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Pranzatelli TJ, Perez P, Ku A, Matuck BF, Huynh K, Sakai S, Abed M, Jang SI, Yamada E, Dominick K, Ahmed Z, Oliver A, Wasikowski R, Easter QT, Baer AN, Pelayo E, Khavandgar Z, Gupta S, Kleiner DE, Magone MT, Lessard C, Farris AD, Burbelo PD, Martin D, Morell R, Zheng C, Rachmaninoff N, Maldonado-Ortiz J, Qu X, Aure MH, Dezfulian MH, Lake R, Teichmann S, Barber DL, Tsoi LC, Sowalsky AG, Tyc KM, Liu J, Gudjonsson JE, Byrd KM, Johnson PL, Chiorini JA, Warner BM. GZMK+CD8+ T cells Target A Specific Acinar Cell Type in Sjögren's Disease. RESEARCH SQUARE 2024:rs.3.rs-3601404. [PMID: 38196575 PMCID: PMC10775371 DOI: 10.21203/rs.3.rs-3601404/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Sjögren's Disease (SjD) is a systemic autoimmune disease without a clear etiology or effective therapy. Utilizing unbiased single-cell and spatial transcriptomics to analyze human minor salivary glands in health and disease we developed a comprehensive understanding of the cellular landscape of healthy salivary glands and how that landscape changes in SjD patients. We identified novel seromucous acinar cell types and identified a population of PRR4+CST3+WFDC2- seromucous acinar cells that are particularly targeted in SjD. Notably, GZMK +CD8 T cells, enriched in SjD, exhibited a cytotoxic phenotype and were physically associated with immune-engaged epithelial cells in disease. These findings shed light on the immune response's impact on transitioning acinar cells with high levels of secretion and explain the loss of this specific cell population in SjD. This study explores the complex interplay of varied cell types in the salivary glands and their role in the pathology of Sjögren's Disease.
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nat Methods 2024; 21:1349-1363. [PMID: 38849569 DOI: 10.1038/s41592-024-02298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 05/03/2024] [Indexed: 06/09/2024]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Fairlie Reese
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA
- Cherokee Nation System Solutions, contractor to the US Geological Survey-Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Matthew S Adams
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Gabriela Balderrama-Gutierrez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Amit K Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jose M Gonzalez Martinez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Flomics Biotech, SL, Barcelona, Spain
| | - Cindy E Liang
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - David A Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Andrey D Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Ashley M Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Muhammed Hasan Çelik
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R M Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian-Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew E Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andre D Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Brandon Y Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Andrew E Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | | | - Alyssa Cousineau
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Energy, Installations & Environment, Office of the Assistant Secretary of Defense, Washington, DC, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Nedka G Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Margaret E Hunter
- US Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - Rene Maehr
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yin Shen
- Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Hagen U Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, NY, USA
| | - Barbara J Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
- UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
| | - Angela N Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
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3
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Currey J, Ellsworth C, Khatun MS, Wang C, Chen Z, Liu S, Midkiff C, Xiao M, Ren M, Liu F, Elgazzaz M, Fox S, Maness NJ, Rappaport J, Lazartigues E, Blair R, Kolls JK, Mauvais-Jarvis F, Qin X. Upregulation of inflammatory genes and pathways links obesity to severe COVID-19. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167322. [PMID: 38942338 DOI: 10.1016/j.bbadis.2024.167322] [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: 11/28/2023] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024]
Abstract
Obesity is a risk factor for developing severe COVID-19. However, the mechanism underlying obesity-accelerated COVID-19 remains unclear. Here, we report results from a study in which 2-3-month-old K18-hACE2 (K18) mice were fed a western high-fat diet (WD) or normal chow (NC) over 3 months before intranasal infection with a sublethal dose of SARS-CoV2 WA1 (a strain ancestral to the Wuhan variant). After infection, the WD-fed K18 mice lost significantly more body weight and had more severe lung inflammation than normal chow (NC)-fed mice. Bulk RNA-seq analysis of lungs and adipose tissue revealed a diverse landscape of various immune cells, inflammatory markers, and pathways upregulated in the infected WD-fed K18 mice when compared with the infected NC-fed control mice. The transcript levels of IL-6, an important marker of COVID-19 disease severity, were upregulated in the lung at 6-9 days post-infection in the WD-fed mice when compared to NC-fed mice. Transcriptome analysis of the lung and adipose tissue obtained from deceased COVID-19 patients found that the obese patients had an increase in the expression of genes and the activation of pathways associated with inflammation as compared to normal-weight patients (n = 2). The K18 mouse model and human COVID-19 patient data support a link between inflammation and an obesity-accelerated COVID-19 disease phenotype. These results also indicate that obesity-accelerated severe COVID-19 caused by SARS-CoV-2 WA1 infection in the K18 mouse model would be a suitable model for dissecting the cellular and molecular mechanisms underlying pathogenesis.
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Affiliation(s)
- Joshua Currey
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Calder Ellsworth
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mst Shamima Khatun
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Chenxiao Wang
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Zheng Chen
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Shumei Liu
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Cecily Midkiff
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Mark Xiao
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mi Ren
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Fengming Liu
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Mona Elgazzaz
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Sharon Fox
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Nicholas J Maness
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jay Rappaport
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Eric Lazartigues
- Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Robert Blair
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Jay K Kolls
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA; Department of Pulmonary Critical Care and Environmental Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Franck Mauvais-Jarvis
- Department of Medicine, Section of Endocrinology and Metabolism, Tulane University School of Medicine, New Orleans, LA 70112, USA; Southeast Louisiana VA Medical Center, New Orleans, LA 70119, USA
| | - Xuebin Qin
- Tulane National Primate Research Center, Covington, LA 70433, USA; Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA.
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Li Z, Xie Q, Zhao F, Huo X, Ren D, Liu Z, Zhou X, Shen G, Zhao J. Exploring GZMK as a prognostic marker and predictor of immunotherapy response in breast cancer: unveiling novel insights into treatment outcomes. J Cancer Res Clin Oncol 2024; 150:286. [PMID: 38833021 PMCID: PMC11150209 DOI: 10.1007/s00432-024-05791-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Granzyme K (GZMK) is a crucial mediator released by immune cells to eliminate tumor cells, playing significant roles in inflammation and tumorigenesis. Despite its importance, the specific role of GZMK in breast cancer and its mechanisms are not well understood. METHODS We utilized data from the TCGA and GEO databases and employed a range of analytical methods including GO, KEGG, GSEA, ssGSEA, and PPI to investigate the impact of GZMK on breast cancer. In vitro studies, including RT-qPCR, CCK-8 assay, cell cycle experiments, apoptosis assays, Celigo scratch assays, Transwell assays, and immunohistochemical methods, were conducted to validate the effects of GZMK on breast cancer cells. Additionally, Cox regression analysis integrating TCGA and our clinical data was used to develop an overall survival (OS) prediction model. RESULTS Analysis of clinical pathological features revealed significant correlations between GZMK expression and lymph node staging, differentiation grade, and molecular breast cancer subtypes. High GZMK expression was associated with improved OS, progression-free survival (PFS), and recurrence-free survival (RFS), as confirmed by multifactorial Cox regression analysis. Functional and pathway enrichment analyses of genes positively correlated with GZMK highlighted involvement in lymphocyte differentiation, T cell differentiation, and T cell receptor signaling pathways. A robust association between GZMK expression and T cell presence was noted in the breast cancer tumor microenvironment (TME), with strong correlations with ESTIMATEScore (Cor = 0.743, P < 0.001), ImmuneScore (Cor = 0.802, P < 0.001), and StromalScore (Cor = 0.516, P < 0.001). GZMK also showed significant correlations with immune checkpoint molecules, including CTLA4 (Cor = 0.856, P < 0.001), PD-1 (Cor = 0.82, P < 0.001), PD-L1 (Cor = 0.56, P < 0.001), CD48 (Cor = 0.75, P < 0.001), and CCR7 (Cor = 0.856, P < 0.001). Studies indicated that high GZMK expression enhances patient responsiveness to immunotherapy, with higher levels observed in responsive patients compared to non-responsive ones. In vitro experiments confirmed that GZMK promotes cell proliferation, cell division, apoptosis, cell migration, and invasiveness (P < 0.05). CONCLUSION Our study provides insights into the differential expression of GZMK in breast cancer and its potential mechanisms in breast cancer pathogenesis. Elevated GZMK expression is associated with improved OS and RFS, suggesting its potential as a prognostic marker for breast cancer survival and as a predictor of the efficacy of immunotherapy.
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Affiliation(s)
- Zitao Li
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, 810000, China
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Qiqi Xie
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Fuxing Zhao
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Xinfa Huo
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Zhilin Liu
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Xiaofeng Zhou
- Pathology Department, Affiliated Hospital of Qinghai University, Xining, 810000, China
| | - Guoshuang Shen
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China.
| | - Jiuda Zhao
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinghai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, 810000, China.
- Breast Disease Diagnosis and Treatment Center of Qinghai University Affiliated Hospital & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China.
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5
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Wang AZ, Mashimo BL, Schaettler MO, Sherpa ND, Leavitt LA, Livingstone AJ, Khan SM, Li M, Anzaldua-Campos MI, Bradley JD, Leuthardt EC, Kim AH, Dowling JL, Chicoine MR, Jones PS, Choi BD, Cahill DP, Carter BS, Petti AA, Johanns TM, Dunn GP. Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population. Cancer Discov 2024; 14:1106-1131. [PMID: 38416133 DOI: 10.1158/2159-8290.cd-23-0913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/20/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
Recent clinical trials have highlighted the limited efficacy of T cell-based immunotherapy in patients with glioblastoma (GBM). To better understand the characteristics of tumor-infiltrating lymphocytes (TIL) in GBM, we performed cellular indexing of transcriptomes and epitopes by sequencing and single-cell RNA sequencing with paired V(D)J sequencing, respectively, on TILs from two cohorts of patients totaling 15 patients with high-grade glioma, including GBM or astrocytoma, IDH-mutant, grade 4 (G4A). Analysis of the CD8+ TIL landscape reveals an enrichment of clonally expanded GZMK+ effector T cells in the tumor compared with matched blood, which was validated at the protein level. Furthermore, integration with other cancer types highlights the lack of a canonically exhausted CD8+ T-cell population in GBM TIL. These data suggest that GZMK+ effector T cells represent an important T-cell subset within the GBM microenvironment and may harbor potential therapeutic implications. SIGNIFICANCE To understand the limited efficacy of immune-checkpoint blockade in GBM, we applied a multiomics approach to understand the TIL landscape. By highlighting the enrichment of GZMK+ effector T cells and the lack of exhausted T cells, we provide a new potential mechanism of resistance to immunotherapy in GBM. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Anthony Z Wang
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryce L Mashimo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maximilian O Schaettler
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ngima D Sherpa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Biological and Biomedical Sciences Graduate Program, Harvard University, Cambridge, Massachusetts
| | - Lydia A Leavitt
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurosurgery, University of Louisville, Louisville, Kentucky
| | - Alexandra J Livingstone
- Department of Medicine, Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Saad M Khan
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mao Li
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Markus I Anzaldua-Campos
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Neuroscience Undergraduate Program, Harvard University, Cambridge, Massachusetts
| | - Joseph D Bradley
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Michael R Chicoine
- Department of Neurological Surgery, University of Missouri-Columbia, Columbia, Missouri
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Allegra A Petti
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tanner M Johanns
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Brain Tumor Center, Washington University School of Medicine/Siteman Cancer Center, St. Louis, Missouri
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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6
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Cigalotto L, Martinvalet D. Granzymes in health and diseases: the good, the bad and the ugly. Front Immunol 2024; 15:1371743. [PMID: 38646541 PMCID: PMC11026543 DOI: 10.3389/fimmu.2024.1371743] [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: 01/16/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Granzymes are a family of serine proteases, composed of five human members: GA, B, H, M and K. They were first discovered in the 1980s within cytotoxic granules released during NK cell- and T cell-mediated killing. Through their various proteolytic activities, granzymes can trigger different pathways within cells, all of which ultimately lead to the same result, cell death. Over the years, the initial consideration of granzymes as mere cytotoxic mediators has changed due to surprising findings demonstrating their expression in cells other than immune effectors as well as new intracellular and extracellular activities. Additional roles have been identified in the extracellular milieu, following granzyme escape from the immunological synapse or their release by specific cell types. Outside the cell, granzyme activities mediate extracellular matrix alteration via the degradation of matrix proteins or surface receptors. In certain contexts, these processes are essential for tissue homeostasis; in others, excessive matrix degradation and extensive cell death contribute to the onset of chronic diseases, inflammation, and autoimmunity. Here, we provide an overview of both the physiological and pathological roles of granzymes, highlighting their utility while also recognizing how their unregulated presence can trigger the development and/or worsening of diseases.
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Affiliation(s)
- Lavinia Cigalotto
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
| | - Denis Martinvalet
- Laboratory of Reactive Oxygen Species and Cytotoxic Immunity, Department Biomedical Sciences, University of Padova, Padova, Italy
- Veneto Institute Of Molecular Medicine (VIMM), Padova, Italy
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7
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Koga R, Maehara T, Aoyagi R, Munemura R, Murakami Y, Doi A, Kono M, Yamamoto H, Niiro H, Kiyoshima T, Tanabe M, Nakano T, Matsukuma Y, Kawano M, Stone JH, Pillai S, Nakamura S, Kawano S. Granzyme K- and amphiregulin-expressing cytotoxic T cells and activated extrafollicular B cells are potential drivers of IgG4-related disease. J Allergy Clin Immunol 2024; 153:1095-1112. [PMID: 38092138 DOI: 10.1016/j.jaci.2023.11.916] [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: 09/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND IgG4-related disease (IgG4-RD), an example of a type I immune disease, is an immune-mediated fibrotic disorder characterized by dysregulated resolution of severe inflammation and wound healing. However, truly dominant or pathognomonic autoantibodies related to IgG4-RD are not identified. OBJECTIVE We sought to perform single-cell RNA sequencing and T-cell receptor and B-cell receptor sequencing to obtain a comprehensive, unbiased view of tissue-infiltrating T and B cells. METHODS We performed unbiased single-cell RNA-sequencing analysis for the transcriptome and T-cell receptor sequencing and B-cell receptor sequencing on sorted CD3+ T or CD19+ B cells from affected tissues of patients with IgG4-RD. We also conducted quantitative analyses of CD3+ T-cell and CD19+ B-cell subsets in 68 patients with IgG4-RD and 30 patients with Sjögren syndrome. RESULTS Almost all clonally expanded T cells in these lesions were either Granzyme K (GZMK)-expressing CD4+ cytotoxic T cells or GZMK+CD8+ T cells. These GZMK-expressing cytotoxic T cells also expressed amphiregulin and TGF-β but did not express immune checkpoints, and the tissue-infiltrating CD8+ T cells were phenotypically heterogeneous. MKI67+ B cells and IgD-CD27-CD11c-CXCR5- double-negative 3 B cells were clonally expanded and infiltrated affected tissue lesions. GZMK+CD4+ cytotoxic T cells colocalized with MKI67+ B cells in the extrafollicular area from affected tissue sites. CONCLUSIONS The above-mentioned cells likely participate in T-B collaborative events, suggesting possible avenues for targeted therapies. Our findings were validated using orthogonal approaches, including multicolor immunofluorescence and the use of comparator disease groups, to support the central role of cytotoxic CD4+ and CD8+ T cells expressing GZMK, amphiregulin, and TGF-β in the pathogenesis of inflammatory fibrotic disorders.
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Affiliation(s)
- Risako Koga
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Takashi Maehara
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan; Dento-craniofacial Development and Regeneration Research Center, Faculty of Dental Science, Kyushu University, Kyushu, Japan.
| | - Ryuichi Aoyagi
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Ryusuke Munemura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Yuka Murakami
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | | | - Michihito Kono
- Department of Rheumatology, Endocrinology and Nephrology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hidetaka Yamamoto
- Graduate School of Medicine, Dentistry & Pharmaceutical Science, Okayama University, Okayama, Japan
| | - Hiroaki Niiro
- Department of Medical Education, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tamotsu Kiyoshima
- Laboratory of Oral Pathology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Mika Tanabe
- Department of Ophthalmology, Graduate School of Medicine Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiaki Nakano
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuta Matsukuma
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mitsuhiro Kawano
- Division of Rheumatology, Department of Internal Medicine, Kanazawa University Hospital, Kanazawa, Japan
| | - John H Stone
- Division of Rheumatology, Allergy, and Immunology, Harvard Medical School, Boston, Mass
| | - Shiv Pillai
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Shintaro Kawano
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
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8
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Liu F, Smith AD, Wang TTY, Pham Q, Hou P, Cheung L, Yang H, Li RW. Phospholipid-rich krill oil promotes intestinal health by strengthening beneficial gut microbial interactions in an infectious colitis model. Food Funct 2024; 15:2604-2615. [PMID: 38356343 DOI: 10.1039/d3fo04980a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Krill oil (KO) is rich in bioactive ingredients including phospholipids, omega-3 fatty acids, and astaxanthin. While health benefits and roles of KO in modulating lipid metabolism are well documented, its ability to alleviate symptoms related to infectious colitis and modulate gut microbial interactions is still largely unknown. Here we used a multi-omics approach, including transcriptome, microbiome, and metabolome analyses, to understand how KO mediates gut microbial interactions and promotes epithelial healing in an infectious colitis model. KO reversed the infection-induced intestinal hyperplasia to baseline. KO dampened intestinal inflammation via multiple targets, mediating several proinflammatory pathways, including IL17 signaling, and reducing luminal histamine levels. KO supplementation enriched butyrate-producing bacteria, including Roseburia and Clostridium, and strengthened beneficial microbial interactions in the gut microbial community. Supplementation with phospholipid-rich KO also increased microbial phylogenetic diversity. KO enhanced mucosal barrier function by increasing the production of Muc6 and the antimicrobial peptide, Leap2. KO played an active role during epithelial healing by inhibiting the expression of granzyme K while increasing the expression of a colitis protective factor, Dclk1. Together, our findings demonstrate that KO rich in omega-3 phospholipids can play a protective role in infectious colitis and should be considered a dietary option for promoting gut health.
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Affiliation(s)
- Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Allen D Smith
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Thomas T Y Wang
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Quynhchi Pham
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Pengfen Hou
- Affilated Hospital of Qingdao Binhai University, Qingdao, China
| | - Lumei Cheung
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Robert W Li
- USDA-ARS, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA
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9
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Rodriguez-Mogeda C, van Ansenwoude CMJ, van der Molen L, Strijbis EMM, Mebius RE, de Vries HE. The role of CD56 bright NK cells in neurodegenerative disorders. J Neuroinflammation 2024; 21:48. [PMID: 38350967 PMCID: PMC10865604 DOI: 10.1186/s12974-024-03040-8] [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: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/15/2024] Open
Abstract
Emerging evidence suggests a potential role for natural killer (NK) cells in neurodegenerative diseases, such as multiple sclerosis, Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. However, the precise function of NK cells in these diseases remains ambiguous. The existence of two NK cell subsets, CD56bright and CD56dim NK cells, complicates the understanding of the contribution of NK cells in neurodegeneration as their functions within the context of neurodegenerative diseases may differ significantly. CD56bright NK cells are potent cytokine secretors and are considered more immunoregulatory and less terminally differentiated than their mostly cytotoxic CD56dim counterparts. Hence, this review focusses on NK cells, specifically on CD56bright NK cells, and their role in neurodegenerative diseases. Moreover, it explores the mechanisms underlying their ability to enter the central nervous system. By consolidating current knowledge, we aim to provide a comprehensive overview on the role of CD56bright NK cells in neurodegenerative diseases. Elucidating their impact on neurodegeneration may have implications for future therapeutic interventions, potentially ameliorating disease pathogenesis.
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Affiliation(s)
- Carla Rodriguez-Mogeda
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Amsterdam, The Netherlands
- MS Center Amsterdam, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Chaja M J van Ansenwoude
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Amsterdam, The Netherlands
- MS Center Amsterdam, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Lennart van der Molen
- IQ Health Science Department, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eva M M Strijbis
- Amsterdam Neuroscience, Amsterdam, The Netherlands
- MS Center Amsterdam, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands
- Department of Neurology, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands
| | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam, The Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Amsterdam Neuroscience, Amsterdam, The Netherlands.
- MS Center Amsterdam, Amsterdam UMC Location Vrije Universiteit, Amsterdam, The Netherlands.
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10
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Mikkilineni L, Natrakul DA, Lam N, Manasanch EE, Mann J, Weissler KA, Wong N, Brudno JN, Goff SL, Yang JC, Ganaden M, Patel R, Zheng Z, Gartner JJ, Martin KR, Wang HW, Yuan CM, Lowe T, Maric I, Shao L, Jin P, Stroncek DF, Highfill SL, Rosenberg SA, Kochenderfer JN. Rapid anti-myeloma activity by T cells expressing an anti-BCMA CAR with a human heavy-chain-only antigen-binding domain. Mol Ther 2024; 32:503-526. [PMID: 38155568 PMCID: PMC10861980 DOI: 10.1016/j.ymthe.2023.12.018] [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: 10/09/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 12/30/2023] Open
Abstract
Multiple myeloma (MM) is a rarely curable malignancy of plasma cells. MM expresses B cell maturation antigen (BCMA). We developed a fully human anti-BCMA chimeric antigen receptor (CAR) with a heavy-chain-only antigen-recognition domain, a 4-1BB domain, and a CD3ζ domain. The CAR was designated FHVH33-CD8BBZ. We conducted the first-in-humans clinical trial of T cells expressing FHVH33-CD8BBZ (FHVH-T). Twenty-five patients with relapsed MM were treated. The stringent complete response rate (sCR) was 52%. Median progression-free survival (PFS) was 78 weeks. Of 24 evaluable patients, 6 (25%) had a maximum cytokine-release syndrome (CRS) grade of 3; no patients had CRS of greater than grade 3. Most anti-MM activity occurred within 2-4 weeks of FHVH-T infusion as shown by decreases in the rapidly changing MM markers serum free light chains, urine light chains, and bone marrow plasma cells. Blood CAR+ cell levels peaked during the time that MM elimination was occurring, between 7 and 15 days after FHVH-T infusion. C-C chemokine receptor type 7 (CCR7) expression on infusion CD4+ FHVH-T correlated with peak blood FHVH-T levels. Single-cell RNA sequencing revealed a shift toward more differentiated FHVH-T after infusion. Anti-CAR antibody responses were detected in 4 of 12 patients assessed. FHVH-T has powerful, rapid, and durable anti-MM activity.
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Affiliation(s)
- Lekha Mikkilineni
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danielle A Natrakul
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Norris Lam
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jennifer Mann
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine A Weissler
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathan Wong
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research in the CCR Collaborative Bioinformatics Resource, National Cancer Institute, Bethesda, MD, USA
| | - Jennifer N Brudno
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie L Goff
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James C Yang
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Micaela Ganaden
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rashmika Patel
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhili Zheng
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jared J Gartner
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kathryn R Martin
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hao-Wei Wang
- Flow Cytometry Unit, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Constance M Yuan
- Flow Cytometry Unit, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Lowe
- Flow Cytometry Unit, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irina Maric
- Hematology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - Lipei Shao
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ping Jin
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David F Stroncek
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Steven L Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James N Kochenderfer
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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11
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Hoeks C, Puijfelik FV, Koetzier SC, Rip J, Corsten CEA, Wierenga-Wolf AF, Melief MJ, Stinissen P, Smolders J, Hellings N, Broux B, van Luijn MM. Differential Runx3, Eomes, and T-bet expression subdivides MS-associated CD4 + T cells with brain-homing capacity. Eur J Immunol 2024; 54:e2350544. [PMID: 38009648 DOI: 10.1002/eji.202350544] [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: 04/28/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Multiple sclerosis (MS) is a common and devastating chronic inflammatory disease of the CNS. CD4+ T cells are assumed to be the first to cross the blood-central nervous system (CNS) barrier and trigger local inflammation. Here, we explored how pathogenicity-associated effector programs define CD4+ T cell subsets with brain-homing ability in MS. Runx3- and Eomes-, but not T-bet-expressing CD4+ memory cells were diminished in the blood of MS patients. This decline reversed following natalizumab treatment and was supported by a Runx3+ Eomes+ T-bet- enrichment in cerebrospinal fluid samples of treatment-naïve MS patients. This transcription factor profile was associated with high granzyme K (GZMK) and CCR5 levels and was most prominent in Th17.1 cells (CCR6+ CXCR3+ CCR4-/dim ). Previously published CD28- CD4 T cells were characterized by a Runx3+ Eomes- T-bet+ phenotype that coincided with intermediate CCR5 and a higher granzyme B (GZMB) and perforin expression, indicating the presence of two separate subsets. Under steady-state conditions, granzyme Khigh Th17.1 cells spontaneously passed the blood-brain barrier in vitro. This was only found for other subsets including CD28- cells when using inflamed barriers. Altogether, CD4+ T cells contain small fractions with separate pathogenic features, of which Th17.1 seems to breach the blood-brain barrier as a possible early event in MS.
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Affiliation(s)
- Cindy Hoeks
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Fabiënne van Puijfelik
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Steven C Koetzier
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jasper Rip
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Cato E A Corsten
- Department of Neurology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Annet F Wierenga-Wolf
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marie-José Melief
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Piet Stinissen
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Joost Smolders
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Neurology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, the Netherlands
| | - Niels Hellings
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Bieke Broux
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
- University MS Center (UMSC), Hasselt, Belgium
| | - Marvin M van Luijn
- Department of Immunology, MS Center ErasMS, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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12
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Zhang Y, Atkinson J, Burd CE, Graves J, Segal BM. Biological aging in multiple sclerosis. Mult Scler 2023; 29:1701-1708. [PMID: 37877740 PMCID: PMC10843499 DOI: 10.1177/13524585231204122] [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] [Indexed: 10/26/2023]
Abstract
Multiple sclerosis (MS) is most likely to adopt a progressive clinical course during middle age or beyond, and the number of older adults with MS is steadily increasing. Developing new strategies to manage progressive forms of MS, which do not respond to currently available disease-modifying therapies (DMTs), will require a deeper understanding of the mechanisms by which biological aging interacts with pathogenic pathways to propel disability accumulation. In experimental autoimmune encephalomyelitis (EAE), a widely used preclinical mouse model of MS, middle-aged animals experience a more severe and protracted clinical course than their younger counterparts. This exacerbated disease course is accompanied by persistent neuroinflammation. Clinical studies of age-related biomarkers, such as telomere length, senescence markers, and DNA methylation, suggest that biological aging is accelerated in people with MS compared with age- and sex-matched healthy controls. Furthermore, distinguishing biological age from chronological may afford more precision in determining aging effects in MS. Here we review the current literature on aging biology and its impact on MS pathogenesis. Future research on this topic may lead to the development of novel biomarkers and senotherapy agents that slow neurological decline in people with progressive MS by targeting relevant aging-related pathways.
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Affiliation(s)
- Yinan Zhang
- Department of Neurology, The Ohio State University Wexner
Medical Center, Columbus, OH
| | - Jeffrey Atkinson
- Department of Neurology, The Ohio State University Wexner
Medical Center, Columbus, OH
| | - Christin E. Burd
- Departments of Molecular Genetics, Cancer Biology and
Genetics, The Ohio State University, Columbus, OH
| | - Jennifer Graves
- Department of Neurosciences, University of California San
Diego, San Diego, CA
| | - Benjamin M. Segal
- Department of Neurology, The Ohio State University Wexner
Medical Center, Columbus, OH
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13
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Xi Z, Yang T, Huang T, Zhou J, Yang P. Identification and Preliminary Clinical Validation of Key Extracellular Proteins as the Potential Biomarkers in Hashimoto's Thyroiditis by Comprehensive Analysis. Biomedicines 2023; 11:3127. [PMID: 38137348 PMCID: PMC10740579 DOI: 10.3390/biomedicines11123127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/04/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Hashimoto's thyroiditis (HT) is an autoimmune disruption manifested by immune cell infiltration in thyroid tissue and the production of antibodies against thyroid-specific antigens, such as the thyroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TGAb). TPOAb and TGAb are commonly used in clinical tests; however, handy indicators of the diagnosis and progression of HT are still scarce. Extracellular proteins are glycosylated and are likely to enter body fluids and become readily available and detectable biomarkers. Our research aimed to discover extracellular biomarkers and potential treatment targets associated with HT through integrated bioinformatics analysis and clinical sample validations. A total of 19 extracellular protein-differentially expressed genes (EP-DEGs) were screened by the GSE138198 dataset from the Gene Expression Omnibus (GEO) database and protein annotation databases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the function and pathway of EP-DEGs. STRING, Cytoscape, MCODE, and Cytohubba were used to construct a protein-protein interaction (PPI) network and screen key EP-DEGs. Six key EP-DEGs (CCL5, GZMK, CXCL9, CXCL10, CXCL11, and CXCL13) were further validated in the GSE29315 dataset and the diagnostic curves were evaluated, which all showed high diagnostic accuracy (AUC > 0.95) for HT. Immune profiling revealed the correlation of the six key EP-DEGs and the pivotal immune cells in HT, such as CD8+ T cells, dendritic cells, and Th2 cells. Further, we also confirmed the key EP-DEGs in clinical thyroid samples. Our study may provide bioinformatics and clinical evidence for revealing the pathogenesis of HT and improving the potential diagnosis biomarkers and therapeutic strategies for HT.
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Affiliation(s)
| | | | | | - Jun Zhou
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Peng Yang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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14
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Shchukina I, Bohacova P, Artyomov MN. T cell control of inflammaging. Semin Immunol 2023; 70:101818. [PMID: 37611324 DOI: 10.1016/j.smim.2023.101818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/25/2023]
Abstract
T cells are a critical component of the immune system, found in abundance in blood, secondary lymphoid organs, and peripheral tissues. As individuals age, T cells are particularly susceptible to changes, making them one of the most affected immune subsets. These changes can have significant implications for age-related dysregulations, including the development of low-grade inflammation - a hallmark of aging known as inflammaging. In this review, we first present age-related changes in the functionality of the T cell compartment, including dysregulation of cytokine and chemokine production and cytotoxicity. Next, we discuss how these changes can contribute to the development and maintenance of inflammaging. Furthermore, we will summarize the mechanisms through which age-related changes in T cells may drive abnormal physiological outcomes.
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Affiliation(s)
- Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Pavla Bohacova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
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15
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de Fàbregues O, Sellés M, Ramos-Vicente D, Roch G, Vila M, Bové J. Relevance of tissue-resident memory CD8 T cells in the onset of Parkinson's disease and examination of its possible etiologies: infectious or autoimmune? Neurobiol Dis 2023; 187:106308. [PMID: 37741513 DOI: 10.1016/j.nbd.2023.106308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/05/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023] Open
Abstract
Tissue-resident memory CD8 T cells are responsible for local immune surveillance in different tissues, including the brain. They constitute the first line of defense against pathogens and cancer cells and play a role in autoimmunity. A recently published study demonstrated that CD8 T cells with markers of residency containing distinct granzymes and interferon-γ infiltrate the parenchyma of the substantia nigra and contact dopaminergic neurons in an early premotor stage of Parkinson's disease. This infiltration precedes α-synuclein aggregation and neuronal loss in the substantia nigra, suggesting a relevant role for CD8 T cells in the onset of the disease. To date, the nature of the antigen that initiates the adaptive immune response remains unknown. This review will discuss the role of tissue-resident memory CD8 T cells in brain immune homeostasis and in the onset of Parkinson's disease and other neurological diseases. We also discuss how aging and genetic factors can affect the CD8 T cell immune response and how animal models can be misleading when studying human-related immune response. Finally, we speculate about a possible infectious or autoimmune origin of Parkinson's disease.
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Affiliation(s)
- Oriol de Fàbregues
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain; Movement Disorders Unit, Neurology Department, Vall d'Hebron University Hospital
| | - Maria Sellés
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain
| | - David Ramos-Vicente
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain
| | - Gerard Roch
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain
| | - Miquel Vila
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain; Department of Biochemistry and Molecular Biology, Autonomous University of Barcelona, Barcelona, Catalonia, Spain; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
| | - Jordi Bové
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute, Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Barcelona, Catalonia, Spain.
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16
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Kurtz SL, Rydén P, Elkins KL. Transcriptional signatures measured in whole blood correlate with protection against tuberculosis in inbred and outbred mice. PLoS One 2023; 18:e0289358. [PMID: 37535648 PMCID: PMC10399789 DOI: 10.1371/journal.pone.0289358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
Although BCG has been used for almost 100 years to immunize against Mycobacterium tuberculosis, TB remains a global public health threat. Numerous clinical trials are underway studying novel vaccine candidates and strategies to improve or replace BCG, but vaccine development still lacks a well-defined set of immune correlates to predict vaccine-induced protection against tuberculosis. This study aimed to address this gap by examining transcriptional responses to BCG vaccination in C57BL/6 inbred mice, coupled with protection studies using Diversity Outbred mice. We evaluated relative gene expression in blood obtained from vaccinated mice, because blood is easily accessible, and data can be translated to human studies. We first determined that the average peak time after vaccination is 14 days for gene expression of a small subset of immune-related genes in inbred mice. We then performed global transcriptomic analyses using whole blood samples obtained two weeks after mice were vaccinated with BCG. Using comparative bioinformatic analyses and qRT-PCR validation, we developed a working correlate panel of 18 genes that were highly correlated with administration of BCG but not heat-killed BCG. We then tested this gene panel using BCG-vaccinated Diversity Outbred mice and revealed associations between the expression of a subset of genes and disease outcomes after aerosol challenge with M. tuberculosis. These data therefore demonstrate that blood-based transcriptional immune correlates measured within a few weeks after vaccination can be derived to predict protection against M. tuberculosis, even in outbred populations.
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Affiliation(s)
- Sherry L Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Patrik Rydén
- Department of Mathematics and Mathematical Statistics, Umeå University, Umeå, Sweden
| | - Karen L Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
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17
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Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez JM, Hunt T, Lagarde J, Liang CE, Li H, Jerryd Meade M, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Hasan Çelik M, Chen Y, Du MR, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Liang Li J, Lienhard M, Mikheenko A, Mulligan D, Ming Nip K, Pertea M, Ritchie ME, Sim AD, Tang AD, Kei Wan Y, Wang C, Wong BY, Yang C, Barnes I, Berry A, Capella S, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Goetz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Laird Smith M, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Fai Au K, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550582. [PMID: 37546854 PMCID: PMC10402094 DOI: 10.1101/2023.07.25.550582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from cDNA and direct RNA datasets, encompassing human, mouse, and manatee species, using different protocols and sequencing platforms. These data were utilized by developers to address challenges in transcript isoform detection and quantification, as well as de novo transcript isoform identification. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. When aiming to detect rare and novel transcripts or when using reference-free approaches, incorporating additional orthogonal data and replicate samples are advised. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.
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Affiliation(s)
- Francisco J. Pardo-Palacios
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- These authors contributed equally to this work
| | - Dingjie Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Fairlie Reese
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Sílvia Carbonell-Sala
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- These authors contributed equally to this work
| | - Brian Williams
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- These authors contributed equally to this work
| | - Jane E. Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Maite De María
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Matthew S. Adams
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Gabriela Balderrama-Gutierrez
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
- These authors contributed equally to this work
| | - Amit K. Behera
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Jose M. Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- These authors contributed equally to this work
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain
- These authors contributed equally to this work
| | - Cindy E. Liang
- Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA
- These authors contributed equally to this work
| | - Haoran Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
- These authors contributed equally to this work
| | - Marcus Jerryd Meade
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- These authors contributed equally to this work
| | - David A. Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
- These authors contributed equally to this work
| | - Andrey D. Prjibelski
- Department of Computer Science, University of Helsinki, Helsinki, Finland
- Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- These authors contributed equally to this work
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Hamed Bostan
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Ashley M. Brooks
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Muhammed Hasan Çelik
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ying Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mei R,M. Du
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Jonathan Göke
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore
| | - Saber Hafezqorani
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Ralf Herwig
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Hideya Kawaji
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Joseph Lee
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jian Liang Li
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA
| | - Matthias Lienhard
- Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Alla Mikheenko
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Dennis Mulligan
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Mihaela Pertea
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andre D. Sim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alison D. Tang
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Yuk Kei Wan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Changqing Wang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Brandon Y. Wong
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, USA
| | - Chen Yang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | | | - Luis Ferrández-Peral
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Natàlia Garcia-Reyero
- Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA
| | | | | | | | | | | | | | - Jorge Mestre-Tomás
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | - Jonathan M. Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nedka G. Panayotova
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
| | | | - Eric Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Enrique Sapena
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK
| | - Leon Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Melissa Laird Smith
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hazuki Takahashi
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
| | | | - Piero Carninci
- Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan
- Human Technopole, Milano, Italy
| | - Nancy D. Denslow
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA
- Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Margaret E. Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Hagen U. Tilgner
- Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA
| | - Barbara J. Wold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
- Center for Public Health Genomics
- UVA Cancer Center, University of Virginia, Charlottesville, USA
| | - Ali Mortazavi
- Developmental and Cell Biology, University of California, Irvine, Irvine, USA
- Center for Complex Biological Systems, University of California, Irvine, Irvine, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA
| | - Angela N. Brooks
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA
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18
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Bhengu KN, Singh R, Naidoo P, Mpaka-Mbatha MN, Nembe-Mafa N, Mkhize-Kwitshana ZL. Cytokine Responses during Mycobacterium tuberculosis H37Rv and Ascaris lumbricoides Costimulation Using Human THP-1 and Jurkat Cells, and a Pilot Human Tuberculosis and Helminth Coinfection Study. Microorganisms 2023; 11:1846. [PMID: 37513018 PMCID: PMC10384037 DOI: 10.3390/microorganisms11071846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/09/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Helminth infections are widespread in tuberculosis-endemic areas and are associated with an increased risk of active tuberculosis. In contrast to the pro-inflammatory Th1 responses elicited by Mycobacterium tuberculosis (Mtb) infection, helminth infections induce anti-inflammatory Th2/Treg responses. A robust Th2 response has been linked to reduced tuberculosis protection. Several studies show the effect of helminth infection on BCG vaccination and TB, but the mechanisms remain unclear. AIM To determine the cytokine response profiles during tuberculosis and intestinal helminth coinfection. METHODS For the in vitro study, lymphocytic Jurkat and monocytic THP-1 cell lines were stimulated with Mtb H37Rv and Ascaris lumbricoides (A. lumbricoides) excretory-secretory protein extracts for 24 and 48 h. The pilot human ex vivo study consisted of participants infected with Mtb, helminths, or coinfected with both Mtb and helminths. Thereafter, the gene transcription levels of IFN-γ, TNF-α, granzyme B, perforin, IL-2, IL-17, NFATC2, Eomesodermin, IL-4, IL-5, IL-10, TGF-β and FoxP3 in the unstimulated/uninfected controls, singly stimulated/infected and costimulated/coinfected groups were determined using RT-qPCR. RESULTS TB-stimulated Jurkat cells had significantly higher levels of IFN-γ, TNF-α, granzyme B, and perforin compared to unstimulated controls, LPS- and A. lumbricoides-stimulated cells, and A. lumbricoides plus TB-costimulated cells (p < 0.0001). IL-2, IL-17, Eomes, and NFATC2 levels were also higher in TB-stimulated Jurkat cells (p < 0.0001). Jurkat and THP-1 cells singly stimulated with TB had lower IL-5 and IL-4 levels compared to those singly stimulated with A. lumbricoides and those costimulated with TB plus A. lumbricoides (p < 0.0001). A. lumbricoides-singly stimulated cells had higher IL-4 levels compared to TB plus A. lumbricoides-costimulated Jurkat and THP-1 cells (p < 0.0001). TGF-β levels were also lower in TB-singly stimulated cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). IL-10 levels were lower in TB-stimulated Jurkat and THP-1 cells compared to TB plus A. lumbricoides-costimulated cells (p < 0.0001). Similar results were noted for the human ex vivo study, albeit with a smaller sample size. CONCLUSIONS Data suggest that helminths induce a predominant Th2/Treg response which may downregulate critical Th1 responses that are crucial for tuberculosis protection.
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Affiliation(s)
- Khethiwe N Bhengu
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
- Department of Biomedical Sciences, Faculty of Natural Sciences, Mangosuthu University of Technology, Umlazi, Durban 4031, South Africa
| | - Ravesh Singh
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Howard College, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Pragalathan Naidoo
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
| | - Miranda N Mpaka-Mbatha
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
- Department of Biomedical Sciences, Faculty of Natural Sciences, Mangosuthu University of Technology, Umlazi, Durban 4031, South Africa
| | - Nomzamo Nembe-Mafa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
| | - Zilungile L Mkhize-Kwitshana
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Division of Research Capacity Development, South African Medical Research Council (SAMRC), Cape Town 7505, South Africa
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19
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Aybay E, Ryu J, Fu Z, Akula S, Enriquez EM, Hallgren J, Wernersson S, Olsson AK, Hellman L. Extended cleavage specificities of human granzymes A and K, two closely related enzymes with conserved but still poorly defined functions in T and NK cell-mediated immunity. Front Immunol 2023; 14:1211295. [PMID: 37497217 PMCID: PMC10366535 DOI: 10.3389/fimmu.2023.1211295] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023] Open
Abstract
Granzymes A and K are two highly homologous serine proteases expressed by mammalian cytotoxic T cells (CTL) and natural killer cells (NK). Granzyme A is the most abundant of the different granzymes (gzms) expressed by these two cell types. Gzms A and K are found in all jawed vertebrates and are the most well conserved of all hematopoietic serine proteases. Their potential functions have been studied extensively for many years, however, without clear conclusions. Gzm A was for many years thought to serve as a key component in the defense against viral infection by the induction of apoptosis in virus-infected cells, similar to gzm B. However, later studies have questioned this role and instead indicated that gzm A may act as a potent inducer of inflammatory cytokines and chemokines. Gzms A and K form clearly separate branches in a phylogenetic tree indicating separate functions. Transcriptional analyses presented here demonstrate the presence of gzm A and K transcripts in both CD4+ and CD8+ T cells. To enable screening for their primary biological targets we have made a detailed analysis of their extended cleavage specificities. Phage display analysis of the cleavage specificity of the recombinant enzymes showed that both gzms A and K are strict tryptases with high selectivity for Arg over Lys in the P1 position. The major differences in the specificities of these two enzymes are located N-terminally of the cleavage site, where gzm A prefers small amino acids such as Gly in the P3 position and shows a relatively relaxed selectivity in the P2 position. In contrast, gzm K prefers large amino acids such as Phe, Tyr, and Trp in both the P2 and P3 positions and does not tolerate negatively charged residues in the P2 position. This major distinction in extended specificities is likely reflected also in preferred in vivo targets of these two enzymes. This information can now be utilized for high-precision screening of primary targets for gzms A and K in search of their highly conserved but still poorly defined functions in vertebrate immunity.
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Affiliation(s)
- Erdem Aybay
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Jinhye Ryu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Zhirong Fu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
| | - Srinivas Akula
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erika Mendez Enriquez
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Jenny Hallgren
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Sara Wernersson
- Department of Anatomy, Physiology, and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, The Biomedical Center, Uppsala, Sweden
| | - Lars Hellman
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, The Biomedical Center, Uppsala, Sweden
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20
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Cheon IS, Son YM, Sun J. Tissue-resident memory T cells and lung immunopathology. Immunol Rev 2023; 316:63-83. [PMID: 37014096 PMCID: PMC10524334 DOI: 10.1111/imr.13201] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
Abstract
Rapid reaction to microbes invading mucosal tissues is key to protect the host against disease. Respiratory tissue-resident memory T (TRM ) cells provide superior immunity against pathogen infection and/or re-infection, due to their presence at the site of pathogen entry. However, there has been emerging evidence that exuberant TRM -cell responses contribute to the development of various chronic respiratory conditions including pulmonary sequelae post-acute viral infections. In this review, we have described the characteristics of respiratory TRM cells and processes underlying their development and maintenance. We have reviewed TRM -cell protective functions against various respiratory pathogens as well as their pathological activities in chronic lung conditions including post-viral pulmonary sequelae. Furthermore, we have discussed potential mechanisms regulating the pathological activity of TRM cells and proposed therapeutic strategies to alleviate TRM -cell-mediated lung immunopathology. We hope that this review provides insights toward the development of future vaccines or interventions that can harness the superior protective abilities of TRM cells, while minimizing the potential for immunopathology, a particularly important topic in the era of coronavirus disease 2019 (COVID-19) pandemic.
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Affiliation(s)
- In Su Cheon
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Young Min Son
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi-do, Republic of Korea 17546
| | - Jie Sun
- Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA
- Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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21
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Chuwatthanakhajorn S, Chang CS, Ganapathy K, Tang PC, Chen CF. Comparison of Immune-Related Gene Expression in Two Chicken Breeds Following Infectious Bronchitis Virus Vaccination. Animals (Basel) 2023; 13:ani13101642. [PMID: 37238072 DOI: 10.3390/ani13101642] [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: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
This study aims to identify the immune-related genes and the corresponding biological pathways following infectious bronchitis virus vaccination in Taiwan Country and White Leghorn chicken breeds. Transcriptomic analyses of the spleen of these two breeds were conducted by next-generation sequencing. Compared to White Leghorn chicken, Taiwan Country chicken showed a significantly higher level of anti-infectious bronchitis virus (IBV) antibodies at 14 and 21 days pos vaccination. At 7 days post vaccination, in the Taiwan Country chicken, higher expression of mitogen-activated protein kinase 10, Major histocompatibility complex class 1, and V-set pre-B cell surrogate light chain 3 were found. In contrast, the White Leghorn chicken had a high expression of interleukin 4 induced 1, interleukin 6, and interleukin 22 receptor subunit alpha 2. These findings have highlighted the variations in immune induction between chickens with distinct genetic background and provided biological pathways and specific genes involved in immune responses against live attenuated IBV vaccine.
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Affiliation(s)
- Schwann Chuwatthanakhajorn
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
- Faculty of Veterinary Science, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Chi-Sheng Chang
- Department of Animal Science, Chinese Culture University, Taipei 111, Taiwan
| | - Kannan Ganapathy
- Institute of Infection, Veterinary & Ecological Sciences (IVES), University of Liverpool, Neston CH64 7TE, UK
| | - Pin-Chi Tang
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
- Smart Sustainable New Agriculture Research Center (SMARTer), Taichung 402, Taiwan
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22
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Cuesta LM, Verna A, Pérez S. Modulation of granzymes mRNA expression in neural tissue of BoAHV-1 and BoAHV-5-infected cattle. Vet Immunol Immunopathol 2023; 260:110610. [PMID: 37196596 DOI: 10.1016/j.vetimm.2023.110610] [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: 04/20/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Bovine alphaherpesviruses (BoAHV)-1 and 5 are neurotropic viruses of cattle which differ in their neuropathogenic potential. BoAHV-5 is responsible for non-suppurative meningoencephalitis in calves while BoAHV-1 can occasionally cause encephalitis. Granzymes (GZMs) are serine-proteases that participate in CD8+ T cells-mediated killing of virally-infected cells upon release through perforin (PFN)-formed pores in the cell membrane. Recently, six GZMs have been identified in cattle (A, B, K, H, M and O). However, their expression in bovine tissues has not been evaluated. In this study, the mRNA expression levels of PFN and GZMs A, B, K, H and M in the nervous system of calves experimentally-inoculated with BoAHV-1 or BoAHV-5 were analyzed at the three distinct stages of the infectious cycle of alphaherpesviruses: acute infection, latency and reactivation. This is the first report describing the expression of GZMs in bovine neural tissue and the first analysis of GZM expression in the context of bovine alphaherpesviruses neuropathogenesis. The findings revealed that PFN and GZM K are upregulated during BoAHV-1 or BoAHV-5 acute infection. In contrast to BoAHV-1, during BoAHV-5 latency a significant up-regulation of PFN, GZM K and GZM H was detected. PFN and GZM A, K and H expression was also up-regulated during BoAHV-5 reactivation. Therefore, a distinct pattern of PFN and GZM expression is evident along the infectious cycle of each alphaherpesvirus and this might contribute to the differences in BoAHV-1 and BoAHV-5 neuropathogenesis.
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Affiliation(s)
- Lucía Martínez Cuesta
- Centro de Investigación Veterinaria de Tandil (CIVETAN)-CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, Tandil 7000, Argentina
| | - Andrea Verna
- Área de Producción Animal, Instituto de Innovación para la Producción Agropecuaria y Desarrollo Sostenible (IPADS, CONICET-INTA), Ruta Nacional 226 km 73,5, Balcarce, 7620 Buenos Aires, Argentina
| | - Sandra Pérez
- Centro de Investigación Veterinaria de Tandil (CIVETAN)-CONICET, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Paraje Arroyo Seco S/N, Tandil 7000, Argentina.
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23
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Wong SL, Kardia E, Vijayan A, Umashankar B, Pandzic E, Zhong L, Jaffe A, Waters SA. Molecular and Functional Characteristics of Airway Epithelium under Chronic Hypoxia. Int J Mol Sci 2023; 24:ijms24076475. [PMID: 37047450 PMCID: PMC10095024 DOI: 10.3390/ijms24076475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/14/2023] Open
Abstract
Localized and chronic hypoxia of airway mucosa is a common feature of progressive respiratory diseases, including cystic fibrosis (CF). However, the impact of prolonged hypoxia on airway stem cell function and differentiated epithelium is not well elucidated. Acute hypoxia alters the transcription and translation of many genes, including the CF transmembrane conductance regulator (CFTR). CFTR-targeted therapies (modulators) have not been investigated in vitro under chronic hypoxic conditions found in CF airways in vivo. Nasal epithelial cells (hNECs) derived from eight CF and three non-CF participants were expanded and differentiated at the air-liquid interface (26-30 days) at ambient and 2% oxygen tension (hypoxia). Morphology, global proteomics (LC-MS/MS) and function (barrier integrity, cilia motility and ion transport) of basal stem cells and differentiated cultures were assessed. hNECs expanded at chronic hypoxia, demonstrating epithelial cobblestone morphology and a similar proliferation rate to hNECs expanded at normoxia. Hypoxia-inducible proteins and pathways in stem cells and differentiated cultures were identified. Despite the stem cells' plasticity and adaptation to chronic hypoxia, the differentiated epithelium was significantly thinner with reduced barrier integrity. Stem cell lineage commitment shifted to a more secretory epithelial phenotype. Motile cilia abundance, length, beat frequency and coordination were significantly negatively modulated. Chronic hypoxia reduces the activity of epithelial sodium and CFTR ion channels. CFTR modulator drug response was diminished. Our findings shed light on the molecular pathophysiology of hypoxia and its implications in CF. Targeting hypoxia can be a strategy to augment mucosal function and may provide a means to enhance the efficacy of CFTR modulators.
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Affiliation(s)
- Sharon L Wong
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Egi Kardia
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Abhishek Vijayan
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bala Umashankar
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW 2052, Australia
| | - Adam Jaffe
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW 2052, Australia
| | - Shafagh A Waters
- School of Biomedical Sciences, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales, Sydney, NSW 2052, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2052, Australia
- Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW 2052, Australia
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24
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Bozorgmehr N, Hnatiuk M, Peters AC, Elahi S. Depletion of polyfunctional CD26 highCD8 + T cells repertoire in chronic lymphocytic leukemia. Exp Hematol Oncol 2023; 12:13. [PMID: 36707896 PMCID: PMC9881277 DOI: 10.1186/s40164-023-00375-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND CD8+ T cells play an essential role against tumors but the role of human CD8+CD26+ T cell subset against tumors, in particular, haematological cancers such as chronic lymphocytic leukemia (CLL) remains unknown. Although CD4+CD26high T cells are considered for adoptive cancer immunotherapy, the role of CD8+CD26+ T cells is ill-defined. Therefore, further studies are required to better determine the role of CD8+CD26+ T cells in solid tumors and haematological cancers. METHODS We studied 55 CLL and 44 age-sex-matched healthy controls (HCs). The expression of CD26 on different T cell subsets (e.g. naïve, memory, effector, and etc.) was analyzed. Also, functional properties of CD8+CD26+ and CD8+CD26- T cells were evaluated. Finally, the plasma cytokine/chemokine and Galectin-9 (Gal-9) levels were examined. RESULTS CD26 expression identifies three CD8+ T cell subsets with distinct immunological properties. While CD26negCD8+ T cells are mainly transitional, effector memory and effectors, CD26lowCD8+ T cells are mainly naïve, stem cell, and central memory but CD26high T cells are differentiated to transitional and effector memory. CD26+CD8+ T cells are significantly reduced in CLL patients versus HCs. CD26high cells are enriched with Mucosal Associated Invariant T (MAIT) cells co-expressing CD161TVα7.2 and IL-18Rα. Also, CD26high cells have a rich chemokine receptor profile (e.g. CCR5 and CCR6), profound cytokine (TNF-α, IFN-γ, and IL-2), and cytolytic molecules (Granzyme B, K, and perforin) expression upon stimulation. CD26high and CD26low T cells exhibit significantly lower frequencies of CD160, 2B4, TIGIT, ICOS, CD39, and PD-1 but higher levels of CD27, CD28, and CD73 versus CD26neg cells. To understand the mechanism linked to CD26high depletion, we found that malignant B cells by shedding Galectin-9 (Gal-9) contribute to the elevation of plasma Gal-9 in CLL patients. In turn, Gal-9 and the inflammatory milieu (IL-18, IL-12, and IL-15) in CLL patients contribute to increased apoptosis of CD26high T cells. CONCLUSIONS Our results demonstrate that CD26+ T cells possess a natural polyfunctionality to traffic and exhibit effector functions and resist exhaustion. Therefore, they can be proposed for adoptive cancer immunotherapy. Finally, neutralizing and/or inhibiting Gal-9 may preserve CD26highCD8+ T cells in CLL.
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Affiliation(s)
- Najmeh Bozorgmehr
- grid.17089.370000 0001 2190 316XSchool of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Mark Hnatiuk
- grid.17089.370000 0001 2190 316XDepatment of Medicine Division of Hematology, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Anthea C. Peters
- grid.17089.370000 0001 2190 316XDepartment of Oncology, Division of Medical Oncology, University of Alberta, Edmonton, AB T6G 2E1 Canada
| | - Shokrollah Elahi
- grid.17089.370000 0001 2190 316XSchool of Dentistry, Division of Foundational Sciences, University of Alberta, Edmonton, AB T6G 2E1 Canada ,grid.17089.370000 0001 2190 316XDepartment of Oncology, Division of Medical Oncology, University of Alberta, Edmonton, AB T6G 2E1 Canada ,grid.17089.370000 0001 2190 316XLi Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2E1 Canada
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25
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Verschoor CP, Picard E, Andrew MK, Haynes L, Loeb M, Pawelec G, Kuchel GA. NK- and T-cell granzyme B and K expression correlates with age, CMV infection and influenza vaccine-induced antibody titres in older adults. FRONTIERS IN AGING 2023; 3:1098200. [PMID: 36685324 PMCID: PMC9849551 DOI: 10.3389/fragi.2022.1098200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023]
Abstract
Granzymes are a family of serine-proteases that act as critical mediators in the cytolytic and immunomodulatory activities of immune cells such as CD8+ T-cells and natural killer (NK) cells. Previous work indicates that both granzyme B (GZB) and K (GZK) are increased with age in CD8+ T-cells, and in the case of GZB, contribute to dysfunctional immune processes observed in older adults. Here, we sought to determine how GZB and GZK expression in NK-cells, and CD4+, CD8+, and gamma-delta T-cells, quantified in terms of positive cell frequency and mean fluorescence intensity (MFI), differed with age, age-related health-traits and the antibody response to high-dose influenza vaccine. We found that the frequency and MFI of GZB-expressing NK-cells, and CD8+ and Vδ1+ T-cells, and GZK-expressing CD8+ T-cells was significantly higher in older (66-97 years old; n = 75) vs. younger (24-37 years old; n = 10) adults by up to 5-fold. There were no significant associations of GZB/GZK expression with sex, frailty or plasma levels of TNF or IL-6 in older adults, but those who were seropositive for cytomegalovirus (CMV) exhibited significantly higher frequencies of GZB+ NK-cells, and CD4+, CD8+ and Vδ1+ T-cells, and GZK+ CD8+ T-cells (Cohen's d = .5-1.5). Pre-vaccination frequencies of GZB+ NK-cells were positively correlated with vaccine antibody responses against A/H3N2 (d = .17), while the frequencies of GZK+ NK and CD8+ T-cells were inversely associated with A/H1N1 (d = -0.18 to -0.20). Interestingly, GZK+ NK-cell frequency was inversely correlated with pre-vaccination A/H1N1 antibody titres, as well as those measured over the previous 4 years, further supporting a role for this subset in influencing vaccine antibody-responses. These findings further our understanding of how granzyme expression in different lymphoid cell-types may change with age, while suggesting that they influence vaccine responsiveness in older adults.
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Affiliation(s)
- Chris P. Verschoor
- Health Sciences North Research Institute, Sudbury, ON, Canada,Northern Ontario School of Medicine, Sudbury, ON, Canada,*Correspondence: Chris P. Verschoor,
| | - Emilie Picard
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | | | - Laura Haynes
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
| | - Mark Loeb
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Graham Pawelec
- Health Sciences North Research Institute, Sudbury, ON, Canada,Department of Immunology, University of Tübingen, Tübingen, Germany
| | - George A. Kuchel
- UConn Center on Aging, University of Connecticut School of Medicine, Farmington, CT, United States
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26
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Graves JS, Krysko KM, Hua LH, Absinta M, Franklin RJM, Segal BM. Ageing and multiple sclerosis. Lancet Neurol 2023; 22:66-77. [PMID: 36216015 DOI: 10.1016/s1474-4422(22)00184-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/09/2022] [Accepted: 04/20/2022] [Indexed: 11/07/2022]
Abstract
The factor that is most relevant and strongly associated with the clinical course of multiple sclerosis is chronological age. Very young patients exclusively have relapsing remitting disease, whereas those with later onset disease face a more rapid development of permanent disability. For people with progressive multiple sclerosis, the poor response to current disease modifying therapies might be related to ageing in the immune system and CNS. Ageing is also associated with increased risks of side-effects caused by some multiple sclerosis therapies. Both somatic and reproductive ageing processes might contribute to development of progressive multiple sclerosis. Understanding the role of ageing in immune and neural cell function in patients with multiple sclerosis might be key to halting non-relapse-related progression. The growing literature on potential therapies that target senescent cells and ageing processes might provide effective strategies for remyelination and neuroprotection.
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Affiliation(s)
- Jennifer S Graves
- Department of Neurosciences, University of California, San Diego, CA, USA; Pediatric Multiple Sclerosis Center, Rady Children's Hospital, San Diego, CA, USA; Department of Neurology, San Diego VA Hospital, San Diego, CA, USA.
| | - Kristen M Krysko
- Division of Neurology, Department of Medicine, Li Ka Shing Knowledge Institute, St Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Le H Hua
- Department of Neurology, Cleveland Clinic, Lou Ruvo Center for Brain Health, Las Vegas, NV, USA
| | - Martina Absinta
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA; Division of Neuroscience, IRCCS San Raffaele Scientific Institute and Vita-Salute San Raffaele University, Milan, Italy
| | - Robin J M Franklin
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Benjamin M Segal
- Department of Neurology and the Neuroscience Research Institute, The Ohio State University, Columbus, OH, USA
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27
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Zheng Y, Zhao J, Shan Y, Guo S, Schrodi SJ, He D. Role of the granzyme family in rheumatoid arthritis: Current Insights and future perspectives. Front Immunol 2023; 14:1137918. [PMID: 36875082 PMCID: PMC9977805 DOI: 10.3389/fimmu.2023.1137918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Rheumatoid arthritis (RA) is a complex autoimmune disease characterized by chronic inflammation that affects synovial tissues of multiple joints. Granzymes (Gzms) are serine proteases that are released into the immune synapse between cytotoxic lymphocytes and target cells. They enter target cells with the help of perforin to induce programmed cell death in inflammatory and tumor cells. Gzms may have a connection with RA. First, increased levels of Gzms have been found in the serum (GzmB), plasma (GzmA, GzmB), synovial fluid (GzmB, GzmM), and synovial tissue (GzmK) of patients with RA. Moreover, Gzms may contribute to inflammation by degrading the extracellular matrix and promoting cytokine release. They are thought to be involved in RA pathogenesis and have the potential to be used as biomarkers for RA diagnosis, although their exact role is yet to be fully elucidated. The purpose of this review was to summarize the current knowledge regarding the possible role of the granzyme family in RA, with the aim of providing a reference for future research on the mechanisms of RA and the development of new therapies.
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Affiliation(s)
- Yixin Zheng
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Jianan Zhao
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yu Shan
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven J Schrodi
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China.,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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28
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Nüssing S, Sutton VR, Trapani JA, Parish IA. Beyond target cell death - Granzyme serine proteases in health and disease. Mol Aspects Med 2022; 88:101152. [PMID: 36368281 DOI: 10.1016/j.mam.2022.101152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 10/06/2022] [Accepted: 10/22/2022] [Indexed: 11/09/2022]
Abstract
Granzymes are a family of small (∼32 kDa) serine proteases with a range of substrate specificities that are stored in, and released from, the cytoplasmic secretory vesicles ('granules') of cytotoxic T lymphocytes and natural killer cells. Granzymes are not digestive proteases but finely tuned processing enzymes that target their substrates in specific ways to activate various signalling pathways, or to inactivate viral proteins and other targets. Great emphasis has been placed on studying the pro-apoptotic functions of granzymes, which largely depend on their synergy with the pore-forming protein perforin, on which they rely for penetration into the target cell cytosol to access their substrates. While a critical role for granzyme B in target cell apoptosis is undisputed, both it and the remaining granzymes also influence a variety of other biological processes (including important immunoregulatory functions), which are discussed in this review. This includes the targeting of many extracellular as well as intracellular substrates, and can also lead to deleterious outcomes for the host if granzyme expression or function are dysregulated or abrogated. A final important consideration is that granzyme repertoire, biochemistry and function vary considerably across species, probably resulting from the pressures applied by viruses and other pathogens across evolutionary time. This has implications for the interpretation of granzyme function in preclinical models of disease.
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Affiliation(s)
- Simone Nüssing
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Vivien R Sutton
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Joseph A Trapani
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia.
| | - Ian A Parish
- Peter MacCallum Cancer Centre, Melbourne, Victoria, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3052, Australia; John Curtin School of Medical Research, ANU, ACT, Australia.
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29
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Melsen JE, van Ostaijen-ten Dam MM, Schoorl DJA, Schol PJ, van den Homberg DAL, Lankester AC, Lugthart G, Schilham MW. Single-cell transcriptomics in bone marrow delineates CD56 dimGranzymeK + subset as intermediate stage in NK cell differentiation. Front Immunol 2022; 13:1044398. [PMID: 36505452 PMCID: PMC9730327 DOI: 10.3389/fimmu.2022.1044398] [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: 09/14/2022] [Accepted: 11/03/2022] [Indexed: 11/25/2022] Open
Abstract
Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56brightCD16+, CD56dimCD16+ and CD69+CXCR6+ lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56dimGzmK+ subset was identified that shared features with CD56bright and CD56dimGzmK- NK cells based on transcriptome, phenotype (NKG2AhighCD16lowKLRG1highTIGIThigh) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56bright, CD56dimGzmK+ and CD56dimGzmK- cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34+ progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells.
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30
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Richardson KC, Jung K, Pardo J, Turner CT, Granville DJ. Noncytotoxic Roles of Granzymes in Health and Disease. Physiology (Bethesda) 2022; 37:323-348. [PMID: 35820180 DOI: 10.1152/physiol.00011.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Granzymes are serine proteases previously believed to play exclusive and somewhat redundant roles in lymphocyte-mediated target cell death. However, recent studies have challenged this paradigm. Distinct substrate profiles and functions have since emerged for each granzyme while their dysregulated proteolytic activities have been linked to diverse pathologies.
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Affiliation(s)
- Katlyn C Richardson
- International Collaboration on Repair Discoveries (ICORD), British Columbia Professional Firefighters' Wound Healing Laboratory, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Jung
- International Collaboration on Repair Discoveries (ICORD), British Columbia Professional Firefighters' Wound Healing Laboratory, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julian Pardo
- Fundación Instituto de Investigación Sanitaria Aragón (IIS Aragón), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain.,Department of Microbiology, Radiology, Pediatrics and Public Health, University of Zaragoza, Zaragoza, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Zaragoza, Spain
| | - Christopher T Turner
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia.,Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - David J Granville
- International Collaboration on Repair Discoveries (ICORD), British Columbia Professional Firefighters' Wound Healing Laboratory, Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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31
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Jia F, Jiang S, Zhang J, Fu Q, Zhang X, Ye Y. A Preliminary Study of Frequency and Clinical Relevance of Cytotoxic Peripheral CD4 and CD8 T Cells in Patients with Anti-MDA5 Positive Dermatomyositis. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:136-142. [PMID: 36788974 PMCID: PMC9895870 DOI: 10.2478/rir-2022-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/06/2022] [Indexed: 06/18/2023]
Abstract
OBJECTIVES Anti-melanoma differentiation-associated gene 5-positive dermatomyositis (MDA5+DM) is an autoimmune disease frequently accompanied by rapidly progressive interstitial lung disease (RP-ILD) with high mortality. T cells are implicated in the pathogenesis of MDA5+DM and this study aims to measure the frequency and clinical relevance of cytotoxic CD4 and CD8 T cells in this disease. METHODS T cells expressing Perforin, Granzyme B (GZMB) and Granzyme K (GZMK) were analyzed by flow cytometry from peripheral blood of 19 patients with active MDA5+DM and 19 age- and sex-matched healthy donors (HDs). The frequency of CD4 and CD8 T cells and the cytotoxic subsets were compared between patients with MDA5+DM and HDs. Correlations within T cell subsets and between T cell subsets and clinical parameters of lactate dehydrogenase (LDH), ferritin, neutrophil-to-lymphocyte ratio (NLR), and Myositis Intention-to-Treat Index (MITAX) were evaluated. RESULTS Compared with HDs, patients with active MDA5+DM significantly had increased frequency of CD4 T cells, and reduced frequency of GZMK+GZMB- CD8 T cells. Furthermore, the frequency of GZMK+GZMB- CD8 T cells positively correlated with serum ferritin levels in active MDA5+DM patients. Notably, the patients in the Dead group of MDA5+DM had a significant higher frequency of GZMK+GZMB- CD4 and CD8 T cells. CONCLUSION Substantial changes of cytotoxic T cell subsets are observed in active MDA5+DM patients. In addition, a high frequency of GZMK+GZMB- CD4 and CD8 T cells is associated with unfavorable prognosis in MDA5+DM. More studies are warranted to further explore the roles of cytotoxic T cells in MDA5+DM.
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Affiliation(s)
- Fengyun Jia
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai/University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200031, China
| | - Shan Jiang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai/University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200031, China
| | - Jiamin Zhang
- Blood Group Reference Laboratory, Shanghai Blood Center, Shanghai200051, China
| | - Qiong Fu
- Department of Rheumatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai200001, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai/University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai200031, China
| | - Yan Ye
- Department of Rheumatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai200001, China
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32
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Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. J Exp Med 2022; 219:e20220038. [PMID: 35938989 PMCID: PMC9365674 DOI: 10.1084/jem.20220038] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.
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Affiliation(s)
- Sara A. Rubin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Chloé S. Baron
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Cecilia Pessoa Rodrigues
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexandra F. Corbin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Song P. Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA
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33
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Ramírez-Labrada A, Pesini C, Santiago L, Hidalgo S, Calvo-Pérez A, Oñate C, Andrés-Tovar A, Garzón-Tituaña M, Uranga-Murillo I, Arias MA, Galvez EM, Pardo J. All About (NK Cell-Mediated) Death in Two Acts and an Unexpected Encore: Initiation, Execution and Activation of Adaptive Immunity. Front Immunol 2022; 13:896228. [PMID: 35651603 PMCID: PMC9149431 DOI: 10.3389/fimmu.2022.896228] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/20/2022] [Indexed: 12/12/2022] Open
Abstract
NK cells are key mediators of immune cell-mediated cytotoxicity toward infected and transformed cells, being one of the main executors of cell death in the immune system. NK cells recognize target cells through an array of inhibitory and activating receptors for endogenous or exogenous pathogen-derived ligands, which together with adhesion molecules form a structure known as immunological synapse that regulates NK cell effector functions. The main and best characterized mechanisms involved in NK cell-mediated cytotoxicity are the granule exocytosis pathway (perforin/granzymes) and the expression of death ligands. These pathways are recognized as activators of different cell death programmes on the target cells leading to their destruction. However, most studies analyzing these pathways have used pure recombinant or native proteins instead of intact NK cells and, thus, extrapolation of the results to NK cell-mediated cell death might be difficult. Specially, since the activation of granule exocytosis and/or death ligands during NK cell-mediated elimination of target cells might be influenced by the stimulus received from target cells and other microenvironment components, which might affect the cell death pathways activated on target cells. Here we will review and discuss the available experimental evidence on how NK cells kill target cells, with a special focus on the different cell death modalities that have been found to be activated during NK cell-mediated cytotoxicity; including apoptosis and more inflammatory pathways like necroptosis and pyroptosis. In light of this new evidence, we will develop the new concept of cell death induced by NK cells as a new regulatory mechanism linking innate immune response with the activation of tumour adaptive T cell responses, which might be the initiating stimulus that trigger the cancer-immunity cycle. The use of the different cell death pathways and the modulation of the tumour cell molecular machinery regulating them might affect not only tumour cell elimination by NK cells but, in addition, the generation of T cell responses against the tumour that would contribute to efficient tumour elimination and generate cancer immune memory preventing potential recurrences.
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Affiliation(s)
- Ariel Ramírez-Labrada
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Unidad de Nanotoxicología e Inmunotoxicología (UNATI), Centro de Investigación Biomédica de Aragón (CIBA), Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Cecilia Pesini
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Llipsy Santiago
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Instituto de Carboquimica (ICB), CSIC, Zaragoza, Spain
| | - Sandra Hidalgo
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Adanays Calvo-Pérez
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Carmen Oñate
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Alejandro Andrés-Tovar
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain
| | - Marcela Garzón-Tituaña
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Iratxe Uranga-Murillo
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Maykel A Arias
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain
| | - Eva M Galvez
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain.,Instituto de Carboquimica (ICB), CSIC, Zaragoza, Spain
| | - Julián Pardo
- Immunotherapy, Inflammation and Cancer, Aragón Health Research Institute (IIS Aragón), Biomedical Research Centre of Aragón (CIBA), Zaragoza, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Zaragoza, Spain.,Department of Microbiology, Preventive Medicine and Public Health, Fundación Agencia Aragonesa para la Investigación y el Desarrollo ARAID Foundation, University of Zaragoza, Zaragoza, Spain
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34
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Lavergne M, Hernández-Castañeda MA, Mantel PY, Martinvalet D, Walch M. Oxidative and Non-Oxidative Antimicrobial Activities of the Granzymes. Front Immunol 2021; 12:750512. [PMID: 34707614 PMCID: PMC8542974 DOI: 10.3389/fimmu.2021.750512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/23/2021] [Indexed: 01/11/2023] Open
Abstract
Cell-mediated cytotoxicity is an essential immune defense mechanism to fight against viral, bacterial or parasitic infections. Upon recognition of an infected target cell, killer lymphocytes form an immunological synapse to release the content of their cytotoxic granules. Cytotoxic granules of humans contain two membrane-disrupting proteins, perforin and granulysin, as well as a homologous family of five death-inducing serine proteases, the granzymes. The granzymes, after delivery into infected host cells by the membrane disrupting proteins, may contribute to the clearance of microbial pathogens through different mechanisms. The granzymes can induce host cell apoptosis, which deprives intracellular pathogens of their protective niche, therefore limiting their replication. However, many obligate intracellular pathogens have evolved mechanisms to inhibit programed cells death. To overcome these limitations, the granzymes can exert non-cytolytic antimicrobial activities by directly degrading microbial substrates or hijacked host proteins crucial for the replication or survival of the pathogens. The granzymes may also attack factors that mediate microbial virulence, therefore directly affecting their pathogenicity. Many mechanisms applied by the granzymes to eliminate infected cells and microbial pathogens rely on the induction of reactive oxygen species. These reactive oxygen species may be directly cytotoxic or enhance death programs triggered by the granzymes. Here, in the light of the latest advances, we review the antimicrobial activities of the granzymes in regards to their cytolytic and non-cytolytic activities to inhibit pathogen replication and invasion. We also discuss how reactive oxygen species contribute to the various antimicrobial mechanisms exerted by the granzymes.
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Affiliation(s)
- Marilyne Lavergne
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Maria Andrea Hernández-Castañeda
- Division Infectious Disease and International Medicine, Department of Medicine, Center for Immunology, Minneapolis, MN, United States
| | - Pierre-Yves Mantel
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Denis Martinvalet
- Department of Biomedical Sciences, Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Biomedical Sciences, University of Padua, Padova, Italy
| | - Michael Walch
- Department of Oncology, Microbiology and Immunology, Anatomy Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
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35
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Casalegno Garduño R, Däbritz J. New Insights on CD8 + T Cells in Inflammatory Bowel Disease and Therapeutic Approaches. Front Immunol 2021; 12:738762. [PMID: 34707610 PMCID: PMC8542854 DOI: 10.3389/fimmu.2021.738762] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
CD8+ T cells are involved in the pathogenesis of inflammatory bowel disease (IBD), a complex multifactorial chronic disease. Here, we present an overview of the current research with the controversial findings of CD8+ T cell subsets and discuss some possible perspectives on their therapeutic value in IBD. Studies on the role of CD8+ T cells in IBD have contradictory outcomes, which might be related to the heterogeneity of the cells. Recent data suggest that cytotoxic CD8+ T cells (Tc1) and interleukin (IL) 17-producing CD8+ (Tc17) cells contribute to the pathogenesis of IBD. Moreover, subsets of regulatory CD8+ T cells are abundant at sites of inflammation and can exhibit pro-inflammatory features. Some subsets of tissue resident memory CD8+ T cells (Trm) might be immunosuppressant, whereas others might be pro-inflammatory. Lastly, exhausted T cells might indicate a positive outcome for patients. The function and plasticity of different subsets of CD8+ T cells in health and IBD remain to be further investigated in a challenging field due to the limited availability of mucosal samples and adequate controls.
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Affiliation(s)
- Rosaely Casalegno Garduño
- Mucosal Immunology Group, Department of Pediatrics, Rostock University Medical Center, Rostock, Germany
| | - Jan Däbritz
- Mucosal Immunology Group, Department of Pediatrics, Rostock University Medical Center, Rostock, Germany.,Center for Immunobiology, Blizard Institute, The Barts and the London School of Medicine and Dentistry, Queen Mary University, London, United Kingdom
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36
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Li S, van Dijk CGM, Meeldijk J, Kok HM, Blommestein I, Verbakel ALF, Kotte M, Broekhuizen R, Laclé MM, Goldschmeding R, Cheng C, Bovenschen N. Extracellular Granzyme K Modulates Angiogenesis by Regulating Soluble VEGFR1 Release From Endothelial Cells. Front Oncol 2021; 11:681967. [PMID: 34178673 PMCID: PMC8220216 DOI: 10.3389/fonc.2021.681967] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/19/2021] [Indexed: 01/02/2023] Open
Abstract
Angiogenesis is crucial for normal development and homeostasis, but also plays a role in many diseases including cardiovascular diseases, autoimmune diseases, and cancer. Granzymes are serine proteases stored in the granules of cytotoxic cells, and have predominantly been studied for their pro-apoptotic role upon delivery in target cells. A growing body of evidence is emerging that granzymes also display extracellular functions, which largely remain unknown. In the present study, we show that extracellular granzyme K (GrK) inhibits angiogenesis and triggers endothelial cells to release soluble VEGFR1 (sVEGFR1), a decoy receptor that inhibits angiogenesis by sequestering VEGF-A. GrK does not cleave off membrane-bound VEGFR1 from the cell surface, does not release potential sVEGFR1 storage pools from endothelial cells, and does not trigger sVEGFR1 release via protease activating receptor-1 (PAR-1) activation. GrK induces de novo sVEGFR1 mRNA and protein expression and subsequent release of sVEGFR1 from endothelial cells. GrK protein is detectable in human colorectal tumor tissue and its levels positively correlate with sVEGFR1 protein levels and negatively correlate with T4 intratumoral angiogenesis and tumor size. In conclusion, extracellular GrK can inhibit angiogenesis via secretion of sVEGFR1 from endothelial cells, thereby sequestering VEGF-A and impairing VEGFR signaling. Our observation that GrK positively correlates with sVEGFR1 and negatively correlates with angiogenesis in colorectal cancer, suggest that the GrK-sVEGFR1-angiogenesis axis may be a valid target for development of novel anti-angiogenic therapies in cancer.
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Affiliation(s)
- Shuang Li
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Christian G M van Dijk
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jan Meeldijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Helena M Kok
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Isabelle Blommestein
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Annick L F Verbakel
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Marit Kotte
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Roel Broekhuizen
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Miangela M Laclé
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Roel Goldschmeding
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Caroline Cheng
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, Netherlands
| | - Niels Bovenschen
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands.,Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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