Pewe
- Department of Pathology, University of Iowa, Iowa City, IA52246
| | - Mariah Hassert
- Department of Pathology, University of Iowa, Iowa City, IA52246
| | - SungRye Park
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - Hai-Hui Xue
- Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ07110
| | - John T. Harty
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
| | - Vladimir P. Badovinac
- Department of Pathology, University of Iowa, Iowa City, IA52246
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52246
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5
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Evrard M, Becht E, Fonseca R, Obers A, Park SL, Ghabdan-Zanluqui N, Schroeder J, Christo SN, Schienstock D, Lai J, Burn TN, Clatch A, House IG, Beavis P, Kallies A, Ginhoux F, Mueller SN, Gottardo R, Newell EW, Mackay LK. Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts. Immunity 2023:S1074-7613(23)00262-5. [PMID: 37392736 DOI: 10.1016/j.immuni.2023.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/08/2023] [Accepted: 06/07/2023] [Indexed: 07/03/2023]
Abstract
Memory CD8+ T cells can be broadly divided into circulating (TCIRCM) and tissue-resident memory T (TRM) populations. Despite well-defined migratory and transcriptional differences, the phenotypic and functional delineation of TCIRCM and TRM cells, particularly across tissues, remains elusive. Here, we utilized an antibody screening platform and machine learning prediction pipeline (InfinityFlow) to profile >200 proteins in TCIRCM and TRM cells in solid organs and barrier locations. High-dimensional analyses revealed unappreciated heterogeneity within TCIRCM and TRM cell lineages across nine different organs after either local or systemic murine infection models. Additionally, we demonstrated the relative effectiveness of strategies allowing for the selective ablation of TCIRCM or TRM populations across organs and identified CD55, KLRG1, CXCR6, and CD38 as stable markers for characterizing memory T cell function during inflammation. Together, these data and analytical framework provide an in-depth resource for memory T cell classification in both steady-state and inflammatory conditions.
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Affiliation(s)
- Maximilien Evrard
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
| | - Etienne Becht
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raissa Fonseca
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Simone L Park
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Nagela Ghabdan-Zanluqui
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Jan Schroeder
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Susan N Christo
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Dominik Schienstock
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Junyun Lai
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Thomas N Burn
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Imran G House
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Paul Beavis
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia; Cancer Immunology Program, Peter MacCallum Cancer Centre, Parkville, VIC 3010, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore
| | - Scott N Mueller
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Centre Hospitalier Universitaire du Vaud and University of Lausanne, Lausanne 1011, Switzerland
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3010, Australia.
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6
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Altendorfer B, Unger MS, Poupardin R, Hoog A, Asslaber D, Gratz IK, Mrowetz H, Benedetti A, de Sousa DMB, Greil R, Egle A, Gate D, Wyss-Coray T, Aigner L. Transcriptomic Profiling Identifies CD8 + T Cells in the Brain of Aged and Alzheimer's Disease Transgenic Mice as Tissue-Resident Memory T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1272-1285. [PMID: 36165202 PMCID: PMC9515311 DOI: 10.4049/jimmunol.2100737] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 07/20/2022] [Indexed: 12/13/2022]
Abstract
Peripheral immune cell infiltration into the brain is a prominent feature in aging and various neurodegenerative diseases such as Alzheimer's disease (AD). As AD progresses, CD8+ T cells infiltrate into the brain parenchyma, where they tightly associate with neurons and microglia. The functional properties of CD8+ T cells in the brain are largely unknown. To gain further insights into the putative functions of CD8+ T cells in the brain, we explored and compared the transcriptomic profile of CD8+ T cells isolated from the brain and blood of transgenic AD (APPswe/PSEN1dE9, line 85 [APP-PS1]) and age-matched wild-type (WT) mice. Brain CD8+ T cells of APP-PS1 and WT animals had similar transcriptomic profiles and substantially differed from blood circulating CD8+ T cells. The gene signature of brain CD8+ T cells identified them as tissue-resident memory (Trm) T cells. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the significantly upregulated genes revealed overrepresentation of biological processes involved in IFN-β signaling and the response to viral infections. Furthermore, brain CD8+ T cells of APP-PS1 and aged WT mice showed similar differentially regulated genes as brain Trm CD8+ T cells in mouse models with acute virus infection, chronic parasite infection, and tumor growth. In conclusion, our profiling of brain CD8+ T cells suggests that in AD, these cells exhibit similar adaptive immune responses as in other inflammatory diseases of the CNS, potentially opening the door for immunotherapy in AD.
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Affiliation(s)
- Barbara Altendorfer
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Michael Stefan Unger
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Rodolphe Poupardin
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
- Experimental and Clinical Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Anna Hoog
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
- Experimental and Clinical Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Daniela Asslaber
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Iris Karina Gratz
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Heike Mrowetz
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Ariane Benedetti
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
- Institute of Experimental Neuroregeneration, Paracelsus Medical University, Salzburg, Austria
| | - Diana Marisa Bessa de Sousa
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Richard Greil
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Alexander Egle
- IIIrd Medical Department with Hematology and Medical Oncology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
- Salzburg Cancer Research Institute with Laboratory of Immunological and Molecular Cancer Research and Center for Clinical Cancer and Immunology Trials, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA; and
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA; and
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria;
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
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