1
|
Ghita L, Yao Z, Xie Y, Duran V, Cagirici HB, Samir J, Osman I, Rebellón-Sánchez DE, Agudelo-Rojas OL, Sanz AM, Sahoo MK, Robinson ML, Gelvez-Ramirez RM, Bueno N, Luciani F, Pinsky BA, Montoya JG, Estupiñan-Cardenas MI, Villar-Centeno LA, Rojas-Garrido EM, Rosso F, Quake SR, Zanini F, Einav S. Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach. Nat Immunol 2023; 24:2150-2163. [PMID: 37872316 PMCID: PMC10863980 DOI: 10.1038/s41590-023-01654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023]
Abstract
Severe dengue (SD) is a major cause of morbidity and mortality. To define dengue virus (DENV) target cells and immunological hallmarks of SD progression in children's blood, we integrated two single-cell approaches capturing cellular and viral elements: virus-inclusive single-cell RNA sequencing (viscRNA-Seq 2) and targeted proteomics with secretome analysis and functional assays. Beyond myeloid cells, in natural infection, B cells harbor replicating DENV capable of infecting permissive cells. Alterations in cell type abundance, gene and protein expression and secretion as well as cell-cell communications point towards increased immune cell migration and inflammation in SD progressors. Concurrently, antigen-presenting cells from SD progressors demonstrate intact uptake yet impaired interferon response and antigen processing and presentation signatures, which are partly modulated by DENV. Increased activation, regulation and exhaustion of effector responses and expansion of HLA-DR-expressing adaptive-like NK cells also characterize SD progressors. These findings reveal DENV target cells in human blood and provide insight into SD pathogenesis beyond antibody-mediated enhancement.
Collapse
Affiliation(s)
- Luca Ghita
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhiyuan Yao
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yike Xie
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Veronica Duran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA
| | - Halise Busra Cagirici
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Jerome Samir
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Ilham Osman
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Ana Maria Sanz
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Makeda L Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Nathalia Bueno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI/Fundacion INFOVIDA), Bucaramanga, Colombia
| | - Fabio Luciani
- School of Biomedical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Benjamin A Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose G Montoya
- Palo Alto Medical Foundation and Dr. Jack S. Remington Laboratory for Speciality Diagnostics, Palo Alto, CA, USA
| | | | - Luis Angel Villar-Centeno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI/Fundacion INFOVIDA), Bucaramanga, Colombia
| | - Elsa Marina Rojas-Garrido
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI/Fundacion INFOVIDA), Bucaramanga, Colombia
| | - Fernando Rosso
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
- Division of Infectious Diseases, Department of Internal Medicine, Fundación Valle del Lili, Cali, Colombia
| | - Stephen R Quake
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Fabio Zanini
- School of Clinical Medicine, UNSW Sydney, Sydney, New South Wales, Australia.
- Cellular Genomics Futures Institute, UNSW Sydney, Sydney, New South Wales, Australia.
- Evolution and Ecology Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
2
|
Louie RHY, Cai C, Samir J, Singh M, Deveson IW, Ferguson JM, Amos TG, McGuire HM, Gowrishankar K, Adikari T, Balderas R, Bonomi M, Ruella M, Bishop D, Gottlieb D, Blyth E, Micklethwaite K, Luciani F. CAR + and CAR - T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies. Nat Commun 2023; 14:7767. [PMID: 38012187 PMCID: PMC10682404 DOI: 10.1038/s41467-023-43656-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is effective in treating B cell malignancies, but factors influencing the persistence of functional CAR+ T cells, such as product composition, patients' lymphodepletion, and immune reconstitution, are not well understood. To shed light on this issue, here we conduct a single-cell multi-omics analysis of transcriptional, clonal, and phenotypic profiles from pre- to 1-month post-infusion of CAR+ and CAR- T cells from patients from a CARTELL study (ACTRN12617001579381) who received a donor-derived 4-1BB CAR product targeting CD19. Following infusion, CAR+ T cells and CAR- T cells shows similar differentiation profiles with clonally expanded populations across heterogeneous phenotypes, demonstrating clonal lineages and phenotypic plasticity. We validate these findings in 31 patients with large B cell lymphoma treated with CD19 CAR T therapy. For these patients, we identify using longitudinal mass-cytometry data an association between NK-like subsets and clinical outcomes at 6 months with both CAR+ and CAR- T cells. These results suggest that non-CAR-derived signals can provide information about patients' immune recovery and be used as correlate of clinically relevant parameters.
Collapse
Affiliation(s)
- Raymond Hall Yip Louie
- School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW, Australia
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Curtis Cai
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Ira W Deveson
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | | | - Timothy G Amos
- Garvan Institute for Medical Research, Sydney, NSW, Australia
| | - Helen Marie McGuire
- Ramaciotti Facility for Human Systems Biology, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
- Infection, Immunity and Inflammation Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Kavitha Gowrishankar
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Thiruni Adikari
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | | | - Martina Bonomi
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia
- Department of Physics, University of Bologna, Bologna, Italy
| | - Marco Ruella
- Division of Hematology and Oncology, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - David Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Kenneth Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
- NSW Health Pathology Blood Transplant and Cell Therapies Laboratory - ICPMR Westmead, Sydney, NSW, Australia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW, Australia.
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia.
- Garvan Institute for Medical Research, Sydney, NSW, Australia.
| |
Collapse
|
3
|
van de Sandt CE, Nguyen THO, Gherardin NA, Crawford JC, Samir J, Minervina AA, Pogorelyy MV, Rizzetto S, Szeto C, Kaur J, Ranson N, Sonda S, Harper A, Redmond SJ, McQuilten HA, Menon T, Sant S, Jia X, Pedrina K, Karapanagiotidis T, Cain N, Nicholson S, Chen Z, Lim R, Clemens EB, Eltahla A, La Gruta NL, Crowe J, Lappas M, Rossjohn J, Godfrey DI, Thomas PG, Gras S, Flanagan KL, Luciani F, Kedzierska K. Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan. Nat Immunol 2023; 24:1890-1907. [PMID: 37749325 PMCID: PMC10602853 DOI: 10.1038/s41590-023-01633-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/24/2023] [Indexed: 09/27/2023]
Abstract
CD8+ T cells provide robust antiviral immunity, but how epitope-specific T cells evolve across the human lifespan is unclear. Here we defined CD8+ T cell immunity directed at the prominent influenza epitope HLA-A*02:01-M158-66 (A2/M158) across four age groups at phenotypic, transcriptomic, clonal and functional levels. We identify a linear differentiation trajectory from newborns to children then adults, followed by divergence and a clonal reset in older adults. Gene profiles in older adults closely resemble those of newborns and children, despite being clonally distinct. Only child-derived and adult-derived A2/M158+CD8+ T cells had the potential to differentiate into highly cytotoxic epitope-specific CD8+ T cells, which was linked to highly functional public T cell receptor (TCR)αβ signatures. Suboptimal TCRαβ signatures in older adults led to less proliferation, polyfunctionality, avidity and recognition of peptide mutants, although displayed no signs of exhaustion. These data suggest that priming T cells at different stages of life might greatly affect CD8+ T cell responses toward viral infections.
Collapse
Affiliation(s)
- Carolien E van de Sandt
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Simone Rizzetto
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Christopher Szeto
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jasveen Kaur
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Nicole Ranson
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Sabrina Sonda
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Alice Harper
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
| | - Samuel J Redmond
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Hayley A McQuilten
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Tejas Menon
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Sneha Sant
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Xiaoxiao Jia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kate Pedrina
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Theo Karapanagiotidis
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Natalie Cain
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ratana Lim
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Auda Eltahla
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole L La Gruta
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, Victoria, Australia
| | - Martha Lappas
- Obstetrics, Nutrition and Endocrinology Group, Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jamie Rossjohn
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Dale I Godfrey
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephanie Gras
- Viral and Structural Immunology Laboratory, Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Katie L Flanagan
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, Tasmania, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, Victoria, Australia
- Tasmanian Vaccine Trial Centre, Clifford Craig Foundation, Launceston General Hospital, Launceston, Tasmania, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| |
Collapse
|
4
|
Cai C, Samir J, Adikari T, Peters T, Luciani F. The functional and molecular determinants of HCV-specific CD8 T cell responses during early infection. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.169.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
T-cell exhaustion is a hallmark of hepatitis C virus (HCV) infection and limits protective immunity in chronic viral infections and cancer. However, limited knowledge exists of the initial dynamics that establish exhaustion in humans. We studied longitudinal blood samples from a unique cohort of primary HCV infection subjects using single cell multi-omics and viral dynamics to identify the functions and phenotypes of HCV-specific CD8+ T cells.
The magnitude of IFN-γ production against the transmitted virus was associated with the rate of immune escape, larger clonal expansion, and a molecular profile consistent with a progenitor of early-exhaustion. Lineage tracing within clones revealed fate plasticity through the course of the infection and differentiation fates of progenitor exhausted subsets. This study provides new insights on the contribution of CD8+ T cells to HCV disease outcome and exhaustion, and supports future studies on early T-cell differentiation in human infections.
Supported by grants from the NHMCR and scholarships from the Australian Government Research Training Program.
Collapse
Affiliation(s)
- Curtis Cai
- 1Centre for Infectious Medicine, Karolinska Institutet, Sweden
- 2The Kirby Institute, University of New South Wales, Australia
| | - Jerome Samir
- 2The Kirby Institute, University of New South Wales, Australia
| | - Thiruni Adikari
- 2The Kirby Institute, University of New South Wales, Australia
| | - Tim Peters
- 3Garvan Institute of Medical Research, Australia
| | - Fabio Luciani
- 2The Kirby Institute, University of New South Wales, Australia
- 3Garvan Institute of Medical Research, Australia
| |
Collapse
|
5
|
Sullivan LC, Nguyen THO, Harpur CM, Stankovic S, Kanagarajah AR, Koutsakos M, Saunders PM, Cai Z, Gray JA, Widjaja JML, Lin J, Pietra G, Mingari MC, Moretta L, Samir J, Luciani F, Westall GP, Malmberg KJ, Kedzierska K, Brooks AG. Natural killer cell receptors regulate responses of HLA-E-restricted T cells. Sci Immunol 2021; 6:eabe9057. [PMID: 33893172 DOI: 10.1126/sciimmunol.abe9057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Human cytomegalovirus (CMV) infection can stimulate robust human leukocyte antigen (HLA)-E-restricted CD8+ T cell responses. These T cells recognize a peptide from UL40, which differs by as little as a single methyl group from self-peptides that also bind HLA-E, challenging their capacity to avoid self-reactivity. Unexpectedly, we showed that the UL40/HLA-E T cell receptor (TCR) repertoire included TCRs that had high affinities for HLA-E/self-peptide. However, paradoxically, lower cytokine responses were observed from UL40/HLA-E T cells bearing TCRs with high affinity for HLA-E. RNA sequencing and flow cytometric analysis revealed that these T cells were marked by the expression of inhibitory natural killer cell receptors (NKRs) KIR2DL1 and KIR2DL2/L3. On the other hand, UL40/HLA-E T cells bearing lower-affinity TCRs expressed the activating receptor NKG2C. Activation of T cells bearing higher-affinity TCRs was regulated by the interaction between KIR2D receptors and HLA-C. These findings identify a role for NKR signaling in regulating self/non-self discrimination by HLA-E-restricted T cells, allowing for antiviral responses while avoiding contemporaneous self-reactivity.
Collapse
Affiliation(s)
- Lucy C Sullivan
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Christopher M Harpur
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Sanda Stankovic
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Abbie R Kanagarajah
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Zhangying Cai
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - James A Gray
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jacqueline M L Widjaja
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Gabriella Pietra
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Maria Cristina Mingari
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa 16132, Italy
| | - Lorenzo Moretta
- Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, 00165 Roma, Italy
| | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Glen P Westall
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Karl J Malmberg
- KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo 0318, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
| |
Collapse
|
6
|
Zhao Y, Cai C, Samir J, Palgen JL, Keoshkerian E, Li H, Bull RA, Luciani F, An H, Lloyd AR. Human CD8 T-stem cell memory subsets phenotypic and functional characterization are defined by expression of CD122 or CXCR3. Eur J Immunol 2021; 51:1732-1747. [PMID: 33844287 DOI: 10.1002/eji.202049057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2021] [Accepted: 04/07/2021] [Indexed: 11/12/2022]
Abstract
Long-lived T-memory stem cells (TSCM ) are key to both naturally occurring and vaccine-conferred protection against infection. These cells are characterized by the CD45RA+ CCR7+ CD95+ phenotype. Significant heterogeneity within the TSCM population is recognized, but distinguishing surface markers and functional characterization of potential subsets are lacking. Human CD8 TSCM subsets were identified in healthy subjects who had been previously exposed to CMV or Influenza (Flu) virus in flow cytometry by expression of CD122 or CXCR3, and then characterized in proliferation, multipotency, self-renewal, and intracellular cytokine production (TNF-α, IL-2, IFN-γ), together with transcriptomic profiles. The TSCM CD122hi -expressing subset (versus CD122lo ) demonstrated greater proliferation, greater multipotency, and enhanced polyfunctionality with higher frequencies of triple positive (TNF-α, IL-2, IFN-γ) cytokine-producing cells upon exposure to recall antigen. The TSCM CXCR3lo subpopulation also had increased proliferation and polyfunctional cytokine production. Transcriptomic analysis further showed that the TSCM CD122hi population had increased expression of activation and homing molecules, such as Ccr6, Cxcr6, Il12rb, and Il18rap, and downregulated cell proliferation inhibitors, S100A8 and S100A9. These data reveal that the TSCM CD122hi phenotype is associated with increased proliferation, enhanced multipotency and polyfunctionality with an activated memory-cell like transcriptional profile, and hence, may be favored for induction by immunization and for adoptive immunotherapy.
Collapse
Affiliation(s)
- Yanran Zhao
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Curtis Cai
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Jerome Samir
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Jean-Louis Palgen
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Elizabeth Keoshkerian
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Hui Li
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Fabio Luciani
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Hongyan An
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| | - Andrew R Lloyd
- Viral Immunology Systems Program (VISP), The Kirby Institute, University of New South Wales, Sydney, Australia
| |
Collapse
|
7
|
Bagaev DV, Vroomans RMA, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov ES, Zvyagin IV, Babel N, Cole DK, Godkin AJ, Sewell AK, Kesmir C, Chudakov DM, Luciani F, Shugay M. VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Nucleic Acids Res 2020; 48:D1057-D1062. [PMID: 31588507 PMCID: PMC6943061 DOI: 10.1093/nar/gkz874] [Citation(s) in RCA: 204] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/17/2019] [Accepted: 09/29/2019] [Indexed: 01/11/2023] Open
Abstract
Here, we report an update of the VDJdb database with a substantial increase in the number of T-cell receptor (TCR) sequences and their cognate antigens. The update further provides a new database infrastructure featuring two additional analysis modes that facilitate database querying and real-world data analysis. The increased yield of TCR specificity identification methods and the overall increase in the number of studies in the field has allowed us to expand the database more than 5-fold. Furthermore, several new analysis methods are included. For example, batch annotation of TCR repertoire sequencing samples allows for annotating large datasets on-line. Using recently developed bioinformatic methods for TCR motif mining, we have built a reduced set of high-quality TCR motifs that can be used for both training TCR specificity predictors and matching against TCRs of interest. These additions enhance the versatility of the VDJdb in the task of exploring T-cell antigen specificities. The database is available at https://vdjdb.cdr3.net.
Collapse
Affiliation(s)
- Dmitry V Bagaev
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Renske M A Vroomans
- Origins Center, Groningen, The Netherlands.,Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,School of Medical Sciences, UNSW Sydney, Sydney, Australia
| | - Ulrik Stervbo
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - Cristina Rius
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Garry Dolton
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Meriem Attaf
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Evgeny S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ivan V Zvyagin
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Nina Babel
- Center for Translational Medicine, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin, Germany
| | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.,Immunocore Ltd., Abingdon, OX14 4RY, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Can Kesmir
- Theoretical Biology and Bioinformatics Department, Science Faculty, Utrecht University, Utrecht, Netherlands
| | - Dmitriy M Chudakov
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,School of Medical Sciences, UNSW Sydney, Sydney, Australia
| | - Mikhail Shugay
- Pirogov Russian Medical State University, Moscow, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| |
Collapse
|
8
|
Abstract
Background Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information. Results We developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8+ T cells with available gene expression, TCR sequences, quantification of 15 surface proteins, and 44 antigen specificities (across viruses, cancer, and self-antigens). We performed quality control, filtering of tetramer non-specific cells, clustering, random sampling and hypothesis testing to discover antigen specific gene signatures which were associated with immune cell differentiation states and clonal expansion across the pathogen specific T cells. We also analysed 563 single cells (plate-based sorted) obtained from 11 subjects, revealing clonally expanded T and B cells across primary cancer tissues and metastatic lymph-node. These immune cells clustered with distinct gene signatures according to the breast cancer molecular subtype. VDJView has been tested in lab meetings and peer-to-peer discussions, showing effective data generation and discussion without the need to consult bioinformaticians. Conclusions VDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview.
Collapse
Affiliation(s)
- Jerome Samir
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,Garvan Institute of Medical Research, Sydney, Australia
| | - Simone Rizzetto
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia
| | - Money Gupta
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia.,Garvan Institute of Medical Research, Sydney, Australia
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, Australia. .,Garvan Institute of Medical Research, Sydney, Australia.
| |
Collapse
|
9
|
Rizzetto S, Koppstein DNP, Samir J, Singh M, Reed JH, Cai CH, Lloyd AR, Eltahla AA, Goodnow CC, Luciani F. B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle. Bioinformatics 2019; 34:2846-2847. [PMID: 29659703 DOI: 10.1093/bioinformatics/bty203] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/04/2018] [Indexed: 01/07/2023] Open
Abstract
Motivation The B-cell receptor (BCR) performs essential functions for the adaptive immune system including recognition of pathogen-derived antigens. The vast repertoire and adaptive variation of BCR sequences due to V(D)J recombination and somatic hypermutation necessitates single-cell characterization of BCR sequences. Single-cell RNA sequencing presents the opportunity for simultaneous capture of paired BCR heavy and light chains and the transcriptomic signature. Results We developed VDJPuzzle, a novel bioinformatic tool that reconstructs productive, full-length B-cell receptor sequences of both heavy and light chains and extract somatic mutations on the VDJ region. VDJPuzzle successfully reconstructed BCRs from 100% (n=117) human and 96.5% (n=200) murine B cells. The reconstructed BCRs were successfully validated with single-cell Sanger sequencing. Availability and implementation VDJPuzzle is available at https://bitbucket.org/kirbyvisp/vdjpuzzle2. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Simone Rizzetto
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia
| | - David N P Koppstein
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia
| | - Jerome Samir
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia
| | - Mandeep Singh
- Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Joanne H Reed
- Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Curtis H Cai
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia
| | | | - Auda A Eltahla
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia
| | | | - Fabio Luciani
- Kirby Institute for Infection and Immunity, Sydney, Australia.,School of Medical Sciences, UNSW, Sydney, Australia.,Immunogenomics, Garvan Institute of Medical Research, Sydney, Australia
| |
Collapse
|
10
|
Qarro A, Assebane M, Bazine K, Samir J, Najoui M, Guenoun F, Beddouch A, Lezrek M, Alami M. Masse rénale avec image stellaire centrale: Quel est votre diagnostic? African Journal of Urology 2013. [DOI: 10.1016/j.afju.2012.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
11
|
Asseban M, Jaafari H, Qarro A, Ammani A, Samir J, Bazine K, Najoui M, Alami M. Adénome de prostate révélé par des hypoglycémies profondes: A propos d'un cas. African Journal of Urology 2013. [DOI: 10.1016/j.afju.2012.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
12
|
Qarro A, Ghoundale O, Bazine K, Asseban M, Najoui M, Samir J, Ouhbi Y, Beddouch A, Lezrek M, Alami M. Score de Gleason des biopsies prostatiques et celui des pièces de prostatectomies: Quelle corrélation? African Journal of Urology 2012. [DOI: 10.1016/j.afju.2012.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|