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Muñoz Sandoval D, Bach FA, Ivens A, Harding AC, Smith NL, Mazurczyk M, Themistocleous Y, Edwards NJ, Silk SE, Barrett JR, Cowan GJ, Napolitani G, Savill NJ, Draper SJ, Minassian AM, Nahrendorf W, Spence PJ. Plasmodium falciparum infection induces T cell tolerance that is associated with decreased disease severity upon re-infection. J Exp Med 2025; 222:e20241667. [PMID: 40214640 PMCID: PMC11987708 DOI: 10.1084/jem.20241667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 11/18/2024] [Accepted: 03/12/2025] [Indexed: 04/14/2025] Open
Abstract
Immunity to severe malaria is acquired quickly, operates independently of pathogen load, and represents a highly effective form of disease tolerance. The mechanism that underpins tolerance remains unknown. We used a human rechallenge model of falciparum malaria in which healthy adult volunteers were infected three times over a 12 mo period to track the development of disease tolerance in real-time. We found that parasitemia triggered a hardwired innate immune response that led to systemic inflammation, pyrexia, and hallmark symptoms of clinical malaria across the first three infections of life. In contrast, a single infection was sufficient to reprogram T cell activation and reduce the number and diversity of effector cells upon rechallenge. Crucially, this did not silence stem-like memory cells but instead prevented the generation of cytotoxic effectors associated with autoinflammatory disease. Tolerized hosts were thus able to prevent collateral tissue damage in the absence of antiparasite immunity.
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Affiliation(s)
- Diana Muñoz Sandoval
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
- Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Florian A. Bach
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Adam C. Harding
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Natasha L. Smith
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Michalina Mazurczyk
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | | | - Sarah E. Silk
- The Jenner Institute, University of Oxford, Oxford, UK
- Department of Biochemistry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Jordan R. Barrett
- The Jenner Institute, University of Oxford, Oxford, UK
- Department of Biochemistry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Graeme J.M. Cowan
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Giorgio Napolitani
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nicholas J. Savill
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Simon J. Draper
- The Jenner Institute, University of Oxford, Oxford, UK
- Department of Biochemistry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Angela M. Minassian
- The Jenner Institute, University of Oxford, Oxford, UK
- Department of Biochemistry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Wiebke Nahrendorf
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Philip J. Spence
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
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2
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Bagkou Dimakou D, Tamblyn J, Lissauer D, Richter A. Evaluation of peripheral NK tests offered to women with recurrent pregnancy loss and a search for novel candidate biomarkers. J Reprod Immunol 2025; 169:104522. [PMID: 40112444 DOI: 10.1016/j.jri.2025.104522] [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: 10/08/2024] [Revised: 01/28/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025]
Abstract
Recurrent pregnancy loss (RPL) is a common condition of largely undetermined pathogenesis. There is prior evidence of association with immune dysregulation linked to elevated NK cell levels and cytotoxicity. However, experimental findings remain contentious, hindering clinical adoption of immunological testing. Given their importance in healthy pregnancy, this study set out to determine the clinical utility of NK cell assays in 100 non-pregnant women with RPL and 80 healthy control women and establish an exploratory mass cytometry panel for in-depth NK phenotyping. As previously described, peripheral NK cell elevation was observed with RPL. The augmented NK cell cytotoxicity, often referenced, was undetectable, although enhanced degranulation was observed. Reduced cytolytic molecule secretion by PBMCs was seen in RPL, possibly counterbalancing the increased NK cell degranulation. Mass cytometry was employed for the detailed investigation of NK cell phenotype, focused on inhibitory and activating receptor expression. Augmented prevalence of CD57+ mature cytotoxic NK cells was present in the RPL cohort. This was accompanied by elevated prevalence of subsets lacking inhibitory receptor expression, indicating enhanced NK cell responsiveness to activating signalling. Additionally, CXCR3/CXCR4+ subset reduction, suggested potential uterine migration defects. This extensive analysis of peripheral NK cells in RPL has revealed significant dysregulation affecting both total number and potential activity. The extent to which this dysregulation is reflected in utero requires further examination. Current findings will be used to guide subsequent investigations on paired peripheral and endometrial samples as well as biomarker discovery to improve our capacity to estimate risk of a following loss.
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Affiliation(s)
- Danai Bagkou Dimakou
- Department of Clinical Immunology Service, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, United Kingdom; Tommy's National Centre for Miscarriage Research, United Kingdom.
| | - Jennifer Tamblyn
- Tommy's National Centre for Miscarriage Research, United Kingdom; University of Birmingham, School of Medical Sciences, United Kingdom; Leeds NHS Teaching Hospital Trust, United Kingdom
| | - David Lissauer
- University of Liverpool, Institute of Life Course and Medical Sciences, United Kingdom
| | - Alex Richter
- Department of Clinical Immunology Service, School of Infection, Inflammation and Immunology, College of Medicine and Health, University of Birmingham, United Kingdom
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3
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Willsmore ZN, Booth L, Patel A, Di Meo A, Prassas I, Chauhan J, Wu Y, Fitzpartick A, Stoker K, Kapiris M, Biswas D, Perucha E, Whittaker S, Tsoka S, Diamandis EP, Middleton GW, Tull TJ, Papa S, Lacy KE, Karagiannis SN. Circulating immunoregulatory B cell and autoreactive antibody profiles predict lack of toxicity to anti-PD-1 checkpoint inhibitor treatment in advanced melanoma. J Immunother Cancer 2025; 13:e011682. [PMID: 40449958 DOI: 10.1136/jitc-2025-011682] [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] [Accepted: 05/13/2025] [Indexed: 06/03/2025] Open
Abstract
BACKGROUND The majority of patients with melanoma develop immune-related adverse events (irAEs), and over half do not respond to anti-PD-1 (Programmed cell death protein 1) checkpoint inhibitor (CPI) immunotherapy. Accurate predictive biomarkers for both response to therapy and development of irAEs are currently lacking in clinical practice. Here, we conduct deep immunophenotyping of circulating regulatory and class-switched B cell and antibody immune states in patients with advanced stage III/IV melanoma prior to and longitudinally during CPI. METHODS Mass cytometry, serum antibody isotyping and immuno-mass spectrometry proteome-wide screening evaluations to identify autoreactive antibodies were undertaken to profile circulating humoral immunity features in patients and healthy subjects and interrogate pretreatment B cell and antibody signatures that predict toxicity and response to anti-PD-1 therapy. In paired blood samples pretreatment and post-treatment, these humoral immune response profiles were monitored and correlated with the onset of toxicity. RESULTS We found increased circulating IL-10+ (Interleukin-10+) plasmablasts and double-negative (DN) B cell frequencies, higher PD-L1 (programmed death ligand 1), TGFβ (Transforming Growth Factorβ) and CD95 expression by B cells, alongside higher IgG4 and IgE serum levels in patients with stage III/IV melanoma. This suggests enhanced B regulatory and Th2 (Thelper2)-driven responses in advanced disease. Increased baseline frequency of DN2 B cells, plasmablasts, and serum IgE, IgA and antibody autoreactivity were observed in patients who did not develop irAE. During treatment, higher IL-10+class-switched memory B cell, plasmablast and IgG1, IgG3 and IgE, alongside reduced IgG2, IgG4, IgA and IgM levels, were observed. A reduction in autoantibodies targeting tubulins was observed during treatment. Increased frequency of class-switched memory B cells predicted improved survival, while reduced transitional and PD-L1+TGFβ+ naive B cell frequencies and higher IgG4 and IgE levels predicted lower survival, on anti-PD-1 therapy. CONCLUSIONS Distinct B cell and antibody reactivities in patients with advanced melanoma share features with extrafollicular B cell responses in autoimmune diseases, may be protective from irAE and help predict outcomes to anti-PD-1.
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Affiliation(s)
- Zena N Willsmore
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Lucy Booth
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Akshay Patel
- Institute of Immunology and Immunotherapy (III), College of Medicine and Health, University of Birmingham, Birmingham, UK
| | - Ashley Di Meo
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Ioannis Prassas
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Jitesh Chauhan
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Yin Wu
- Department of Medical Oncology, Guy's and St Thomas' Hospitals NHS Trust, London, UK
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbial Sciences, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Amanda Fitzpartick
- Department of Medical Oncology, Guy's and St Thomas' Hospitals NHS Trust, London, UK
| | - Katie Stoker
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, Strand Campus, King's College London, London, UK
| | - Matthaios Kapiris
- Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
| | - Dhruva Biswas
- Cardiovascular Data Science (CarDS) Lab, Research Faculty, Yale School of Medicine, New Haven, Connecticut, USA
- School of Cardiovascular and Metabolic Medicine & Sciences, James Black Centre, King's College London, London, UK
| | - Esperanza Perucha
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbial Sciences, King's College London, London, UK
- Centre for Rheumatic Diseases, King's College London, London, UK
| | - Sean Whittaker
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, Strand Campus, King's College London, London, UK
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gary W Middleton
- Institute of Immunology and Immunotherapy (III), College of Medicine and Health, University of Birmingham, Birmingham, UK
| | - Thomas J Tull
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
- St John's Institute of Dermatology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sophie Papa
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Katie E Lacy
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
| | - Sophia N Karagiannis
- St John's Institute of Dermatology, School of Basic and Medical Biosciences and KHP Centre for Translational Medicine, Guy's Hospital, King's College London, London, UK
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, Innovation Hub, Guy's Cancer Centre, King's College London, London, UK
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4
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Wang M, Otto C, Fernández Zapata C, Dehlinger A, Gallaccio G, Diekmann LM, Niederschweiberer M, Schindler P, Körtvélyessy P, Kunkel D, Paul F, Ruprecht K, Böttcher C. Comprehensive analysis of B cell repopulation in ocrelizumab-treated patients with multiple sclerosis by mass cytometry and proteomics. iScience 2025; 28:112383. [PMID: 40322080 PMCID: PMC12049848 DOI: 10.1016/j.isci.2025.112383] [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: 05/14/2024] [Revised: 09/30/2024] [Accepted: 04/04/2025] [Indexed: 05/08/2025] Open
Abstract
Ocrelizumab, an anti-CD20 antibody, depletes CD20+ B cells, which subsequently repopulate over months. Little is known about changes in other immune cell populations and molecular markers associated with B cell repopulation. Here, we performed a comprehensive characterization of immune cells from ocrelizumab-treated patients with multiple sclerosis (MS) using mass cytometry. About 50% of patients showed naive B cell repopulation after 6 months mainly with a transitional phenotype, whereas CD27+ memory B cells only rarely repopulated. This repopulation was associated with a reduction of memory T cells and activated myeloid cells, as well as reduced expression of activation/migration markers in both cell types. A plasma proteomics analysis identified proteins including TNFRSF13C, associated with B cell depletion and repopulation. Plasma levels of neurofilament light-chain protein declined after ocrelizumab treatment was not linked with B cell repopulation. These findings identify potential soluble markers for monitoring of ocrelizumab treatment in MS.
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Affiliation(s)
- Meng Wang
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Carolin Otto
- Department of Neurology with Experimental Neurology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - Camila Fernández Zapata
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Adeline Dehlinger
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Gerardina Gallaccio
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Lisa-Marie Diekmann
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Moritz Niederschweiberer
- Department of Neurology with Experimental Neurology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - Patrick Schindler
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Neurology with Experimental Neurology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
- Neuroscience Clinical Research Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - Peter Körtvélyessy
- Department of Neurology, Center for ALS and Other Motor Neuron Disorders, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Desiree Kunkel
- Flow & MassCytometry Core Facility, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin 13353, Germany
| | - Friedemann Paul
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Neurology with Experimental Neurology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
- Neuroscience Clinical Research Center, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - Klemens Ruprecht
- Department of Neurology with Experimental Neurology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
| | - Chotima Böttcher
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, Berlin 13125, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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5
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Galvez-Cancino F, Navarrete M, Beattie G, Puccio S, Conde-Gallastegi E, Foster K, Morris Y, Sahwangarrom T, Karagianni D, Liu J, Lee AJX, Garyfallos DA, Simpson AP, Mastrokalos GT, Nannini F, Costoya C, Anantharam V, Cianciotti BC, Bradley L, Garcia-Diaz C, Clements M, Shroff A, Vahid Dastjerdi F, Rota EM, Sheraz S, Bentham R, Uddin I, Walczak H, Lladser A, Reading JL, Chester KA, Pule MA, Brennan PM, Marguerat S, Parrinello S, Peggs KS, McGranahan N, Lugli E, Litchfield K, Pollard SM, Quezada SA. Regulatory T cell depletion promotes myeloid cell activation and glioblastoma response to anti-PD1 and tumor-targeting antibodies. Immunity 2025; 58:1236-1253.e8. [PMID: 40280128 DOI: 10.1016/j.immuni.2025.03.021] [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: 06/26/2023] [Revised: 10/28/2024] [Accepted: 03/31/2025] [Indexed: 04/29/2025]
Abstract
Glioblastoma is invariably lethal and responds poorly to immune checkpoint blockade. Here, we examined the impact of regulatory T (Treg) cell depletion on glioblastoma progression and immunotherapy responsiveness. In human glioblastoma, elevated Treg cell signatures correlated with poorer survival outcomes, with these cells expressing high levels of CD25. In Nf1-/-Pten-/-EGFRvIII+ glioblastoma-bearing mice, a single dose of non-interleukin-2 (IL-2) blocking (NIB) anti-CD25 (anti-CD25NIB) antibody depleted Treg cells and promoted CD8+ T cell clonal expansion and partial tumor control, further enhanced by programmed cell death-1 (PD1)-blockade. Treg cell depletion induced interferon-γ (IFN-γ)-dependent tumor microenvironment remodeling, increasing Fcγ receptor (FcγR) expression on intratumoral myeloid cells and enhancing phagocytosis. Combination of anti-CD25NIB with anti-EGFRvIII tumor-targeting antibodies resulted in complete tumor control. Anti-human CD25NIB treatment of glioblastoma patient-derived tumor fragments effectively depleted Treg cells and activated CD8+ T cells. These findings underscore the therapeutic relevance of Treg targeting in glioblastoma and unveil potent combination strategies for anti-CD25NIB based on innate cell activation.
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Affiliation(s)
- Felipe Galvez-Cancino
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK; Immune Regulation Laboratory, Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Mariela Navarrete
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Gordon Beattie
- CRUK City of London Centre Single Cell Genomics Facility, UCL Cancer Institute, University College London, London, UK; Bioinformatics Hub, UCL Cancer Institute, University College London, London, UK
| | - Simone Puccio
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy; Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, via Manzoni 56, Rozzano, Milan 20089, Italy
| | - Enrique Conde-Gallastegi
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Kane Foster
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Yasmin Morris
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Teerapon Sahwangarrom
- Pre-Cancer Immunology Laboratory, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Despoina Karagianni
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Jiali Liu
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Alvin J X Lee
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Dimitrios A Garyfallos
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Alexander P Simpson
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Gerasimos-Theodoros Mastrokalos
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Francesco Nannini
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Cristobal Costoya
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Varshaa Anantharam
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | | | - Leanne Bradley
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Claudia Garcia-Diaz
- Neurogenesis and Brain Cancer Group, Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Melanie Clements
- Neurogenesis and Brain Cancer Group, Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Aditya Shroff
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, London WC1E 6DD, UK
| | | | - Enrique Miranda Rota
- Recombinant Antibody Therapeutics Group, UCL Cancer Institute, London WC1E 6DD, UK
| | - Shahida Sheraz
- Pre-Cancer Immunology Laboratory, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK
| | - Robert Bentham
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Imran Uddin
- CRUK City of London Centre Single Cell Genomics Facility, UCL Cancer Institute, University College London, London, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer and Inflammation (CCCI), UCL Cancer Institute, London WC1E 6DD, UK; Institute of Biochemistry I & CECAD Cluster of Excellence, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Alvaro Lladser
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - James L Reading
- Pre-Cancer Immunology Laboratory, Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kerry A Chester
- Recombinant Antibody Therapeutics Group, UCL Cancer Institute, London WC1E 6DD, UK
| | - Martin A Pule
- Research Department of Haematology, Cancer Institute, University College London, Paul O'Gorman Building, London WC1E 6DD, UK
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Samuel Marguerat
- Bioinformatics Hub, UCL Cancer Institute, University College London, London, UK
| | - Simona Parrinello
- Neurogenesis and Brain Cancer Group, Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, London WC1E 6DD, UK
| | - Karl S Peggs
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Enrico Lugli
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Kevin Litchfield
- The Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London WC1E 6DD, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine and Institute for Regeneration and Repair, & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Sergio A Quezada
- Immune Regulation and Tumour Immunotherapy Laboratory, Cancer Immunology Unit, Research Department of Haematology, UCL Cancer Institute, University College London, London WC1E 6DD, UK.
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6
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Qi Y, Ge H, Sun X, Wei Y, Zhai J, Qian H, Mo H, Ma F. Systemic immune characteristics predicting toxicity to immune checkpoint inhibitors in patients with advanced breast cancer. J Autoimmun 2025; 153:103423. [PMID: 40267835 DOI: 10.1016/j.jaut.2025.103423] [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: 01/30/2025] [Revised: 04/12/2025] [Accepted: 04/14/2025] [Indexed: 04/25/2025]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are among the most promising treatment options for cancer. However, frequent and sometimes life-threatening immune-related adverse events (irAEs) are associated with ICI treatment. Therefore, it is imperative to establish a model for predicting the risk of irAEs to identify high-risk groups, enable more accurate clinical risk‒benefit analysis for ICI treatment and decrease the incidence of irAEs. However, no ideal model for predicting irAEs has been applied in clinical practice. The aim of this study was to analyze the systemic immune characteristics of patients with irAEs and establish a model for predicting the risk of irAEs. METHODS We conducted a study to monitor irAEs in patients with advanced breast cancer undergoing immunotherapy during and following the treatment course. Peripheral blood mononuclear cells (PBMCs) were collected before and after two cycles of therapy. Mass cytometry time-of-flight (CyTOF) was employed to identify baseline and posttreatment immune cell subpopulations, and the relationships between the proportions of cells in these subpopulations and the occurrence of irAEs were explored. Additionally, we conducted subgroup analyses stratified by the anatomic location and time of onset of irAEs. Furthermore, we developed a logistic regression model to predict the risk of irAEs and validated this model using two independent validation cohorts from the Gene Expression Omnibus (GEO) database (accession numbers GSE189125 and GSE186143). RESULTS By analyzing 106 blood samples and samples from two independent validation cohorts (n = 16 and 60 patients), we found that high proportions of CXCR3+CCR6+CD4+ T cells and CD38+CD86+CXCR3+CCR6+CD8+ T cells and a low proportion of CXCR3lowCD56dim natural killer (NK) cells at baseline were significantly correlated with the incidence of irAEs (P = 0.0029, P < 0.001, and P = 0.0017, respectively). In the subgroup analysis, we observed consistent results in patients with immune-related pneumonitis (ir-pneumonitis) and immune-related thyroiditis (ir-thyroiditis). In the early irAE group, the baseline proportion of CXCR3+CCR6+CD4+ T cells was greater than that in the late irAE group (P = 0.011). An analysis of PBMCs before and after ICI treatment revealed thatthe dynamic changes in the proportions of naïve CD4+ T cells and CXCR3lowCD56dim NK cells were closely related to irAE occurrence. Finally, we ultimately developed a model for predicting the risk of irAEs, which yielded an area under the receiver operating characteristic curve (AUROC) of 0.79 in the training cohort and an AUROC of 0.75 in the single-cell validation cohort (GSE189125). CONCLUSIONS These findings indicate that different populations of immune cells are associated with different irAEs and that characterization of these cells may be used as biomarkers to predict the risk of specific toxicities. This will facilitate the management of irAEs and may lead to a reduction in the incidence of irAEs.
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Affiliation(s)
- Yalong Qi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Hewei Ge
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiaoying Sun
- Department of Medical Oncology, Cancer Hospital of HuanXing ChaoYang District, Beijing, China.
| | - Yuhan Wei
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jingtong Zhai
- Department of Oncology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Hongnan Mo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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7
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Christopher BN, Golick L, Basar A, Reyes L, Robinson RM, Angerstein AO, Krieg C, Hobbs GA, Guttridge DC, O’Bryan JP, Dolloff NG. Modulating the CXCR2 Signaling Axis Using Engineered Chemokine Fusion Proteins to Disrupt Myeloid Cell Infiltration in Pancreatic Cancer. Biomolecules 2025; 15:645. [PMID: 40427538 PMCID: PMC12108577 DOI: 10.3390/biom15050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2025] [Revised: 04/16/2025] [Accepted: 04/24/2025] [Indexed: 05/29/2025] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has one of the lowest 5-year survival rates of all cancers, and limited treatment options exist. Immunotherapy is effective in some cancer types, but the immunosuppressive tumor microenvironment (TME) of PDAC is a barrier to effective immunotherapy. CXCR2+ myeloid-derived suppressor cells (MDSCs) are abundant in PDAC tumors in humans and in mouse models. MDSCs suppress effector cell function, making them attractive targets for restoring anti-tumor immunity. In this study, we show that the most abundant soluble factors released from a genetically diverse set of human and mouse PDAC cells are CXCR2 ligands, including CXCL8, CXCL5, and CXCL1. Expression of CXCR2 ligands is at least partially dependent on mutant KRAS and NFκB signaling, which are two of the most commonly dysregulated pathways in PDAC. We show that MDSCs are the most prevalent immune cells in PDAC tumors. MDSCs expressed high levels of CXCR2, and we found that myeloid cells readily migrate toward conditioned media (CM) prepared from PDAC cultures. We designed CXCR2 ligand-Fc fusion proteins to modulate the CXCR2 chemotactic signaling axis. Unexpectedly, these fusion proteins were superior to native chemokines in binding and activation of CXCR2 on myeloid cells. These "superkines" were potent inhibitors of PDAC CM-induced myeloid cell migration and were superior to CXCR2 small-molecule inhibitors and neutralizing antibodies. Our findings suggest that CXCR2 superkines may disrupt myeloid cell recruitment to PDAC tumors, ultimately improving immunotherapy outcomes in patients with PDAC.
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Affiliation(s)
- Benjamin N. Christopher
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Lena Golick
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Ashton Basar
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Leticia Reyes
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Reeder M. Robinson
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Aaron O. Angerstein
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
| | - Carsten Krieg
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - G. Aaron Hobbs
- Department of Biochemistry, Medical University of South Carolina, Charleston, SC 29425, USA; (G.A.H.); (J.P.O.)
- MUSC Hollings Cancer Center, Charleston, SC 29425, USA;
| | - Denis C. Guttridge
- MUSC Hollings Cancer Center, Charleston, SC 29425, USA;
- MUSC Darby Children’s Research Institute, Charleston, SC 29425, USA
- Department of Pediatrics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - John P. O’Bryan
- Department of Biochemistry, Medical University of South Carolina, Charleston, SC 29425, USA; (G.A.H.); (J.P.O.)
- MUSC Hollings Cancer Center, Charleston, SC 29425, USA;
| | - Nathan G. Dolloff
- Department of Pharmacology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (B.N.C.); (L.G.); (A.B.); (L.R.); (R.M.R.); (A.O.A.)
- MUSC Hollings Cancer Center, Charleston, SC 29425, USA;
- Zucker Institute for Innovation Commercialization, Charleston, SC 29425, USA
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8
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Morrison TA, Vigee J, Tovar KA, Talley TA, Mujal AM, Kono M, Philips R, Nagashima H, Brooks SR, Dada H, Rozich I, Hudspeth K, Lau CM, Yao C, Sciumè G, Sun HW, Bonifacino JS, Kanno Y, Dustin ML, Randazzo D, Proia RL, Sun JC, Shih HY, O'Shea JJ. Selective requirement of glycosphingolipid synthesis for natural killer and cytotoxic T cells. Cell 2025:S0092-8674(25)00409-X. [PMID: 40306279 DOI: 10.1016/j.cell.2025.04.007] [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: 12/22/2024] [Revised: 03/11/2025] [Accepted: 04/03/2025] [Indexed: 05/02/2025]
Abstract
Cell identity genes that exhibit complex regulation are marked by super-enhancer (SE) architecture. Assessment of SEs in natural killer (NK) cells identified Ugcg, encoding the enzyme responsible for glycosphingolipid (GSL) synthesis. Conditional deletion of Ugcg in early hematopoiesis abrogated NK cell generation while sparing other lineages. Pharmacological inhibition of UGCG disrupted cytotoxic granules and cytotoxicity, reduced expansion after viral infection, and promoted apoptosis. B4galt5 transcribes an enzyme downstream of UGCG and possesses SE structure. Addition of its product, lactosylceramide (LacCer), reversed apoptosis due to UGCG inhibition. By contrast, complex GSLs, such as asialo-GM1, were not required for NK cell viability and granule integrity. Ugcg and B4galt5 were upregulated in CD8+ T cells during viral infection, correlating with the acquisition of cytotoxic machinery. Antigen-specific CD8+ T cells lacking Ugcg failed to expand during infection. Our study reveals a selective and essential role of GSL metabolism in NK and CD8+ T cell biology.
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Affiliation(s)
- Tasha A Morrison
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA; Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA.
| | - Jaelyn Vigee
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Kevin A Tovar
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Taylor A Talley
- Lymphocyte Signaling Unit, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD, USA
| | - Adriana M Mujal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mari Kono
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Rachael Philips
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Hiroyuki Nagashima
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Hannah Dada
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Isaiah Rozich
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kelly Hudspeth
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Colleen M Lau
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Chen Yao
- Department of Immunology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, "Sapienza" University of Rome, Rome, Italy
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Juan S Bonifacino
- Division of Neurosciences and Cellular Structure, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | | | - Richard L Proia
- Genetics of Development and Disease Section, Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Han-Yu Shih
- Neuro-immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH), Bethesda, MD, USA.
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9
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Cheng JN, Jin Z, Su C, Jiang T, Zheng X, Guo J, Li X, Chu H, Jia J, Zhou Q, Ding X, Zhang Y, Xu S, Dong F, Zhang Q, Yang X, Yang T, Cheng X, Zha H, Chen D, Wan YY, Liu X, Ye L, Tang H, Symonds ALJ, Li QJ, Jia Q, Zhu B. Bone metastases diminish extraosseous response to checkpoint blockade immunotherapy through osteopontin-producing osteoclasts. Cancer Cell 2025:S1535-6108(25)00137-0. [PMID: 40280123 DOI: 10.1016/j.ccell.2025.03.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 01/23/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025]
Abstract
Bone metastatic lesions typically associate with suboptimal responses to immune checkpoint blockade (ICB) therapies. In this study, we observed that across multiple clinical cohorts and a variety of mouse models, the presence of osseous metastases induces ICB resistance in extraosseous tumors. Mechanistically, this long-distance communication is mediated by osseous tumor-conditioned osteoclasts producing osteopontin (OPN). Through circulation, OPN reprograms the extraosseous tumor microenvironment and impairs T cell recruitment and differentiation of CD8+TCF1+ precursor cells, an essential population for ICB efficacy. In mice, ICB responsiveness is restored by αRANKL blockade of osteoclastogenesis, neutralization of OPN in circulation, or tissue-specific depletion of OPN in osteoclasts. Both the mode of action and therapeutic benefit were validated in clinical cohorts with the αRANKL-ICB combinatory regimen. These findings establish bone as a specific immunoregulatory organ exploited by tumor metastasis and suggest osteoclastogenesis as a promising target to improve ICB prognosis in patients with bone metastasis.
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Affiliation(s)
- Jia-Nan Cheng
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Zheng Jin
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China; Research Institute, GloriousMed Clinical Laboratory (Shanghai) Co., Ltd., Shanghai 201318, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Shanghai 200433, China
| | - Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No.507, Zhengmin Road, Shanghai 200433, China
| | - Xiaobin Zheng
- Department of Thoracic Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou 350014, China
| | - Jinming Guo
- College of Basic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Xingyi Li
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China; Department of Oncology, The General Hospital of Western Theater Command, Chengdu, Sichuan Province 610083, China
| | - Han Chu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Jia Jia
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Qin Zhou
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Xiaofang Ding
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Yiwen Zhang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Shouxia Xu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China; School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Fancong Dong
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China; Department of Oncology, The Affiliated Dongnan Hospital of Xiamen University, Zhangzhou 363000, China
| | - Qiao Zhang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China; The 988th Hospital of Joint Logistic Support Force of PLA, Zhengzhou, Henan 450042, China
| | - Xinxin Yang
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Tao Yang
- Department of Oncology, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan 572013, China
| | - Xiaoming Cheng
- Department of Respiratory Diseases, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Haoran Zha
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China; Department of Oncology, PLA Rocket Force Characteristic Medical Center, Beijing 100088, China
| | - Degao Chen
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China
| | - Yisong Y Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xindong Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing 400038, China
| | - Haidong Tang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Alistair L J Symonds
- Blizard Institute, Barts and London School of Medicine and Dentistry, University of London, London E12AT, UK
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology (IMCB) & Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138668, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138668, Singapore.
| | - Qingzhu Jia
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Immunotherapy, Chongqing 400037, China.
| | - Bo Zhu
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Advanced Pathology Research Institute, Jinfeng Laboratory, Chongqing 401329, China; Institute of Immunological Innovation and Translation, Chongqing Medical University, Chongqing 400016, China.
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10
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Li X, Pan L, Li W, Liu B, Xiao C, Chew V, Zhang X, Long W, Ginhoux F, Loscalzo J, Buggert M, Zhang X, Sheng R, Wang Z. Deciphering immune predictors of immunotherapy response: A multiomics approach at the pan-cancer level. Cell Rep Med 2025; 6:101992. [PMID: 40054456 PMCID: PMC12047473 DOI: 10.1016/j.xcrm.2025.101992] [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: 08/03/2024] [Revised: 01/15/2025] [Accepted: 02/05/2025] [Indexed: 04/18/2025]
Abstract
Immune checkpoint blockade (ICB) therapy has transformed cancer treatment, yet many patients fail to respond. Employing single-cell multiomics, we unveil T cell dynamics influencing ICB response across 480 pan-cancer and 27 normal tissue samples. We identify four immunotherapy response-associated T cells (IRATs) linked to responsiveness or resistance and analyze their pseudotemporal patterns, regulatory mechanisms, and T cell receptor clonal expansion profiles specific to each response. Notably, transforming growth factor β1 (TGF-β1)+ CD4+ and Temra CD8+ T cells negatively correlate with therapy response, in stark contrast to the positive response associated with CXCL13+ CD4+ and CD8+ T cells. Validation with a cohort of 23 colorectal cancer (CRC) samples confirms the significant impact of TGF-β1+ CD4+ and CXCL13+ CD4+ and CD8+ T cells on ICB efficacy. Our study highlights the effectiveness of single-cell multiomics in pinpointing immune markers predictive of immunotherapy outcomes, providing an important resource for crafting targeted immunotherapies for successful ICB treatment across cancers.
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Affiliation(s)
- Xuexin Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, Liaoning 110032, China; Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning 110122, China; Department of Physiology and Pharmacology, Karolinska Institutet, 171 65 Solna, Sweden.
| | - Lu Pan
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Sweden
| | - Weiyuan Li
- School of Medicine, Yunnan University, Kunming, Yunnan 650091, China; Department of Reproductive Medicine, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650021, China
| | - Bingyang Liu
- Department of Endocrinology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Chunjie Xiao
- School of Medicine, Yunnan University, Kunming, Yunnan 650091, China
| | - Valerie Chew
- Translational Immunology Institute (TII), SingHealth-Duke NUS Academic Medical Centre, Singapore 169856, Singapore
| | - Xuan Zhang
- Department of Colorectal Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, China
| | - Wang Long
- Department of Pathology, Nihon University, Tokyo 102-0074, Japan
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore 138648, Singapore; Institut Gustave Roussy, INSERM U1015, Bâtiment de Médecine Moléculaire 114 rue Edouard Vaillant, 94800 Villejuif, France; Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden
| | - Xiaolu Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Shenzhen Research Institute of Shandong University, Shenzhen, Guangdong 518057, China.
| | - Ren Sheng
- College of Life and Health Sciences, Northeastern University, Shenyang, Liaoning 110819, China; School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China.
| | - Zhenning Wang
- Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, China; Institute of Health Sciences, China Medical University, Shenyang, Liaoning 110122, China; The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China.
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11
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Boselli D, Clemente F, Di Terlizzi S, Pagiatakis C, Papa L, Del Zotto G, Villa C, Ramirez GA, Maugeri N, Manfredi AA, Anselmo A. Unravelling Plasma Extracellular Vesicle Diversity With Optimised Spectral Flow Cytometry. JOURNAL OF EXTRACELLULAR BIOLOGY 2025; 4:e70045. [PMID: 40292386 PMCID: PMC12025886 DOI: 10.1002/jex2.70045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 02/27/2025] [Accepted: 03/13/2025] [Indexed: 04/30/2025]
Abstract
Extracellular vesicles (EVs) are crucial for intercellular communication and are found in various biological fluids. The identification and immunophenotyping of such small particles continue to pose significant challenges. Here, we have developed a workflow for the optimisation of a next-generation panel for in-depth immunophenotyping of circulating plasma EVs using spectral flow cytometry. Our data collection followed a multistep optimisation phase for both instrument setup and 21-colour panel design, thus maximising fluorescent signal recovery. This spectral approach enabled the identification of novel EV subpopulations. Indeed, besides common EVs released by erythrocytes, platelets, leukocytes and endothelial cells, we observed rare and poorly known EV subsets carrying antigens related to cell activation or exhaustion. Notably, the unsupervised data analysis of major EV subsets revealed subpopulations expressing up to five surface antigens simultaneously. However, the majority of EVs expressed only a single surface antigen, suggesting they may not fully represent the phenotype of their parent cells. This is likely due to the small surface area or the biogenesis of EVs rather than antibody steric hindrance. Finally, we tested our workflow by analysing the plasma EV landscape in a cohort of systemic lupus erythematosus (SLE) patients. Interestingly, we observed a significant increase in CD54+ EVs, supporting the notion of elevated circulating ICAM under SLE conditions. To our knowledge, these are the first data highlighting the importance of a spectral flow cytometry approach in deciphering the heterogeneity of plasma EVs paving the way for the routine use of a high-dimensional immunophenotyping in EV research.
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Affiliation(s)
- Daniela Boselli
- Experimental Imaging Center, FRACTAL, Flow cytometry Resource, Advanced Cytometry Technical Applications LaboratoryIRCCS Ospedale San RaffaeleMilanItaly
| | - Francesca Clemente
- Experimental Imaging Center, FRACTAL, Flow cytometry Resource, Advanced Cytometry Technical Applications LaboratoryIRCCS Ospedale San RaffaeleMilanItaly
| | - Simona Di Terlizzi
- Experimental Imaging Center, FRACTAL, Flow cytometry Resource, Advanced Cytometry Technical Applications LaboratoryIRCCS Ospedale San RaffaeleMilanItaly
| | - Christina Pagiatakis
- Department of Cardiovascular MedicineIRCCS Humanitas Research HospitalRozzanoMilanItaly
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Laura Papa
- Department of Cardiovascular MedicineIRCCS Humanitas Research HospitalRozzanoMilanItaly
| | - Genny Del Zotto
- Department of Research and DiagnosticsIRCCS Istituto Giannina GasliniGenoaItaly
| | - Chiara Villa
- Experimental Imaging Center, FRACTAL, Flow cytometry Resource, Advanced Cytometry Technical Applications LaboratoryIRCCS Ospedale San RaffaeleMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
| | - Giuseppe Alvise Ramirez
- Unit of Immunology, Rheumatology, Allergy and Rare DiseasesIRCCS Ospedale San RaffaeleMilanItaly
- Division of Immunology, Transplantation and Infectious DiseasesIRCCS Ospedale San RaffaeleMilanItaly
| | - Norma Maugeri
- Università Vita‐Salute San RaffaeleMilanItaly
- Division of Immunology, Transplantation and Infectious DiseasesIRCCS Ospedale San RaffaeleMilanItaly
| | - Angelo A. Manfredi
- Università Vita‐Salute San RaffaeleMilanItaly
- Unit of Immunology, Rheumatology, Allergy and Rare DiseasesIRCCS Ospedale San RaffaeleMilanItaly
- Division of Immunology, Transplantation and Infectious DiseasesIRCCS Ospedale San RaffaeleMilanItaly
| | - Achille Anselmo
- Experimental Imaging Center, FRACTAL, Flow cytometry Resource, Advanced Cytometry Technical Applications LaboratoryIRCCS Ospedale San RaffaeleMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
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12
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Xiao L, Duan R, Liu W, Zhang C, Ma X, Xian M, Wang Q, Guo Q, Xiong W, Su P, Ye L, Li Y, Zhong L, Qian J, Lu Y, Zhao Z, Yi Q. Adoptively transferred tumor-specific IL-9-producing cytotoxic CD8 + T cells activate host CD4 + T cells to control tumors with antigen loss. NATURE CANCER 2025; 6:718-735. [PMID: 40181089 DOI: 10.1038/s43018-025-00935-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/19/2025] [Indexed: 04/05/2025]
Abstract
Host effector CD4+ T cells emerge as critical mediators for tumor regression but whether they can be activated by adoptively transferred CD8+ T cells remains unknown. We previously reported that adoptive transfer of interleukin 9 (IL-9)-producing cytotoxic CD8+ T (Tc9) cells achieved long-term control of tumor growth. Here, we demonstrate that murine tumor-specific Tc9 cells control the outgrowth of antigen-loss relapsed tumors by recruiting and activating host effector CD4+ T cells. Tc9 cells secreted IL-24 and recruited CCR7-expressing conventional type 2 dendritic cells (cDC2 cells) into tumor-draining lymph nodes to prime host CD4+ T cells against relapsed tumors. Host CD4+ T cell or cDC2 deficiency impaired the ability of Tc9 cells to control relapsed tumor outgrowth. Additionally, intratumoral IL24 expression correlates with cDC2 and CD4+ T cell gene signatures in human cancers and their expression is associated with better patient survival. This study reports a mechanism for activation of tumor-specific CD4+ T cells in vivo.
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Affiliation(s)
- Liuling Xiao
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA.
- First Affiliated Hospital, School of Basic Medicine, Chongqing Medical University, Chongqing, China.
| | - Rui Duan
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Wendao Liu
- The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Chuanchao Zhang
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Xingzhe Ma
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Miao Xian
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Qiang Wang
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Qi Guo
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Wei Xiong
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Pan Su
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Lingqun Ye
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Yabo Li
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Ling Zhong
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Jianfei Qian
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Yong Lu
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
| | - Zhongming Zhao
- The University of Texas MD Anderson Cancer Center, UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Qing Yi
- Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA.
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13
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Moshkelgosha S, Levy L, Safavi S, Karunagaran S, Wilson G, Renaud-Picard B, Madu G, Ramchandani R, Oliver J, Watanabe T, Bei KF, Joe B, Li Q, Huszti E, Cheung M, Hedley D, Yeung J, Keshavjee S, Martinu T, Juvet S. Emergence of a senescent and inflammatory pulmonary CD4 + T cell population prior to lung allograft failure. SCIENCE ADVANCES 2025; 11:eadp9052. [PMID: 40117366 PMCID: PMC11927631 DOI: 10.1126/sciadv.adp9052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 02/14/2025] [Indexed: 03/23/2025]
Abstract
Survival after lung transplantation is limited by chronic lung allograft dysfunction (CLAD), an alloimmune fibrotic process leading to death or retransplantation after a median of 6 years. Immunosuppression fails to prevent CLAD, suggesting the existence of drug-resistant alloimmune pathways. We used time-of-flight mass cytometry to identify cells enriched in the bronchoalveolar lavage of patients with subsequent acute lung allograft dysfunction (ALAD), a risk factor for CLAD. We show that CD4+CD57+PD1+ T cells emerge in stable patients, conferring risks for ALAD, CLAD, and death. These cells are senescent, secrete inflammatory cytokines, and fall into two oligoclonal subsets with putative cytotoxic and follicular helper functions. Last, they are associated with fibrosis in mouse and human lung allografts, where they localize near airway epithelium and B cells. Together, our findings reveal an inflammatory T cell population that predicts future lung allograft dysfunction and may represent a rational therapeutic target.
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Affiliation(s)
- Sajad Moshkelgosha
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Liran Levy
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Sheba Medical Center, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shahideh Safavi
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Barts Health NHS Trust, London, UK
| | - Sumiha Karunagaran
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Gavin Wilson
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Benjamin Renaud-Picard
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Nouvel Hôpital Civil, Strasbourg, France
| | - Goodness Madu
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Rashi Ramchandani
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Jillian Oliver
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Tatsuaki Watanabe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Thoracic Surgery, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ke Fan Bei
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Betty Joe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Qixuan Li
- Biostatistics Department, University Health Network, Toronto, ON, Canada
| | - Ella Huszti
- Biostatistics Department, University Health Network, Toronto, ON, Canada
| | - May Cheung
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - David Hedley
- Division of Medical Oncology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Jonathan Yeung
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Shaf Keshavjee
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Tereza Martinu
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- Division of Respirology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Stephen Juvet
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- Division of Respirology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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14
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Hauchamps P, Delandre S, Temmerman ST, Lin D, Gatto L. Visual Quality Control With CytoMDS , a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances. Cytometry A 2025; 107:177-186. [PMID: 40035132 DOI: 10.1002/cyto.a.24921] [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: 07/08/2024] [Revised: 12/09/2024] [Accepted: 01/30/2025] [Indexed: 03/05/2025]
Abstract
Quality Control (QC) of samples is an essential preliminary step in cytometry data analysis. Notably, the identification of potential batch effects and outlying samples is paramount to avoid mistaking these effects for true biological signals in downstream analyses. However, this task can prove to be delicate and tedious, especially for datasets with dozens of samples. Here, we present CytoMDS, a Bioconductor package implementing a dedicated method for low-dimensional representation of cytometry samples composed of marker expressions for up to millions of single cells. This method allows a global representation of all samples of a study, with one single point per sample, in such a way that projected distances can be visually interpreted. CytoMDS uses Earth Mover's Distance for assessing dissimilarities between multi-dimensional distributions of marker expression and Multi-Dimensional Scaling for low-dimensional projection of distances. Some additional visualization tools, both for projection quality diagnosis and for user interpretation of the projection coordinates, are also provided in the package. We demonstrate the strengths and advantages of CytoMDS for QC of cytometry data on three real biological datasets, revealing the presence of low-quality samples, batch effects, and biological signal between sample groups.
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Affiliation(s)
- Philippe Hauchamps
- Computational Biology and Bioinformatics, de Duve Institute UCLouvain, Woluwe-Saint-Lambert, Belgium
| | | | | | | | - Laurent Gatto
- Computational Biology and Bioinformatics, de Duve Institute UCLouvain, Woluwe-Saint-Lambert, Belgium
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15
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Kuett L, Bollhagen A, Tietscher S, Sobottka B, Eling N, Varga Z, Moch H, de Souza N, Bodenmiller B. Distant Metastases of Breast Cancer Resemble Primary Tumors in Cancer Cell Composition but Differ in Immune Cell Phenotypes. Cancer Res 2025; 85:15-31. [PMID: 39437149 DOI: 10.1158/0008-5472.can-24-1211] [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: 04/17/2024] [Revised: 07/02/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
Abstract
Breast cancer is the most commonly diagnosed cancer in women, with distant metastasis being the main cause of breast cancer-related deaths. Elucidating the changes in the tumor and immune ecosystems that are associated with metastatic disease is essential to improve understanding and ultimately treatment of metastasis. Here, we developed an in-depth, spatially resolved single-cell atlas of the phenotypic diversity of tumor and immune cells in primary human breast tumors and matched distant metastases, using imaging mass cytometry to analyze a total of 75 unique antibody targets. Although the same tumor cell phenotypes were typically present in primary tumors and metastatic sites, suggesting a strong founder effect of the primary tumor, their proportions varied between matched samples. Notably, the metastatic site did not influence tumor phenotype composition, except for the brain. Metastatic sites exhibited a lower number of immune cells overall but had a higher proportion of myeloid cells as well as exhausted and cytotoxic T cells. Myeloid cells showed distinct tissue-specific compositional signatures and increased presence of potentially matrix remodeling phenotypes in metastatic sites. This analysis of tumor and immune cell phenotypic composition of metastatic breast cancer highlights the heterogeneity of the disease within patients and across distant metastatic sites, indicating myeloid cells as the predominant immune modulators that could potentially be targeted at these sites. Significance: Multiplex imaging analysis of matched primary and metastatic breast tumors provides a phenotypic and spatial map of tumor microenvironments, revealing similar compositions of cancer cells and divergent immunologic features between matched samples.
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Affiliation(s)
- Laura Kuett
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Alina Bollhagen
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Sandra Tietscher
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Nils Eling
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
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16
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Arceneaux JS, Brockman AA, Khurana R, Chalkley MBL, Geben LC, Krbanjevic A, Vestal M, Zafar M, Weatherspoon S, Mobley BC, Ess KC, Ihrie RA. Multiparameter quantitative analyses of diagnostic cells in brain tissues from tuberous sclerosis complex. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2025; 108:35-54. [PMID: 38953209 PMCID: PMC11693778 DOI: 10.1002/cyto.b.22194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
The advent of high-dimensional imaging offers new opportunities to molecularly characterize diagnostic cells in disorders that have previously relied on histopathological definitions. One example case is found in tuberous sclerosis complex (TSC), a developmental disorder characterized by systemic growth of benign tumors. Within resected brain tissues from patients with TSC, detection of abnormally enlarged balloon cells (BCs) is pathognomonic for this disorder. Though BCs can be identified by an expert neuropathologist, little is known about the specificity and broad applicability of protein markers for these cells, complicating classification of proposed BCs identified in experimental models of this disorder. Here, we report the development of a customized machine learning pipeline (BAlloon IDENtifier; BAIDEN) that was trained to prospectively identify BCs in tissue sections using a histological stain compatible with high-dimensional cytometry. This approach was coupled to a custom 36-antibody panel and imaging mass cytometry (IMC) to explore the expression of multiple previously proposed BC marker proteins and develop a descriptor of BC features conserved across multiple tissue samples from patients with TSC. Here, we present a modular workflow encompassing BAIDEN, a custom antibody panel, a control sample microarray, and analysis pipelines-both open-source and in-house-and apply this workflow to understand the abundance, structure, and signaling activity of BCs as an example case of how high-dimensional imaging can be applied within human tissues.
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Affiliation(s)
- Jerome S. Arceneaux
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College
| | - Asa A. Brockman
- Department of Cell & Developmental Biology, Vanderbilt University
| | - Rohit Khurana
- Department of Cell & Developmental Biology, Vanderbilt University
| | | | | | - Aleksandar Krbanjevic
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center
| | | | | | - Sarah Weatherspoon
- Neuroscience Institute, Le Bonheur Children’s Hospital
- University of Tennessee Health Science Center
| | - Bret C. Mobley
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center
| | - Kevin C. Ess
- Department of Cell & Developmental Biology, Vanderbilt University
- Department of Pediatrics, Vanderbilt University Medical Center
- Department of Neurology, Vanderbilt University Medical Center
- Section of Child Neurology, University of Colorado Anschutz Medical Center
| | - Rebecca A. Ihrie
- Department of Cell & Developmental Biology, Vanderbilt University
- Department of Neurological Surgery, Vanderbilt University Medical Center
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17
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Davids MS, Lin KH, Mohamed AI, Munir T, Eyre TA. Measurable residual disease-driven treatment in first-line chronic lymphocytic leukaemia. Br J Haematol 2025; 206:33-43. [PMID: 39538975 DOI: 10.1111/bjh.19902] [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: 09/05/2024] [Accepted: 11/01/2024] [Indexed: 11/16/2024]
Abstract
The therapeutic paradigm for patients suffering from chronic lymphocytic leukaemia continues to rapidly evolve. Fixed duration therapies continue to develop using novel-novel non-chemotherapeutic combinations. B-cell lymphoma 2 (BCL2) inhibitors in combination with either anti-CD20 antibody or Bruton tyrosine kinase inhibitors are able to achieve deep responses. Levels of attained 'negative' measurable residual disease (MRD, also known as minimal residual disease) have been shown to predict survival outcomes in a number of settings, including following immunochemotherapy and BCL2-combinations. This review will outline the current data supporting fixed duration treatment approaches, the use of MRD in clinical practice, alongside the challenges and possibilities for MRD utility in the future.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Neoplasm, Residual
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Protein Kinase Inhibitors/therapeutic use
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Affiliation(s)
- M S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - K H Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - A I Mohamed
- Department of Haematology, Mid Yorkshire Teaching Hospitals NHS Trust, Wakefield, UK
| | - T Munir
- Department of Haematology, St James's University Hospital, Leeds, UK
| | - T A Eyre
- Department of Haematology, Churchill Hospital, Oxford, UK
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18
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Luo MX, Tan T, Trussart M, Poch A, Nguyen TMH, Speed TP, Hicks DG, Bandala-Sanchez E, Peng H, Chappaz S, Slade C, Utzschneider DT, Koldej RM, Ritchie D, Strasser A, Thijssen R, Ritchie ME, Tam CS, Lindeman GJ, Huang DCS, Lew TE, Anderson MA, Roberts AW, Teh CE, Gray DHD. Venetoclax dose escalation rapidly activates a BAFF/BCL-2 survival axis in chronic lymphocytic leukemia. Blood 2024; 144:2748-2761. [PMID: 39471335 PMCID: PMC11738032 DOI: 10.1182/blood.2024024341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 11/01/2024] Open
Abstract
ABSTRACT Venetoclax, a first-in-class BH3 mimetic drug that targets B-cell lymphoma-2 (BCL-2), has improved the outcomes of patients with chronic lymphocytic leukemia (CLL). Early measurements of the depth of the venetoclax treatment response, assessed by minimal residual disease, are strong predictors of long-term clinical outcomes. However, there are limited data on the early changes induced by venetoclax treatment that might inform strategies to improve responses. To address this gap, we conducted longitudinal mass cytometric profiling of blood cells from patients with CLL during the first 5 weeks of venetoclax monotherapy. At baseline, we resolved CLL heterogeneity at the single-cell level to define multiple subpopulations in all patients based on proliferative, metabolic, and cell survival proteins. Venetoclax induced a significant reduction in all CLL subpopulations and caused rapid upregulation of the prosurvival BCL-2, BCL-extra large, and mantle cell lymphoma-1 proteins in surviving cells, which had reduced sensitivity to the drug. In mouse models, the venetoclax-induced elevation of survival proteins in B cells and CLL-like cells that persisted was recapitulated, and genetic models demonstrated that extensive apoptosis and access to the B-cell cytokine, B-cell activating factor (BAFF), were essential. Accordingly, in patients with CLL who were treated with venetoclax or the anti-CD20 antibody obinutuzumab there was marked elevation in BAFF and an increase in prosurvival proteins in leukemic cells that persisted. Overall, these data highlight the rapid adaptation of CLL cells to targeted therapies through homeostatic factors and support cotargeting of cytokine signals to achieve deeper and more durable long-term responses.
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MESH Headings
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Sulfonamides/pharmacology
- Sulfonamides/administration & dosage
- Sulfonamides/therapeutic use
- Humans
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Proto-Oncogene Proteins c-bcl-2/genetics
- Animals
- Mice
- B-Cell Activating Factor/metabolism
- Antineoplastic Agents/therapeutic use
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/administration & dosage
- Cell Survival/drug effects
- Female
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Meng-Xiao Luo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Tania Tan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marie Trussart
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Annika Poch
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Thi Minh Hanh Nguyen
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Terence P. Speed
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Damien G. Hicks
- School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Melbourne, VIC, Australia
| | - Esther Bandala-Sanchez
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Hongke Peng
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Stéphane Chappaz
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Charlotte Slade
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel T. Utzschneider
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Rachel M. Koldej
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Australian Cancer Research Foundation Translational Research Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - David Ritchie
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Australian Cancer Research Foundation Translational Research Laboratory, The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Haematology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Rachel Thijssen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E. Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Constantine S. Tam
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Alfred Hospital, Melbourne, VIC, Australia
| | - Geoffrey J. Lindeman
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David C. S. Huang
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Thomas E. Lew
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mary Ann Anderson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Andrew W. Roberts
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, The Royal Melbourne Hospital, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Charis E. Teh
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Daniel H. D. Gray
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
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19
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Mazziotta F, Martin LE, Eagan DN, Bar M, Kinsella S, Paulson KG, Voillet V, Lahman MC, Hunter D, Schmitt TM, Duerkopp N, Yeung C, Tang TH, Gottardo R, Asano Y, Wilcox EC, Lee B, Zhang T, Lopedote P, Penter L, Wu CJ, Milano F, Greenberg PD, Chapuis AG. Acute Myeloid Leukemia Skews Therapeutic WT1-specific CD8 TCR-T Cells Towards an NK-like Phenotype that Compromises Function and Persistence. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.12.13.24318504. [PMID: 39763516 PMCID: PMC11702715 DOI: 10.1101/2024.12.13.24318504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2025]
Abstract
Acute myeloid leukemia (AML) that is relapsed and/or refractory post-allogeneic hematopoietic cell transplantation (HCT) is usually fatal. In a prior study, we demonstrated that AML relapse in high-risk patients was prevented by post-HCT immunotherapy with Epstein-Barr virus (EBV)-specific donor CD8+ T cells engineered to express a high-affinity Wilms Tumor Antigen 1 (WT1)-specific T-cell receptor (TTCR-C4). However, in the present study, infusion of EBV- or Cytomegalovirus (CMV)-specific TTCR-C4 did not clearly improve outcomes in fifteen patients with active disease post-HCT. TCRC4-transduced EBV-specific T cells persisted longer post-transfer than CMV-specific T cells. Persisting TTCR-C4 skewed towards dysfunctional natural killer-like terminal differentiation, distinct from the dominant exhaustion programs reported for T-cell therapies targeting solid tumors. In one patient with active AML post-HCT, a sustained TTCR-C4 effector-memory profile correlated with long-term TTCR-C4 persistence and disease control. These findings reveal complex mechanisms underlying AML-induced T-cell dysfunction, informing future therapeutic strategies for addressing post-HCT relapse.
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Affiliation(s)
- Francesco Mazziotta
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Lauren E. Martin
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Daniel N. Eagan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Merav Bar
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
- Bristol Myers Squibb
| | - Sinéad Kinsella
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kelly G. Paulson
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Miranda C. Lahman
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Daniel Hunter
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas M. Schmitt
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Natalie Duerkopp
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Cecilia Yeung
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tzu-Hao Tang
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Raphael Gottardo
- Biomedical Data Science Center, Lausanne University Hospital
- University of Lausanne, Lausanne, Switzerland
- Agora Translational Research Center, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yuta Asano
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elise C. Wilcox
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Bo Lee
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tianzi Zhang
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paolo Lopedote
- Department of Medicine, St. Elizabeth’s Medical Center, Boston University, Boston, MA, USA
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Berlin, Germany
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Filippo Milano
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutch Cancer Center, Seattle, WA, USA
| | - Philip D. Greenberg
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Immunology and Medicine, University of Washington, Seattle, WA, USA
| | - Aude G. Chapuis
- Program in Immunology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutch Cancer Center, Seattle, WA, USA
- Division of Medical Oncology, University of Washington, Seattle, WA, USA
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20
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Nachmany I, Nevo S, Edelheit S, Sarusi-Portuguez A, Friedlander G, Salame TM, Pavlov V, Yakubovsky O, Pencovich N. Myeloid derived suppressor cells mediate hepatocyte proliferation and immune suppression during liver regeneration following resection. Genes Immun 2024; 25:483-491. [PMID: 39488626 DOI: 10.1038/s41435-024-00303-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 10/06/2024] [Accepted: 10/22/2024] [Indexed: 11/04/2024]
Abstract
Liver regeneration following resection is a complex process relying on coordinated pathways and cell types in the remnant organ. Myeloid-Derived Suppressor Cells (MDSCs) have a role in liver regeneration-related angiogenesis but other roles they may play in this process remain to be elucidated. In this study, we sought to examine the effect of G-MDSCs on hepatocytes proliferation and immune modulation during liver regeneration. Global gene expression profiling of regenerating hepatocytes in mice with CD11b+Ly6G+ MDSCs (G-MDSCs) depletion revealed disrupted transcriptional progression from day one to day two after major liver resection. Key genes and pathways related to hepatocyte proliferation and immune response were differentially expressed upon MDSC depletion. Hepatocytes cellularity increased when co-cultured with G-MDSCs, or treated with amphiregulin, which G-MDSCs upregulate during regeneration. Cytometry by time-of-flight (CyTOF) analysis of the intra-liver immune milieu upon MDSC depletion during regeneration demonstrated increased natural killer cell proportions, alongside changes in other immune cell populations. Taken together, these results provide evidence that MDSCs contribute to early liver regeneration by promoting hepatocyte proliferation and modulating the intra-liver immune response, and illuminate the multifaceted role of MDSCs in liver regeneration.
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Affiliation(s)
- Ido Nachmany
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shir Nevo
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sarit Edelheit
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avital Sarusi-Portuguez
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer-Meir Salame
- Mass Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Vera Pavlov
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Oran Yakubovsky
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Niv Pencovich
- The Laboratory of Molecular Biology, Department of Surgery and Transplantation, Sheba Medical Center, Tel-Hashomer, Faculty of Medicine and Medical Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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21
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Tasis A, Papaioannou NE, Grigoriou M, Paschalidis N, Loukogiannaki C, Filia A, Katsiki K, Lamprianidou E, Papadopoulos V, Rimpa CM, Chatzigeorgiou A, Kourtzelis I, Gerasimou P, Kyprianou I, Costeas P, Liakopoulos P, Liapis K, Kolovos P, Chavakis T, Alissafi T, Kotsianidis I, Mitroulis I. Single-Cell Analysis of Bone Marrow CD8+ T Cells in Myeloid Neoplasms Reveals Pathways Associated with Disease Progression and Response to Treatment with Azacitidine. CANCER RESEARCH COMMUNICATIONS 2024; 4:3067-3083. [PMID: 39485042 PMCID: PMC11616010 DOI: 10.1158/2767-9764.crc-24-0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/13/2024] [Accepted: 10/29/2024] [Indexed: 11/03/2024]
Abstract
Immunophenotypic analysis identified a BM CD57+CXCR3+ subset of CD8+ T cells associated with response to AZA in patients with MDS and AML. Single-cell RNA sequencing analysis revealed that IFN signaling is linked to the response to treatment, whereas TGF-β signaling is associated with treatment failure, providing insights into new therapeutic approaches.
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Affiliation(s)
- Athanasios Tasis
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nikos E. Papaioannou
- Laboratory of Immune Regulation, Center of Basic Sciences, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Maria Grigoriou
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Nikolaos Paschalidis
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Catherine Loukogiannaki
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Anastasia Filia
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Laboratory of Autoimmunity and Inflammation, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Kyriaki Katsiki
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eleftheria Lamprianidou
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Vasileios Papadopoulos
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Maria Rimpa
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Chatzigeorgiou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Kourtzelis
- Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | | | - Ioannis Kyprianou
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | - Paul Costeas
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | - Panagiotis Liakopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos Liapis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
- National Center for Tumor Diseases, Partner Site Dresden, Dresden, Germany
| | - Themis Alissafi
- Laboratory of Immune Regulation, Center of Basic Sciences, Biomedical Research Foundation Academy of Athens, Athens, Greece
- Laboratory of Biology, School of Medicine, Athens, Greece
| | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Mitroulis
- Translational Research and Laboratory Medicine Unit, First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
- National Center for Tumor Diseases, Partner Site Dresden, Dresden, Germany
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22
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Liu P, Pan Y, Chang HC, Wang W, Fang Y, Xue X, Zou J, Toothaker JM, Olaloye O, Santiago EG, McCourt B, Mitsialis V, Presicce P, Kallapur SG, Snapper SB, Liu JJ, Tseng GC, Konnikova L, Liu S. Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating. Brief Bioinform 2024; 26:bbae633. [PMID: 39656848 PMCID: PMC11630031 DOI: 10.1093/bib/bbae633] [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: 08/13/2024] [Revised: 11/13/2024] [Accepted: 11/25/2024] [Indexed: 12/17/2024] Open
Abstract
Cytometry is an advanced technique for simultaneously identifying and quantifying many cell surface and intracellular proteins at a single-cell resolution. Analyzing high-dimensional cytometry data involves identifying and quantifying cell populations based on their marker expressions. This study provided a quantitative review and comparison of various ways to phenotype cellular populations within the cytometry data, including manual gating, unsupervised clustering, and supervised auto-gating. Six datasets from diverse species and sample types were included in the study, and manual gating with two hierarchical layers was used as the truth for evaluation. For manual gating, results from five researchers were compared to illustrate the gating consistency among different raters. For unsupervised clustering, 23 tools were quantitatively compared in terms of accuracy with the truth and computing cost. While no method outperformed all others, several tools, including PAC-MAN, CCAST, FlowSOM, flowClust, and DEPECHE, generally demonstrated strong performance. For supervised auto-gating methods, four algorithms were evaluated, where DeepCyTOF and CyTOF Linear Classifier performed the best. We further provided practical recommendations on prioritizing gating methods based on different application scenarios. This study offers comprehensive insights for biologists to understand diverse gating methods and choose the best-suited ones for their applications.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Yuchen Pan
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX 77030, US
| | - Hung-Ching Chang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Wenjia Wang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Yusi Fang
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Xiangning Xue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Jian Zou
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
| | - Jessica M Toothaker
- Department of Immunology, University of Pittsburgh, 5051 Centre Avenue, Pittsburgh, PA 15213, US
- Department of Pediatrics, Yale University, 15 York Street New Haven, CT 06510, US
| | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale University, 15 York Street New Haven, CT 06510, US
| | | | - Black McCourt
- Department of Pediatrics, Yale University, 15 York Street New Haven, CT 06510, US
| | - Vanessa Mitsialis
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, US
- Department of Medicine, Division of Gastroenterology, Hepatology, and Endoscopy, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, US
| | - Pietro Presicce
- Division of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California Los Angeles, 757 Westwood Plaza, Los Angeles, CA 90095, US
| | - Suhas G Kallapur
- Division of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California Los Angeles, 757 Westwood Plaza, Los Angeles, CA 90095, US
| | - Scott B Snapper
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, US
- Department of Medicine, Division of Gastroenterology, Hepatology, and Endoscopy, Brigham & Women’s Hospital and Department of Medicine, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, US
| | - Jia-Jun Liu
- Drug Discovery Institute, School of Medicine, University of Pittsburgh, 700 Technology Dr, Pittsburgh, PA 15219, US
- Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261, US
| | - George C Tseng
- Department of Biostatistics, School of Public Health, University of Pittsburgh, 130 De Soto St., Pittsburgh, PA 15261, US
- Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, US
| | - Liza Konnikova
- Department of Pediatrics, Yale University, 15 York Street New Haven, CT 06510, US
- Division of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California Los Angeles, 757 Westwood Plaza, Los Angeles, CA 90095, US
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, 333 Cedar Street, New Haven, CT 06510, US
- Department of Immunobiology, Yale University, 300 Cedar Street, New Haven, CT 06520, US
- Program in Human and Translational Immunology, Yale University, 300 Cedar Street, New Haven, CT 06520, US
- Program in Translational Biomedicine, Yale University, 300 Cedar Street, New Haven, CT 06520, US
- Center for Systems and Engineering Immunology, Yale University, 100 College St., New Haven, CT 06510, US
| | - Silvia Liu
- Drug Discovery Institute, School of Medicine, University of Pittsburgh, 700 Technology Dr, Pittsburgh, PA 15219, US
- Pittsburgh Liver Research Center, School of Medicine, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15261, US
- Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15213, US
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, 200 Lothrop St., Pittsburgh, PA 15261, US
- Hillman Cancer Center, University of Pittsburgh, 5150 Centre Ave., Pittsburgh, PA 15232, US
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23
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Huang SW, Jiang W, Xu S, Zhang Y, Du J, Wang YQ, Yang KY, Zhang N, Liu F, Zou GR, Jin F, Wu HJ, Zhou YY, Zhu XD, Chen NY, Xu C, Qiao H, Liu N, Sun Y, Ma J, Liang YL, Liu X. Systemic longitudinal immune profiling identifies proliferating Treg cells as predictors of immunotherapy benefit: biomarker analysis from the phase 3 CONTINUUM and DIPPER trials. Signal Transduct Target Ther 2024; 9:285. [PMID: 39438442 PMCID: PMC11496634 DOI: 10.1038/s41392-024-01988-w] [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: 03/19/2024] [Revised: 09/09/2024] [Accepted: 09/24/2024] [Indexed: 10/25/2024] Open
Abstract
The identification of predictors for immunotherapy is often hampered by the absence of control groups in many studies, making it difficult to distinguish between prognostic and predictive biomarkers. This study presents biomarker analyses from the phase 3 CONTINUUM trial (NCT03700476), the first to show that adding anti-PD-1 (aPD1) to chemoradiotherapy (CRT) improves event-free survival (EFS) in patients with locoregionally advanced nasopharyngeal carcinoma. A dynamic single-cell atlas was profiled using mass cytometry on peripheral blood mononuclear cell samples from 12 pairs of matched relapsing and non-relapsing patients in the aPD1-CRT arm. Using a supervised representation learning algorithm, we identified a Ki67+ proliferating regulatory T cells (Tregs) population expressing high levels of activated and immunosuppressive molecules including FOXP3, CD38, HLA-DR, CD39, and PD-1, whose abundance correlated with treatment outcome. The frequency of these Ki67+ Tregs was significantly higher at baseline and increased during treatment in patients who relapsed compared to non-relapsers. Further validation through flow cytometry (n = 120) confirmed the predictive value of this Treg subset. Multiplex immunohistochemistry (n = 249) demonstrated that Ki67+ Tregs in tumors could predict immunotherapy benefit, with aPD1 improving EFS only in patients with low baseline levels of Ki67+ Tregs. These findings were further validated in the multicenter phase 3 DIPPER trial (n = 262, NCT03427827) and the phase 3 OAK trial of anti-PD-L1 immunotherapy in NSCLC, underscoring the predictive value of Ki67+ Treg frequency in identifying the beneficiaries of immunotherapy and potentially guiding personalized treatment strategies.
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Affiliation(s)
- Sai-Wei Huang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Wei Jiang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Sha Xu
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yuan Zhang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Juan Du
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ya-Qin Wang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Kun-Yu Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Ning Zhang
- Department of Radiation Oncology, The First People's Hospital of Foshan, Foshan, PR China
| | - Fang Liu
- Department of Pathology, The First People's Hospital of Foshan, Foshan, PR China
| | - Guo-Rong Zou
- Department of Oncology, Panyu Central Hospital, Guangzhou, PR China
| | - Feng Jin
- Department of Oncology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, PR China
| | - Hai-Jun Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, PR China
| | - Yang-Ying Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, PR China
| | - Xiao-Dong Zhu
- Department of Radiation Oncology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, PR China
| | - Nian-Yong Chen
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, PR China
| | - Cheng Xu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Han Qiao
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Na Liu
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ying Sun
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jun Ma
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Ye-Lin Liang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Xu Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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24
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Hunewald O, Demczuk A, Longworth J, Ollert M. CyCadas: accelerating interactive annotation and analysis of clustered cytometry data. Bioinformatics 2024; 40:btae595. [PMID: 39374546 PMCID: PMC11488975 DOI: 10.1093/bioinformatics/btae595] [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: 02/24/2024] [Revised: 06/19/2024] [Accepted: 10/03/2024] [Indexed: 10/09/2024] Open
Abstract
MOTIVATION Single cell profiling by cytometry has emerged as a key technology in biology, immunology and clinical-translational medicine. The correct annotation, which refers to the identification of clusters as specific cell populations based on their marker expression, of clustered high-dimensional cytometry data, is a critical step of the analysis. Its accuracy determines the correct interpretation of the biological data. Despite the progress in various clustering algorithms, the annotation of clustered data still remains a manual, time consuming and error-prone task. We developed a user-friendly cluster annotation and differential abundance detection tool that can be applied on data generated with Self Organizing Map clustering algorithms, thus simplifying the annotation process of datasets that consist of hundreds or thousands of clusters. RESULTS We present Cytometry Cluster Annotation and Differential Abundance Suite (CyCadas), a semi-automated software tool that facilitates cluster annotation in cytometry data by offering both visual and computational guidance. CyCadas addresses the critical need for efficient and accurate annotation of high-resolution clustered cytometry data, significantly reducing the time needed to perform the analysis compared to both manual gating approaches and manual annotation of clustered data. The tool features a user-friendly interface, visual tools enabling data exploration and automated threshold estimation to separate negative and positive marker expression. It facilitates the definition and annotation of cell phenotypes among multiple clusters in a tree-based data structure. Finally, it calculates the abundance of various cell populations across the conditions with statistical interpretation. It is an ideal resource for researchers aiming to streamline their cytometry workflow. AVAILABILITY AND IMPLEMENTATION CyCadas is available as open source at: https://github.com/DII-LIH-Luxembourg/cycadas.
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Affiliation(s)
- Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
- Bioinformatics & AI, Department of Medical Informatics, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Agnieszka Demczuk
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Joseph Longworth
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
- Immunology & Genetics, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Centre, Odense University Hospital, 5000 Odense, Denmark
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25
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Makatsa MS, Kus A, Wiedeman A, Long SA, Seshadri C. 42-parameter mass cytometry panel to assess cellular and functional phenotypes of leukocytes in bronchoalveolar lavage of Rhesus macaque. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613973. [PMID: 39386621 PMCID: PMC11463637 DOI: 10.1101/2024.09.19.613973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
This Optimized Multiparameter Immunofluorescence Panel (OMIP) reports on the development of a mass cytometry panel for broad immunophenotyping of leukocytes from bronchoalveolar lavage from rhesus macaques. Using this panel, we were able to identify myeloid populations such as macrophages, neutrophils, monocytes, myeloid and plasmacytoid DCs, basophils and lymphoid cell lineages including B cells, natural killer (NK) cells, mucosal associated invariant T (MAIT) cells, γδ T cells, CD4 T cells, CD8 β T cells, CD8 T cells, and innate lymphoid cells (ILCs). We also included markers for defining memory, differentiation (CCR7, CD28, CD45RA), homing potential (CXCR3), cytotoxic potential (perforin, granzyme B, granzyme K), cell activation/differentiation (HLA-DR, CD69, IgD) and effector function (CD154, IFN-γ, TNF, IL-2, IL-17A, IL-6, IL-1β, CCL4 and CD107a). This panel was optimized on cryopreserved, bronchoalveolar lavage and splenocytes collected from rhesus macaques. The antibodies selected in this panel are human-specific antibodies that have been shown to cross-react with non-human primates except for CD45 clone D058-1283 which is specific for non-human primates.
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Affiliation(s)
- Mohau S. Makatsa
- Department of Medicine, University of Washington School of Medicine, Seattle, USA
| | - Anna Kus
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Alice Wiedeman
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - S. Alice Long
- Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, USA
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26
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Régnier P, Montardi C, Maciejewski-Duval A, Marques C, Saadoun D. PUPAID: A R + ImageJ pipeline for thorough and semi-automated processing and analysis of multi-channel immunofluorescence data. PLoS One 2024; 19:e0308970. [PMID: 39298534 DOI: 10.1371/journal.pone.0308970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/02/2024] [Indexed: 09/22/2024] Open
Abstract
PUPAID is a workflow written in R + ImageJ languages which is dedicated to the semi-automated processing and analysis of multi-channel immunofluorescence data. The workflow is designed to extract fluorescence signals within automatically-segmented cells, defined here as Areas of Interest (AOI), on whole multi-layer slides (or eventually cropped sections of them), defined here as Regions of Interest (ROI), in a simple and understandable yet thorough manner. The included (but facultative) R Shiny-based interactive application makes PUPAID also suitable for scientists who are not fluent with R programming. Furthermore, we show that PUPAID identifies significantly more cells, especially in high-density regions, as compared to already published state-of-the-art methods such as StarDist or Cellpose. For extended possibilities and downstream compatibility, single cell information is exported as FCS files (the standardized file format for single cell-based cytometry data) in order to be openable using any third-party cytometry analysis software or any analysis workflow which takes FCS files as input.
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Affiliation(s)
- Paul Régnier
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France
- Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Camille Montardi
- Département de Médecine Interne, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Saclay, Boulogne-Billancourt, France
| | - Anna Maciejewski-Duval
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France
- Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Cindy Marques
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France
- Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Département de Médecine Interne et Immunologie Clinique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France
- Centre National de Référence Maladies Autoimmunes Systémiques Rares, Centre National de Référence Maladies Autoinflammatoires et Amylose Inflammatoire, Inflammation-Immunopathology-Biotherapy Department (DMU 3iD), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France
| | - David Saadoun
- Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France
- Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Département de Médecine Interne et Immunologie Clinique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France
- Centre National de Référence Maladies Autoimmunes Systémiques Rares, Centre National de Référence Maladies Autoinflammatoires et Amylose Inflammatoire, Inflammation-Immunopathology-Biotherapy Department (DMU 3iD), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France
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27
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Arekatla G, Skylaki S, Corredor Suarez D, Jackson H, Schapiro D, Engler S, Auler M, Camargo Ortega G, Hastreiter S, Reimann A, Loeffler D, Bodenmiller B, Schroeder T. Identification of an embryonic differentiation stage marked by Sox1 and FoxA2 co-expression using combined cell tracking and high dimensional protein imaging. Nat Commun 2024; 15:7860. [PMID: 39251590 PMCID: PMC11385471 DOI: 10.1038/s41467-024-52069-z] [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: 05/31/2023] [Accepted: 08/26/2024] [Indexed: 09/11/2024] Open
Abstract
Pluripotent mouse embryonic stem cells (ESCs) can differentiate to all germ layers and serve as an in vitro model of embryonic development. To better understand the differentiation paths traversed by ESCs committing to different lineages, we track individual differentiating ESCs by timelapse imaging followed by multiplexed high-dimensional Imaging Mass Cytometry (IMC) protein quantification. This links continuous live single-cell molecular NANOG and cellular dynamics quantification over 5-6 generations to protein expression of 37 different molecular regulators in the same single cells at the observation endpoints. Using this unique data set including kinship history and live lineage marker detection, we show that NANOG downregulation occurs generations prior to, but is not sufficient for neuroectoderm marker Sox1 upregulation. We identify a developmental cell type co-expressing both the canonical Sox1 neuroectoderm and FoxA2 endoderm markers in vitro and confirm the presence of such a population in the post-implantation embryo. RNASeq reveals cells co-expressing SOX1 and FOXA2 to have a unique cell state characterized by expression of both endoderm as well as neuroectoderm genes suggesting lineage potential towards both germ layers.
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Affiliation(s)
- Geethika Arekatla
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Neurosciences, Leuven Brain Institute (LBI), KU Leuven - University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB Center for Brain & Disease Research, Leuven, Belgium
| | - Stavroula Skylaki
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hartland Jackson
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Health Systems; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Denis Schapiro
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
- Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Translational Spatial Profiling Center (TSPC), Heidelberg, Germany
| | - Stefanie Engler
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Markus Auler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Simon Hastreiter
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Reimann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology and Laboratory Medicine, The University of Tennessee, Memphis, TN, USA
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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28
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Church EC, Bishop E, Fiore-Gartland A, Yu KKQ, Chang M, Jones RM, Brache JK, Ballweber Fleming L, Phan JM, Makatsa MS, Heptinstall J, Chiong K, Dintwe O, Naidoo A, Voillet V, Mayer-Blackwell K, Nwanne G, Andersen-Nissen E, Vary JC, Tomaras GD, McElrath MJ, Sherman DR, Murphy SC, Kublin JG, Seshadri C. Probing Dermal Immunity to Mycobacteria through a Controlled Human Infection Model. Immunohorizons 2024; 8:695-711. [PMID: 39283647 PMCID: PMC11447685 DOI: 10.4049/immunohorizons.2400053] [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: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 09/22/2024] Open
Abstract
Cutaneous mycobacterial infections cause substantial morbidity and are challenging to diagnose and treat. An improved understanding of the dermal immune response to mycobacteria may inspire new therapeutic approaches. We conducted a controlled human infection study with 10 participants who received 2 × 106 CFUs of Mycobacterium bovis bacillus Calmette-Guérin (Tice strain) intradermally and were randomized to receive isoniazid or no treatment. Peripheral blood was collected at multiple time points for flow cytometry, bulk RNA sequencing (RNA-seq), and serum Ab assessments. Systemic immune responses were detected as early as 8 d postchallenge in this M. bovis bacillus Calmette-Guérin-naive population. Injection-site skin biopsies were performed at days 3 and 15 postchallenge and underwent immune profiling using mass cytometry and single-cell RNA-seq, as well as quantitative assessments of bacterial viability and burden. Molecular viability testing and standard culture results correlated well, although no differences were observed between treatment arms. Single-cell RNA-seq revealed various immune and nonimmune cell types in the skin, and communication between them was inferred by ligand-receptor gene expression. Day 3 communication was predominantly directed toward monocytes from keratinocyte, muscle, epithelial, and endothelial cells, largely via the migration inhibitory factor pathway and HLA-E-KLRK1 interaction. At day 15, communication was more balanced between cell types. These data reveal the potential role of nonimmune cells in the dermal immune response to mycobacteria and the utility of human challenge studies to augment our understanding of mycobacterial infections.
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Affiliation(s)
- E. Chandler Church
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Seattle-King County Public Health, Seattle, WA
| | - Emma Bishop
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | | | - Krystle K. Q. Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Ming Chang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - Richard M. Jones
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Justin K. Brache
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | | | - Jolie M. Phan
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Mohau S. Makatsa
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Jack Heptinstall
- Duke Center for Human Systems Immunology, Duke University, Durham, NC
| | - Kelvin Chiong
- Duke Center for Human Systems Immunology, Duke University, Durham, NC
| | - One Dintwe
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Anneta Naidoo
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Valentin Voillet
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | | | - Gift Nwanne
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Cape Town HVTN Immunology Laboratory, Hutchinson Centre Research Institute of South Africa, Cape Town, South Africa
| | - Jay C. Vary
- Department of Dermatology, University of Washington School of Medicine, Seattle, WA
| | | | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - David R. Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA
| | - Sean C. Murphy
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
| | - James G. Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
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29
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Priest DG, Ebihara T, Tulyeu J, Søndergaard JN, Sakakibara S, Sugihara F, Nakao S, Togami Y, Yoshimura J, Ito H, Onishi S, Muratsu A, Mitsuyama Y, Ogura H, Oda J, Okusaki D, Matsumoto H, Wing JB. Atypical and non-classical CD45RB lo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19. Nat Commun 2024; 15:6811. [PMID: 39122676 PMCID: PMC11315995 DOI: 10.1038/s41467-024-50997-4] [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: 11/27/2023] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Resting memory B cells can be divided into classical or atypical groups, but the heterogenous marker expression on activated memory B cells makes similar classification difficult. Here, by longitudinal analysis of mass cytometry and CITE-seq data from cohorts with COVID-19, bacterial sepsis, or BNT162b2 mRNA vaccine, we observe that resting B cell memory consist of classical CD45RB+ memory and CD45RBlo memory, of which the latter contains of two distinct groups of CD11c+ atypical and CD23+ non-classical memory cells. CD45RB levels remain stable in these cells after activation, thereby enabling the tracking of activated B cells and plasmablasts derived from either CD45RB+ or CD45RBlo memory B cells. Moreover, in both COVID-19 patients and mRNA vaccination, CD45RBlo B cells formed the majority of SARS-CoV2 specific memory B cells and correlated with serum antibodies, while CD45RB+ memory are activated by bacterial sepsis. Our results thus identify that stably expressed CD45RB levels can be exploited to trace resting memory B cells and their activated progeny, and suggest that atypical and non-classical CD45RBlo memory B cells contribute to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- David G Priest
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan
| | - Takeshi Ebihara
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Janyerkye Tulyeu
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jonas N Søndergaard
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, IFReC, Osaka University, Suita, Osaka, 563-0793, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, 532-0003, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
- Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
| | - Shunichiro Nakao
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ito
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shinya Onishi
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Arisa Muratsu
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yumi Mitsuyama
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, 558-8558, Japan
| | - Hiroshi Ogura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jun Oda
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okusaki
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Human Immunology (Single Cell Genomics), WPI-IFReC, Osaka University, Suita, 565-0871, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, 565-0871, Japan
| | - Hisatake Matsumoto
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - James B Wing
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan.
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan.
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30
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Gross NE, Zhang Z, Mitchell JT, Charmsaz S, Hernandez AG, Coyne EM, Shin SM, Vargas Carvajal DC, Sidiropoulos DN, Cho Y, Mo G, Yuan X, Cannon C, Suresh Babu J, Lyman MR, Armstrong T, Kagohara LT, Bever KM, Le DT, Jaffee EM, Fertig EJ, Ho WJ. Phosphodiesterase-5 inhibition collaborates with vaccine-based immunotherapy to reprogram myeloid cells in pancreatic ductal adenocarcinoma. JCI Insight 2024; 9:e179292. [PMID: 39106104 PMCID: PMC11457845 DOI: 10.1172/jci.insight.179292] [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: 01/21/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly lethal and resistant to immunotherapy. Although immune recognition can be enhanced with immunomodulatory agents including checkpoint inhibitors and vaccines, few patients experience clinical efficacy because the tumor immune microenvironment (TiME) is dominated by immunosuppressive myeloid cells that impose T cell inhibition. Inhibition of phosphodiesterase-5 (PDE5) was reported to downregulate metabolic regulators arginase and inducible NOS in immunosuppressive myeloid cells and enhance immunity against immune-sensitive tumors, including head and neck cancers. We show for the first time to our knowledge that combining a PDE5 inhibitor, tadalafil, with a mesothelin-specific vaccine, anti-programmed cell death protein 1, and anti-cytotoxic T lymphocyte-associated protein 4 yields antitumor efficacy even against immune-resistant PDAC. To determine immunologic advantages conferred by tadalafil, we profiled the TiME using mass cytometry and single-cell RNA-sequencing analysis with Domino to infer intercellular signaling. Our analyses demonstrated that tadalafil reprograms myeloid cells to be less immunosuppressive. Moreover, tadalafil synergized with the vaccine, enhancing T cell activation including mesothelin-specific T cells. Tadalafil treatment was also associated with myeloid/T cell signaling axes important for antitumor responses (e.g., Cxcr3, Il12). Our study shows that PDE5 inhibition combined with vaccine-based immunotherapy promotes pro-inflammatory states of myeloid cells, activation of T cells, and enhanced myeloid/T cell crosstalk to yield antitumor efficacy against immune-resistant PDAC.
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Affiliation(s)
- Nicole E. Gross
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Zhehao Zhang
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
| | - Jacob T. Mitchell
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
- Department of Genetic Medicine
| | - Soren Charmsaz
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | | | - Erin M. Coyne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Sarah M. Shin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | | | | | - Yeonju Cho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Guanglan Mo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Xuan Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
| | - Courtney Cannon
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
| | | | - Melissa R. Lyman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Todd Armstrong
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
| | - Luciane T. Kagohara
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
| | - Katherine M. Bever
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Bloomberg-Kimmel Institute for Cancer Immunotherapy; and
| | - Dung T. Le
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Bloomberg-Kimmel Institute for Cancer Immunotherapy; and
| | - Elizabeth M. Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
- Bloomberg-Kimmel Institute for Cancer Immunotherapy; and
| | - Elana J. Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
- Department of Genetic Medicine
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
| | - Won Jin Ho
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center
- Convergence Institute
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31
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Wilson GE, Knight J, Liu Q, Shelar A, Stewart E, Wang X, Yan X, Sanders J, Visness C, Gill M, Gruchalla R, Liu AH, Kattan M, Khurana Hershey GK, Togias A, Becker PM, Altman MC, Busse WW, Jackson DJ, Montgomery RR, Chupp GL. Activated sputum eosinophils associated with exacerbations in children on mepolizumab. J Allergy Clin Immunol 2024; 154:297-307.e13. [PMID: 38485057 PMCID: PMC11305967 DOI: 10.1016/j.jaci.2024.01.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND MUPPITS-2 was a randomized, placebo-controlled clinical trial that demonstrated mepolizumab (anti-IL-5) reduced exacerbations and blood and airway eosinophils in urban children with severe eosinophilic asthma. Despite this reduction in eosinophilia, exacerbation risk persisted in certain patients treated with mepolizumab. This raises the possibility that subpopulations of airway eosinophils exist that contribute to breakthrough exacerbations. OBJECTIVE We aimed to determine the effect of mepolizumab on airway eosinophils in childhood asthma. METHODS Sputum samples were obtained from 53 MUPPITS-2 participants. Airway eosinophils were characterized using mass cytometry and grouped into subpopulations using unsupervised clustering analyses of 38 surface and intracellular markers. Differences in frequency and immunophenotype of sputum eosinophil subpopulations were assessed based on treatment arm and frequency of exacerbations. RESULTS Median sputum eosinophils were significantly lower among participants treated with mepolizumab compared with placebo (58% lower, 0.35% difference [95% CI 0.01, 0.74], P = .04). Clustering analysis identified 3 subpopulations of sputum eosinophils with varied expression of CD62L. CD62Lint and CD62Lhi eosinophils exhibited significantly elevated activation marker and eosinophil peroxidase expression, respectively. In mepolizumab-treated participants, CD62Lint and CD62Lhi eosinophils were more abundant in participants who experienced exacerbations than in those who did not (100% higher for CD62Lint, 0.04% difference [95% CI 0.0, 0.13], P = .04; 93% higher for CD62Lhi, 0.21% difference [95% CI 0.0, 0.77], P = .04). CONCLUSIONS Children with eosinophilic asthma treated with mepolizumab had significantly lower sputum eosinophils. However, CD62Lint and CD62Lhi eosinophils were significantly elevated in children on mepolizumab who had exacerbations, suggesting that eosinophil subpopulations exist that contribute to exacerbations despite anti-IL-5 treatment.
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Affiliation(s)
- Gabriella E Wilson
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn
| | - James Knight
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Conn
| | - Qing Liu
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn
| | - Ashish Shelar
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Conn
| | - Emma Stewart
- Committee on Immunology, University of Chicago, Chicago, Ill
| | - Xiaomei Wang
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn
| | - Xiting Yan
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn
| | | | | | - Michelle Gill
- Department of Pediatric Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, Mo
| | - Rebecca Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Andrew H Liu
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colo
| | - Meyer Kattan
- Department of Pediatric Pulmonology, Columbia University Irving Medical Center, New York, NY
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | | | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn
| | - Geoffrey L Chupp
- Department of Internal Medicine, Yale School of Medicine, New Haven, Conn.
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Cai A, Meng Y, Zhou H, Cai H, Shao X, Wang Q, Xu Y, Zhou Y, Zhou W, Chen L, Mou S. Podocyte Pathogenic Bone Morphogenetic Protein-2 Pathway and Immune Cell Behaviors in Primary Membranous Nephropathy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404151. [PMID: 38785168 PMCID: PMC11304328 DOI: 10.1002/advs.202404151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Primary membranous nephropathy (PMN) is one of the leading causes of end-stage renal disease, and the most frequent cause of massive proteinuria in nondiabetic adults, resulting in fatal complications. However, the underlying pathomechanisms of PMN remain largely unclear. Here, single-cell RNA sequencing is employed to analyze kidney biopsies from eleven PMN patients and seven healthy subjects. Profiling 44 060 cells from patients allowed us to characterize the cellular composition and cell-type-specific gene expression in the PMN kidney. The complement-induced BMP2/pSMAD1/COL4 pathway is identified as the pathogenic pathway in podocytes, bridging two key events, i.e., complement system activation and glomerular basement membrane thickening in PMN. Augmented infiltration and activation of myeloid leukocytes and B lymphocytes are found, profiling delicate crosstalk of immune cells in PMN kidneys. Overall, these results provide valuable insights into the roles of podocytes and immune cells in PMN, and comprehensive resources toward the complete understanding of PMN pathophysiology.
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Affiliation(s)
- Anxiang Cai
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yiwei Meng
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- Institute of Molecular Medicine, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Hang Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Hong Cai
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Xinghua Shao
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qin Wang
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yao Xu
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yin Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Wenyan Zhou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai200031China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- School of Life Science and TechnologyShanghai Tech UniversityShanghai201210China
| | - Shan Mou
- Department of Nephrology, Ren Ji Hospital, School of MedicineShanghai Jiao Tong UniversityShanghai200127China
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Wai KC, Okholm TLH, Ha PK, Marquez DM, Tenvooren I, Jones KB, Spitzer MH. The tumor microenvironment of benign and malignant salivary gland tumors. Head Neck 2024; 46:1625-1636. [PMID: 38454566 DOI: 10.1002/hed.27716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/08/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Treatment of salivary gland tumors (SGTs) remains challenging. Little is known about the immune landscape of SGTs. We aimed to characterize the tumor microenvironment in benign and malignant SGTs. METHODS Eleven benign and nine malignant tumors were collected from patients undergoing curative intent surgery. Specimens were analyzed using mass cytometry by time-of-flight. Immune cell populations were manually gated, and T cells were clustered using the FlowSOM algorithm. Population frequencies were compared between high-grade and low-grade malignancies, corrected for multiple hypothesis testing. RESULTS There were trends towards increased CD4+ and CD8+ T cells among malignant tumors. High-grade malignancies exhibited trends towards higher frequencies of CD8+ PD-1+ CD39+ CD103+ exhausted T cells, CD4+ FoxP3+ TCF-1+ CD127- Tregs, and CD69+ CD25- CD4+ T cells compared to low-grade malignancies. CONCLUSION SGTs exhibit significant immunologic diversity. High-grade malignancies tended to have greater infiltration of exhausted CD8+ T cells and Tregs, which may guide future studies for immunotherapy strategies.
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Affiliation(s)
- Katherine C Wai
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Trine Line H Okholm
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Patrick K Ha
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Diana M Marquez
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Iliana Tenvooren
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Kyle B Jones
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
- Pharma Technical Cell and Gene Therapy, Genentech, Inc., South San Francisco, California, USA
| | - Matthew H Spitzer
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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Law C, Wacleche VS, Cao Y, Pillai A, Sowerby J, Hancock B, Horisberger A, Bracero S, Skidanova V, Li Z, Adejoorin I, Dillon E, Benque IJ, Nunez DP, Simmons DP, Keegan J, Chen L, Baker T, Brohawn PZ, Al-Mossawi H, Hao LY, Jones B, Rao N, Qu Y, Alves SE, Jonsson AH, Shaw KS, Vleugels RA, Massarotti E, Costenbader KH, Brenner MB, Lederer JA, Hultquist JF, Choi J, Rao DA. Interferon subverts an AHR-JUN axis to promote CXCL13 + T cells in lupus. Nature 2024; 631:857-866. [PMID: 38987586 PMCID: PMC11628166 DOI: 10.1038/s41586-024-07627-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/30/2024] [Indexed: 07/12/2024]
Abstract
Systemic lupus erythematosus (SLE) is prototypical autoimmune disease driven by pathological T cell-B cell interactions1,2. Expansion of T follicular helper (TFH) and T peripheral helper (TPH) cells, two T cell populations that provide help to B cells, is a prominent feature of SLE3,4. Human TFH and TPH cells characteristically produce high levels of the B cell chemoattractant CXCL13 (refs. 5,6), yet regulation of T cell CXCL13 production and the relationship between CXCL13+ T cells and other T cell states remains unclear. Here, we identify an imbalance in CD4+ T cell phenotypes in patients with SLE, with expansion of PD-1+/ICOS+ CXCL13+ T cells and reduction of CD96hi IL-22+ T cells. Using CRISPR screens, we identify the aryl hydrocarbon receptor (AHR) as a potent negative regulator of CXCL13 production by human CD4+ T cells. Transcriptomic, epigenetic and functional studies demonstrate that AHR coordinates with AP-1 family member JUN to prevent CXCL13+ TPH/TFH cell differentiation and promote an IL-22+ phenotype. Type I interferon, a pathogenic driver of SLE7, opposes AHR and JUN to promote T cell production of CXCL13. These results place CXCL13+ TPH/TFH cells on a polarization axis opposite from T helper 22 (TH22) cells and reveal AHR, JUN and interferon as key regulators of these divergent T cell states.
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Affiliation(s)
- Calvin Law
- Department of Biochemistry and Molecular Genetics, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Human Immunobiology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Vanessa Sue Wacleche
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ye Cao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Arundhati Pillai
- Department of Biochemistry and Molecular Genetics, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Human Immunobiology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - John Sowerby
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Brandon Hancock
- Department of Biochemistry and Molecular Genetics, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Human Immunobiology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center of Synthetic Biology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Alice Horisberger
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sabrina Bracero
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Viktoriya Skidanova
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Zhihan Li
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Ifeoluwakiisi Adejoorin
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Eilish Dillon
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac J Benque
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Diana Pena Nunez
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daimon P Simmons
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Joshua Keegan
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lin Chen
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Ling-Yang Hao
- Discovery Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Brian Jones
- Discovery Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Navin Rao
- Discovery Immunology, Janssen Research & Development, Spring House, PA, USA
| | - Yujie Qu
- Merck & Co., Inc., Rahway, NJ, USA
| | | | - A Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Katharina S Shaw
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ruth Ann Vleugels
- Department of Dermatology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Elena Massarotti
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Karen H Costenbader
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - James A Lederer
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Judd F Hultquist
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jaehyuk Choi
- Department of Biochemistry and Molecular Genetics, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center of Human Immunobiology, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center of Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA.
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
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Giese MA, Bennin DA, Schoen TJ, Peterson AN, Schrope JH, Brand J, Jung HS, Keller NP, Beebe DJ, Dinh HQ, Slukvin II, Huttenlocher A. PTP1B phosphatase dampens iPSC-derived neutrophil motility and antimicrobial function. J Leukoc Biol 2024; 116:118-131. [PMID: 38417030 PMCID: PMC11212797 DOI: 10.1093/jleuko/qiae039] [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: 08/25/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/01/2024] Open
Abstract
Neutrophils are rapidly recruited to sites of infection and are critical for pathogen clearance. Therapeutic use of primary neutrophils has been limited, as they have a short lifespan and are not amenable to genetic manipulation. Human induced pluripotent stem cells (iPSCs) can provide a robust source of neutrophils for infusion and are genetically tractable. However, current work has indicated that dampened intracellular signaling limits iPSC-derived neutrophil (iNeutrophil) cellular activation and antimicrobial response. Here, we show that protein tyrosine phosphatase 1B (PTP1B) inhibits intracellular signaling and dampens iNeutrophil effector function. Deletion of the PTP1B phosphatase increased PI3K and ERK signaling and was associated with increased F-actin polymerization, cell migration, and phagocytosis. In contrast, other effector functions like NETosis and reactive oxygen species production were reduced. PTP1B-deficient neutrophils were more responsive to Aspergillus fumigatus and displayed rapid recruitment and control of hyphal growth. Accordingly, depletion of PTP1B increased production of inflammatory factors including the neutrophil chemokine interleukin-8. Taken together, these findings suggest that PTP1B limits iNeutrophil motility and antimicrobial function.
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Affiliation(s)
- Morgan A Giese
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
- Cellular and Molecular Biology Graduate Program, University of Wisconsin–Madison, 1525 Linden Dr. Madison 53706, WI, United States
| | - David A Bennin
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
| | - Taylor J Schoen
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin–Madison, 2015 Linden Dr. Madison 53706, WI, United States
| | - Ashley N Peterson
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
- Comparative Biomedical Sciences Graduate Program, University of Wisconsin–Madison, 2015 Linden Dr. Madison 53706, WI, United States
| | - Jonathan H Schrope
- Department of Biomedical Engineering, University of Wisconsin–Madison, 1550 Engineering Dr. Madison 53706, WI, United States
| | - Josh Brand
- Cell and Molecular Pathology Graduate Program, University of Wisconsin–Madison, 1685 Highland Ave. Madison 53705, WI, United States
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin–Madison, 1111 Highland Ave. Madison 53705, WI, United States
| | - Ho Sun Jung
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1223 Capitol Ct. Madison 53715, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave. Madison 53705, WI, United States
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
| | - David J Beebe
- Carbone Cancer Center, University of Wisconsin–Madison, 1111 Highland Ave. Madison 53705, WI, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 1685 Highland Ave. Madison 53705, WI, United States
| | - Huy Q Dinh
- Department of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin–Madison, 1111 Highland Ave. Madison 53705, WI, United States
| | - Igor I Slukvin
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, 1223 Capitol Ct. Madison 53715, WI, United States
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, 1111 Highland Ave. Madison 53705, WI, United States
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, 1685 Highland Ave. Madison 53705, WI, United States
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin–Madison, 1550 Linden Dr. Madison 53706, WI, United States
- Department of Pediatrics, University of Wisconsin–Madison, 600 Highland Ave. Madison 53705, WI, United States
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Vardaman D, Ali MA, Bolding C, Tidwell H, Stephens H, Tyrrell DJ. Development of a Spectral Flow Cytometry Analysis Pipeline for High-Dimensional Immune Cell Characterization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599633. [PMID: 38948780 PMCID: PMC11213029 DOI: 10.1101/2024.06.19.599633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Flow cytometry is a widely used technique for immune cell analysis, offering insights into cell composition and function. Spectral flow cytometry allows for high-dimensional analysis of immune cells, overcoming limitations of conventional flow cytometry. However, analyzing data from large antibody panels can be challenging using traditional bi-axial gating strategies. Here, we present a novel analysis pipeline designed to improve analysis of spectral flow cytometry. We employ this method to identify rare T cell populations in aging. We isolated splenocytes from young (2-3 months) and aged (18-19 months) female mice then stained these with a panel of 20 fluorescently labeled antibodies. Spectral flow cytometry was performed, followed by data processing and analysis using Python within a Jupyter Notebook environment to perform batch correction, unsupervised clustering, dimensionality reduction, and differential expression analysis. Our analysis of 3,776,804 T cells from 11 spleens revealed 34 distinct T cell clusters identified by surface marker expression. We observed significant differences between young and aged mice, with certain clusters enriched in one age group over the other. Naïve, effector memory, and central memory CD8+ and CD4+ T cell subsets exhibited age-associated changes in abundance and marker expression. Additionally, γδ T cell clusters showed differential abundance between age groups. By leveraging high-dimensional analysis methods borrowed from single-cell RNA sequencing analysis, we identified age-related differences in T cell subsets, providing insights into the immune aging process. This approach offers a robust, free, and easily implemented analysis pipeline for spectral flow cytometry data that may facilitate the discovery of novel therapeutic targets for age-related immune dysfunction.
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Affiliation(s)
- Donald Vardaman
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Md Akkas Ali
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
- Biochemistry and Structural Biology Theme, Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Chase Bolding
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Harrison Tidwell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Holly Stephens
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
- Immunology Theme, Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Daniel J. Tyrrell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
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37
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Gallaccio G, Wang M, Schlickeiser S, Kunkel D, Böttcher C, Fernández-Zapata C. Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry. STAR Protoc 2024; 5:103038. [PMID: 38678568 PMCID: PMC11068925 DOI: 10.1016/j.xpro.2024.103038] [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: 01/29/2024] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.1.
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Affiliation(s)
- Gerardina Gallaccio
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany
| | - Meng Wang
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany
| | - Stephan Schlickeiser
- Institute of Medical Immunology, BIH-Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, and Berlin Institute of Health Berlin, Berlin, Germany
| | - Desiree Kunkel
- Berlin Institute of Health at Charité - Universitiätsmedizin Berlin, Flow & Mass Cytometry Core Facility, Berlin, Germany
| | - Chotima Böttcher
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany.
| | - Camila Fernández-Zapata
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany.
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Balog JÁ, Horti-Oravecz K, Kövesdi D, Bozsik A, Papp J, Butz H, Patócs A, Szebeni GJ, Grolmusz VK. Peripheral immunophenotyping reveals lymphocyte stimulation in healthy women living with hereditary breast and ovarian cancer syndrome. iScience 2024; 27:109882. [PMID: 38799565 PMCID: PMC11126817 DOI: 10.1016/j.isci.2024.109882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/11/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 (gpath(BRCA1/2)) represent genetic susceptibility for hereditary breast and ovarian cancer syndrome. Tumor-immune interactions are key contributors to breast cancer pathogenesis. Although earlier studies confirmed pro-tumorigenic immunological alterations in breast cancer patients, data are lacking in healthy carriers of gpath(BRCA1/2). Peripheral blood mononuclear cells of 66 women with or without germline predisposition or breast cancer were studied with a mass cytometry panel that identified 4 immune subpopulations of altered frequencies between healthy controls and healthy gpath(BRCA1) carriers, while no difference was observed in healthy gpath(BRCA2) carriers compared to controls. Moreover, 3 (one IgD-CD27+CD95+ B cell subpopulation and two CD45RA-CCR7+CD38+ CD4+ T cell subpopulations) out of these 4 subpopulations were also elevated in triple-negative breast cancer patients compared to controls. Our results reveal an activated peripheral immune phenotype in healthy carriers of gpath(BRCA1) that needs to be further elucidated to be leveraged in risk-reducing strategies.
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Affiliation(s)
- József Ágoston Balog
- Institute of Genetics, Laboratory of Functional Genomics, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Core Facility, HUN-REN Biological Research Center, 6726 Szeged, Hungary
| | - Klaudia Horti-Oravecz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- Semmelweis University, Doctoral School, 1085 Budapest, Hungary
| | - Dorottya Kövesdi
- Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
| | - Janos Papp
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Oncology Biobank, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
| | - Gábor János Szebeni
- Institute of Genetics, Laboratory of Functional Genomics, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Core Facility, HUN-REN Biological Research Center, 6726 Szeged, Hungary
- Department of Internal Medicine, Hematology Centre, Faculty of Medicine University of Szeged, 6725 Szeged, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics and the National Tumorbiology Laboratory, National Institute of Oncology, Comprehensive Cancer Center, 1122 Budapest, Hungary
- HUN-REN-SE Hereditary Cancers Research Group, Hungarian Research Network – Semmelweis University, 1122 Budapest, Hungary
- Department of Laboratory Medicine, Semmelweis University, 1089 Budapest, Hungary
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39
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Van Oekelen O, Amatangelo M, Guo M, Upadhyaya B, Cribbs AP, Kelly G, Patel M, Kim-Schulze S, Flynt E, Lagana A, Gooding S, Merad M, Jagganath S, Pierceall WE, Oppermann U, Thakurta A, Parekh S. Iberdomide increases innate and adaptive immune cell subsets in the bone marrow of patients with relapsed/refractory multiple myeloma. Cell Rep Med 2024; 5:101584. [PMID: 38776911 PMCID: PMC11228551 DOI: 10.1016/j.xcrm.2024.101584] [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: 08/24/2023] [Revised: 02/11/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Iberdomide is a potent cereblon E3 ligase modulator (CELMoD agent) with promising efficacy and safety as a monotherapy or in combination with other therapies in patients with relapsed/refractory multiple myeloma (RRMM). Using a custom mass cytometry panel designed for large-scale immunophenotyping of the bone marrow tumor microenvironment (TME), we demonstrate significant increases of effector T and natural killer (NK) cells in a cohort of 93 patients with multiple myeloma (MM) treated with iberdomide, correlating findings to disease characteristics, prior therapy, and a peripheral blood immune phenotype. Notably, changes are dose dependent, associated with objective response, and independent of prior refractoriness to MM therapies. This suggests that iberdomide broadly induces innate and adaptive immune activation in the TME, contributing to its antitumor efficacy. Our approach establishes a strategy to study treatment-induced changes in the TME of patients with MM and, more broadly, patients with cancer and establishes rational combination strategies for iberdomide with immune-enhancing therapies to treat MM.
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Affiliation(s)
- Oliver Van Oekelen
- Department of Medicine, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Manman Guo
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford, UK
| | - Bhaskar Upadhyaya
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam P Cribbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Geoffrey Kelly
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manishkumar Patel
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, USA
| | - Alessandro Lagana
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah Gooding
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Miriam Merad
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sundar Jagganath
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Udo Oppermann
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Oxford University, Oxford, UK; Oxford Translational Myeloma Centre (OTMC), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, NJ, USA; Oxford Translational Myeloma Centre (OTMC), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Samir Parekh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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40
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Everson RG, Hugo W, Sun L, Antonios J, Lee A, Ding L, Bu M, Khattab S, Chavez C, Billingslea-Yoon E, Salazar A, Ellingson BM, Cloughesy TF, Liau LM, Prins RM. TLR agonists polarize interferon responses in conjunction with dendritic cell vaccination in malignant glioma: a randomized phase II Trial. Nat Commun 2024; 15:3882. [PMID: 38719809 PMCID: PMC11078958 DOI: 10.1038/s41467-024-48073-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
In this randomized phase II clinical trial, we evaluated the effectiveness of adding the TLR agonists, poly-ICLC or resiquimod, to autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination in patients with newly-diagnosed or recurrent WHO Grade III-IV malignant gliomas. The primary endpoints were to assess the most effective combination of vaccine and adjuvant in order to enhance the immune potency, along with safety. The combination of ATL-DC vaccination and TLR agonist was safe and found to enhance systemic immune responses, as indicated by increased interferon gene expression and changes in immune cell activation. Specifically, PD-1 expression increases on CD4+ T-cells, while CD38 and CD39 expression are reduced on CD8+ T cells, alongside an increase in monocytes. Poly-ICLC treatment amplifies the induction of interferon-induced genes in monocytes and T lymphocytes. Patients that exhibit higher interferon response gene expression demonstrate prolonged survival and delayed disease progression. These findings suggest that combining ATL-DC with poly-ICLC can induce a polarized interferon response in circulating monocytes and CD8+ T cells, which may represent an important blood biomarker for immunotherapy in this patient population.Trial Registration: ClinicalTrials.gov Identifier: NCT01204684.
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Affiliation(s)
- Richard G Everson
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Willy Hugo
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Lu Sun
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Joseph Antonios
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Alexander Lee
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Lizhong Ding
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Melissa Bu
- Department of Medicine, Division of Dermatology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Sara Khattab
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Carolina Chavez
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Emma Billingslea-Yoon
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Benjamin M Ellingson
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Timothy F Cloughesy
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Neurology/Neuro-Oncology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Robert M Prins
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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41
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Amarin JZ, Dulek DE, Simmons J, Hayek H, Chappell JD, Nochowicz CH, Kitko CL, Schuster JE, Muñoz FM, Bocchini CE, Moulton EA, Coffin SE, Freedman JL, Ardura MI, Wattier RL, Maron G, Grimley M, Paulsen G, Danziger-Isakov L, Carpenter PA, Englund JA, Halasa NB, Spieker AJ, Kalams SA. Immunophenotypic predictors of influenza vaccine immunogenicity in pediatric hematopoietic cell transplant recipients. Blood Adv 2024; 8:1880-1892. [PMID: 38386973 PMCID: PMC11007439 DOI: 10.1182/bloodadvances.2023012118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
ABSTRACT Pediatric hematopoietic cell transplant (HCT) recipients exhibit poor serologic responses to influenza vaccination early after transplant. To facilitate the optimization of influenza vaccination timing, we sought to identify B- and T-cell subpopulations associated with influenza vaccine immunogenicity in this population. We used mass cytometry to phenotype peripheral blood mononuclear cells collected from pediatric HCT recipients enrolled in a multicenter influenza vaccine trial comparing high- and standard-dose formulations over 3 influenza seasons (2016-2019). We fit linear regression models to estimate relationships between immune cell subpopulation numbers before vaccination and prevaccination to postvaccination geometric mean fold rises in antigen-specific (A/H3N2, A/H1N1, and B/Victoria) serum hemagglutination inhibition antibody titers (28-42 days, and ∼6 months after 2 doses). For cell subpopulations identified as predictive of a response to all 3 antigens, we conducted a sensitivity analysis including time after transplant as an additional covariate. Among 156 HCT recipients, we identified 33 distinct immune cell subpopulations; 7 significantly predicted responses to all 3 antigens 28 to 42 days after a 2-dose vaccine series, irrespective of vaccine dose. We also found evidence that baseline absolute numbers of naïve B cells, naïve CD4+ T cells, and circulating T follicular helper cells predicted peak and sustained vaccine-induced titers irrespective of dose or timing of posttransplant vaccine administration. In conclusion, several B- and T-cell subpopulations predicted influenza vaccine immunogenicity in pediatric HCT recipients. This study provides insights into the immune determinants of vaccine responses and may help guide the development of tailored vaccination strategies for this vulnerable population.
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Affiliation(s)
- Justin Z. Amarin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
- Epidemiology Doctoral Program, School of Medicine, Vanderbilt University, Nashville, TN
| | - Daniel E. Dulek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Joshua Simmons
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Haya Hayek
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Carrie L. Kitko
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Flor M. Muñoz
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
- Department of Molecular Virology and Microbiology, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Claire E. Bocchini
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Elizabeth A. Moulton
- Division of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX
| | - Susan E. Coffin
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L. Freedman
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Monica I. Ardura
- Division of Infectious Diseases and Host Defense Program, Nationwide Children’s Hospital, Columbus, OH
- Department of Pediatrics, The Ohio State University, Columbus, OH
| | - Rachel L. Wattier
- Department of Pediatrics, University of California San Francisco and Benioff Children’s Hospital, San Francisco, CA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN
| | - Michael Grimley
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Grant Paulsen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Lara Danziger-Isakov
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Paul A. Carpenter
- Department of Pediatrics, University of Washington and Seattle Children’s Research Institute, Seattle, WA
| | - Janet A. Englund
- Department of Pediatrics, University of Washington and Seattle Children’s Research Institute, Seattle, WA
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew J. Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Spyros A. Kalams
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN
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42
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Hollands CG, Boyd AL, Zhao X, Reid JC, Henly C, ElRafie A, Boylan D, Broder E, Kalau O, Johnson P, Mark A, McNicol J, Xenocostas A, Berg T, Foley R, Trus M, Leber B, Garcia-Horton A, Campbell C, Bhatia M. Identification of cells of leukemic stem cell origin with non-canonical regenerative properties. Cell Rep Med 2024; 5:101485. [PMID: 38582086 PMCID: PMC11031376 DOI: 10.1016/j.xcrm.2024.101485] [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: 05/19/2023] [Revised: 10/19/2023] [Accepted: 03/04/2024] [Indexed: 04/08/2024]
Abstract
Despite most acute myeloid leukemia (AML) patients entering remission following chemotherapy, outcomes remain poor due to surviving leukemic cells that contribute to relapse. The nature of these enduring cells is poorly understood. Here, through temporal single-cell transcriptomic characterization of AML hierarchical regeneration in response to chemotherapy, we reveal a cell population: AML regeneration enriched cells (RECs). RECs are defined by CD74/CD68 expression, and although derived from leukemic stem cells (LSCs), are devoid of stem/progenitor capacity. Based on REC in situ proximity to CD34-expressing cells identified using spatial transcriptomics on AML patient bone marrow samples, RECs demonstrate the ability to augment or reduce leukemic regeneration in vivo based on transfusion or depletion, respectively. Furthermore, RECs are prognostic for patient survival as well as predictive of treatment failure in AML cohorts. Our study reveals RECs as a previously unknown functional catalyst of LSC-driven regeneration contributing to the non-canonical framework of AML regeneration.
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Affiliation(s)
- Cameron G Hollands
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Allison L Boyd
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Xueli Zhao
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Jennifer C Reid
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Charisa Henly
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Amro ElRafie
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - David Boylan
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Emily Broder
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Olivia Kalau
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Paige Johnson
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Alyssa Mark
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Jamie McNicol
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Anargyros Xenocostas
- Department of Medicine, Division of Hematology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 3K7, Canada; Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada
| | - Tobias Berg
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Ronan Foley
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Michael Trus
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Brian Leber
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Alejandro Garcia-Horton
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Oncology, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Clinton Campbell
- Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Mickie Bhatia
- Michael G. DeGroote School of Medicine, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada; Hematology Exploration and Applications in Leukemia (HEAL) Program, Hamilton, ON, Canada.
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43
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Haddox CL, Nathenson MJ, Mazzola E, Lin JR, Baginska J, Nau A, Weirather JL, Choy E, Marino-Enriquez A, Morgan JA, Cote GM, Merriam P, Wagner AJ, Sorger PK, Santagata S, George S. Phase II Study of Eribulin plus Pembrolizumab in Metastatic Soft-tissue Sarcomas: Clinical Outcomes and Biological Correlates. Clin Cancer Res 2024; 30:1281-1292. [PMID: 38236580 PMCID: PMC10982640 DOI: 10.1158/1078-0432.ccr-23-2250] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/19/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024]
Abstract
PURPOSE Eribulin modulates the tumor-immune microenvironment via cGAS-STING signaling in preclinical models. This non-randomized phase II trial evaluated the combination of eribulin and pembrolizumab in patients with soft-tissue sarcomas (STS). PATIENTS AND METHODS Patients enrolled in one of three cohorts: leiomyosarcoma (LMS), liposarcomas (LPS), or other STS that may benefit from PD-1 inhibitors, including undifferentiated pleomorphic sarcoma (UPS). Eribulin was administered at 1.4 mg/m2 i.v. (days 1 and 8) with fixed-dose pembrolizumab 200 mg i.v. (day 1) of each 21-day cycle, until progression, unacceptable toxicity, or completion of 2 years of treatment. The primary endpoint was the 12-week progression-free survival rate (PFS-12) in each cohort. Secondary endpoints included the objective response rate, median PFS, safety profile, and overall survival (OS). Pretreatment and on-treatment blood specimens were evaluated in patients who achieved durable disease control (DDC) or progression within 12 weeks [early progression (EP)]. Multiplexed immunofluorescence was performed on archival LPS samples from patients with DDC or EP. RESULTS Fifty-seven patients enrolled (LMS, n = 19; LPS, n = 20; UPS/Other, n = 18). The PFS-12 was 36.8% (90% confidence interval: 22.5-60.4) for LMS, 69.6% (54.5-89.0) for LPS, and 52.6% (36.8-75.3) for UPS/Other cohorts. All 3 patients in the UPS/Other cohort with angiosarcoma achieved RECIST responses. Toxicity was manageable. Higher IFNα and IL4 serum levels were associated with clinical benefit. Immune aggregates expressing PD-1 and PD-L1 were observed in a patient that completed 2 years of treatment. CONCLUSIONS The combination of eribulin and pembrolizumab demonstrated promising activity in LPS and angiosarcoma.
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Affiliation(s)
- Candace L. Haddox
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael J. Nathenson
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jia-Ren Lin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Joanna Baginska
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Allison Nau
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason L. Weirather
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edwin Choy
- Division of Hematology Oncology, Massachusetts General Cancer Center, Boston, Massachusetts
| | | | - Jeffrey A. Morgan
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory M. Cote
- Division of Hematology Oncology, Massachusetts General Cancer Center, Boston, Massachusetts
| | - Priscilla Merriam
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J. Wagner
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter K. Sorger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Sandro Santagata
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Suzanne George
- Sarcoma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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44
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Giovenzana A, Bezzecchi E, Bichisecchi A, Cardellini S, Ragogna F, Pedica F, Invernizzi F, Di Filippo L, Tomajer V, Aleotti F, Scotti GM, Socci C, Cesana G, Olmi S, Morelli MJ, Falconi M, Giustina A, Bonini C, Piemonti L, Ruggiero E, Petrelli A. Fat-to-blood recirculation of partially dysfunctional PD-1 +CD4 Tconv cells is associated with dysglycemia in human obesity. iScience 2024; 27:109032. [PMID: 38380252 PMCID: PMC10877684 DOI: 10.1016/j.isci.2024.109032] [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: 08/09/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Obesity is characterized by the accumulation of T cells in insulin-sensitive tissues, including the visceral adipose tissue (VAT), that can interfere with the insulin signaling pathway eventually leading to insulin resistance (IR) and type 2 diabetes. Here, we found that PD-1+CD4 conventional T (Tconv) cells, endowed with a transcriptomic and functional profile of partially dysfunctional cells, are diminished in VAT of obese patients with dysglycemia (OB-Dys), without a concomitant increase in apoptosis. These cells showed enhanced capacity to recirculate into the bloodstream and had a non-restricted TCRβ repertoire divergent from that of normoglycemic obese and lean individuals. PD-1+CD4 Tconv were reduced in the circulation of OB-Dys, exhibited an altered migration potential, and were detected in the liver of patients with non-alcoholic steatohepatitis. The findings suggest a potential role for partially dysfunctional PD-1+CD4 Tconv cells as inter-organ mediators of IR in obese patients with dysglycemic.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Stefano Olmi
- San Marco Hospital GSD, Zingonia, Bergamo, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | | | - Massimo Falconi
- IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Andrea Giustina
- IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Chiara Bonini
- IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Lorenzo Piemonti
- IRCCS Ospedale San Raffaele, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
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45
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Horisberger A, Griffith A, Keegan J, Arazi A, Pulford J, Murzin E, Howard K, Hancock B, Fava A, Sasaki T, Ghosh T, Inamo J, Beuschel R, Cao Y, Preisinger K, Gutierrez-Arcelus M, Eisenhaure TM, Guthridge J, Hoover PJ, Dall'Era M, Wofsy D, Kamen DL, Kalunian KC, Furie R, Belmont M, Izmirly P, Clancy R, Hildeman D, Woodle ES, Apruzzese W, McMahon MA, Grossman J, Barnas JL, Payan-Schober F, Ishimori M, Weisman M, Kretzler M, Berthier CC, Hodgin JB, Demeke DS, Putterman C, Brenner MB, Anolik JH, Raychaudhuri S, Hacohen N, James JA, Davidson A, Petri MA, Buyon JP, Diamond B, Zhang F, Lederer JA, Rao DA. Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.14.575609. [PMID: 38293222 PMCID: PMC10827101 DOI: 10.1101/2024.01.14.575609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.
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46
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Gillard J, Suffiotti M, Brazda P, Venkatasubramanian PB, Versteegen P, de Jonge MI, Kelly D, Bibi S, Pinto MV, Simonetti E, Babiceanu M, Kettring A, Teodosio C, de Groot R, Berbers G, Stunnenberg HG, Schanen B, Fenwick C, Huynen MA, Diavatopoulos DA. Antiviral responses induced by Tdap-IPV vaccination are associated with persistent humoral immunity to Bordetella pertussis. Nat Commun 2024; 15:2133. [PMID: 38459022 PMCID: PMC10923912 DOI: 10.1038/s41467-024-46560-w] [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: 03/01/2022] [Accepted: 03/01/2024] [Indexed: 03/10/2024] Open
Abstract
Many countries continue to experience pertussis epidemics despite widespread vaccination. Waning protection after booster vaccination has highlighted the need for a better understanding of the immunological factors that promote durable protection. Here we apply systems vaccinology to investigate antibody responses in adolescents in the Netherlands (N = 14; NL) and the United Kingdom (N = 12; UK) receiving a tetanus-diphtheria-acellular pertussis-inactivated poliovirus (Tdap-IPV) vaccine. We report that early antiviral and interferon gene expression signatures in blood correlate to persistence of pertussis-specific antibody responses. Single-cell analyses of the innate response identified monocytes and myeloid dendritic cells (MoDC) as principal responders that upregulate antiviral gene expression and type-I interferon cytokine production. With public data, we show that Tdap vaccination stimulates significantly lower antiviral/type-I interferon responses than Tdap-IPV, suggesting that IPV may promote antiviral gene expression. Subsequent in vitro stimulation experiments demonstrate TLR-dependent, IPV-specific activation of the pro-inflammatory p38 MAP kinase pathway in MoDCs. Together, our data provide insights into the molecular host response to pertussis booster vaccination and demonstrate that IPV enhances innate immune activity associated with persistent, pertussis-specific antibody responses.
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Affiliation(s)
- Joshua Gillard
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Madeleine Suffiotti
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Peter Brazda
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Pauline Versteegen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marien I de Jonge
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dominic Kelly
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sagida Bibi
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marta Valente Pinto
- Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, UK
- Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health & Science, Caparica, Almada, Portugal
| | - Elles Simonetti
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Cristina Teodosio
- Leiden University Medical Center, Immunohematology & Blood Transfusion, Leiden, The Netherlands
| | - Ronald de Groot
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Guy Berbers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | | | - Craig Fenwick
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Martijn A Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dimitri A Diavatopoulos
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.
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47
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McDonnell SRP, Nguyen VA, Walton NM, Merkwirth C, Hong F, Berg D, Muensterman ET, Furie RA. Mezagitamab in systemic lupus erythematosus: clinical and mechanistic findings of CD38 inhibition in an autoimmune disease. Lupus Sci Med 2024; 11:e001112. [PMID: 38453421 PMCID: PMC10921479 DOI: 10.1136/lupus-2023-001112] [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: 11/22/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024]
Abstract
OBJECTIVE To evaluate safety and mechanism of action of mezagitamab (TAK-079), an anti-CD38 monoclonal antibody, in patients with moderate to severe systemic lupus erythematosus (SLE). METHODS A phase 1b double-blind, placebo-controlled, multicentre study was conducted in patients with SLE receiving standard background therapy. Eligible patients were adults who met the 2012 SLICC or ACR criteria for diagnosis, had a baseline SLE Disease Activity Index 2000 (SLEDAI-2K) score of ≥6 and were positive for anti-double-stranded DNA antibodies and/or anti-extractable nuclear antigens antibodies. Patients received 45 mg, 90 mg or 135 mg of mezagitamab or placebo every 3 weeks over 12 weeks. Primary endpoints were safety and tolerability. Secondary endpoints included pharmacokinetics and pharmacodynamics. Exploratory assessments included disease activity scales, deep immune profiling and interferon pathway analysis. RESULTS 22 patients received at least one dose of either mezagitamab or placebo. In patients exposed to mezagitamab (n=17), drug was well tolerated. Adverse event (AEs) were balanced across treatment groups, with no treatment emergent AEs exceeding grade 2. Responder analyses for Cutaneous Lupus Erythematosus Disease Area and Severity Index (CLASI) and SLEDAI-2K did not reveal any observable differences across treatment groups. However, there was a trend for more profound skin responses among patients with higher CLASI scores (>10) at baseline. Pharmacodynamic analysis showed median CD38 receptor occupancy up to 88.4% on CD38+ natural killer cells with concurrent depletion of these cells up to 90% in the 135 mg group. Mean reductions in IgG and autoantibodies were less than 20% in all dose groups. Cytometry by time of flight and type 1 interferon gene analysis revealed unique fingerprints that are indicative of a broad immune landscape shift following CD38 targeting. CONCLUSIONS Mezagitamab had a favourable safety profile in patients with moderate to severe SLE and elicited a pharmacodynamic effect consistent with CD38+ cell depletion. These findings reveal novel insights into the drug's mechanism of action and support the continued investigation of mezagitamab in autoimmune diseases.
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Affiliation(s)
| | - Van Anh Nguyen
- Takeda Development Center Americas Inc, Lexington, Massachusetts, USA
| | - Noah M Walton
- Takeda Development Center Americas Inc, Lexington, Massachusetts, USA
| | - Carsten Merkwirth
- Takeda Development Center Americas Inc, Lexington, Massachusetts, USA
| | - Feng Hong
- Takeda Development Center Americas Inc, Lexington, Massachusetts, USA
| | - Deborah Berg
- Clinical Sciences, Takeda Pharmaceuticals America Inc, Lexington, Massachusetts, USA
| | | | - Richard A Furie
- Department of Rheumatology, Northwell Health, Great Neck, New York, USA
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48
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Adine C, Fernando K, Ho NCW, Quah HS, Ho SSW, Wu KZ, Teng KWW, Arcinas C, Li L, Ha K, Chew JWL, Wang C, Too NSH, Yeong JPS, Tan DSW, Tan IBH, Nagadia R, Chia CS, Macalinao D, Bhuvaneswari H, Iyer NG, Fong ELS. Bioengineered hydrogels enhance ex vivo preservation of patient-derived tumor explants for drug evaluation. Biomaterials 2024; 305:122460. [PMID: 38246018 DOI: 10.1016/j.biomaterials.2023.122460] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024]
Abstract
Ex vivo patient-derived tumor slices (PDTS) are currently limited by short-term viability in culture. Here, we show how bioengineered hydrogels enable the identification of key matrix parameters that significantly enhance PDTS viability compared to conventional culture systems. As demonstrated using single-cell RNA sequencing and high-dimensional flow cytometry, hydrogel-embedded PDTS tightly preserved cancer, cancer-associated fibroblast, and various immune cell populations and subpopulations in the corresponding original tumor. Cell-cell communication networks within the tumor microenvironment, including immune checkpoint ligand-receptor interactions, were also maintained. Remarkably, our results from a co-clinical trial suggest hydrogel-embedded PDTS may predict sensitivity to immune checkpoint inhibitors (ICIs) in head and neck cancer patients. Further, we show how these longer term-cultured tumor explants uniquely enable the sampling and detection of temporal evolution in molecular readouts when treated with ICIs. By preserving the compositional heterogeneity and complexity of patient tumors, hydrogel-embedded PDTS provide a valuable tool to facilitate experiments targeting the tumor microenvironment.
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Affiliation(s)
- Christabella Adine
- The N.1 Institute for Health, National University of Singapore, Singapore
| | - Kanishka Fernando
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | | | - Hong Sheng Quah
- National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | | | - Kenny Zhuoran Wu
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | | | - Camille Arcinas
- National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore
| | - Ling Li
- Translational Medicine Research Centre, MSD, Singapore
| | - Kelly Ha
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - Joey Wei Ling Chew
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | - Chenhui Wang
- Department of Biomedical Engineering, National University of Singapore, Singapore
| | | | - Joe Poh Sheng Yeong
- Institute for Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | | | | | - Rahul Nagadia
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore; Department of Oral and Maxillofacial Surgery, National Dental Centre Singapore, Singapore; Department of Dental Medicine, Karolinska Institute, Stockholm, Sweden
| | | | | | | | - N Gopalakrishna Iyer
- National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, National University of Singapore, Singapore.
| | - Eliza Li Shan Fong
- The N.1 Institute for Health, National University of Singapore, Singapore; Department of Biomedical Engineering, National University of Singapore, Singapore; Cancer Science Institute, National University of Singapore, Singapore.
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49
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Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH. High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding. Nat Biomed Eng 2024; 8:310-324. [PMID: 38036616 DOI: 10.1038/s41551-023-01144-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/21/2023] [Indexed: 12/02/2023]
Abstract
Advances in immunology, immuno-oncology, drug discovery and vaccine development demand improvements in the capabilities of flow cytometry to allow it to measure more protein markers per cell at multiple timepoints. However, the size of panels of fluorophore markers is limited by overlaps in fluorescence-emission spectra, and flow cytometers typically perform cell measurements at one timepoint. Here we describe multi-pass high-dimensional flow cytometry, a method leveraging cellular barcoding via microparticles emitting near-infrared laser light to track and repeatedly measure each cell using more markers and fewer colours. By using live human peripheral blood mononuclear cells, we show that the method enables the time-resolved characterization of the same cells before and after stimulation, their analysis via a 10-marker panel with minimal compensation for spectral spillover and their deep immunophenotyping via a 32-marker panel, where the same cells are analysed in 3 back-to-back cycles with 10-13 markers per cycle, reducing overall spillover and simplifying marker-panel design. Cellular barcoding in flow cytometry extends the utility of the technique for high-dimensional multi-pass single-cell analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Han Zhu
- LASE Innovation Inc., Woburn, MA, USA
| | | | | | - Nicola Martino
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA
| | - Seok-Hyun Yun
- Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Cambridge, MA, USA.
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50
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Hauchamps P, Bayat B, Delandre S, Hamrouni M, Toussaint M, Temmerman S, Lin D, Gatto L. CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data. BMC Bioinformatics 2024; 25:80. [PMID: 38378440 PMCID: PMC10877884 DOI: 10.1186/s12859-024-05691-z] [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: 11/10/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps: signal compensation or unmixing, scale transformation, debris, doublets and dead cells removal, batch effect correction, etc. However, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, non standardized diagnostic and visualizations, making objective comparison difficult for the end user. RESULTS Here, we present CytoPipeline and CytoPipelineGUI, two R packages to build, compare and assess pre-processing pipelines for flow cytometry data. To exemplify these new tools, we present the steps involved in designing a pre-processing pipeline on a real life dataset and demonstrate different visual assessment use cases. We also set up a benchmarking comparing two pre-processing pipelines differing by their quality control methods, and show how the package visualization utilities can provide crucial user insight into the obtained benchmark metrics. CONCLUSION CytoPipeline and CytoPipelineGUI are two Bioconductor R packages that help building, visualizing and assessing pre-processing pipelines for flow cytometry data. They increase productivity during pipeline development and testing, and complement benchmarking tools, by providing user intuitive insight into benchmarking results.
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Affiliation(s)
- Philippe Hauchamps
- Computational Biology and Bioinformatics, de duve Institute, UCLouvain, Brussels, Belgium
| | | | | | | | | | | | | | - Laurent Gatto
- Computational Biology and Bioinformatics, de duve Institute, UCLouvain, Brussels, Belgium.
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