1
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Schüller SS, Barman S, Mendez-Giraldez R, Soni D, Daley J, Baden LR, Levy O, Dowling DJ. Immune profiling of age and adjuvant-specific activation of human blood mononuclear cells in vitro. Commun Biol 2024; 7:709. [PMID: 38851856 PMCID: PMC11162429 DOI: 10.1038/s42003-024-06390-4] [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: 09/22/2023] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
Vaccination reduces morbidity and mortality due to infections, but efficacy may be limited due to distinct immunogenicity at the extremes of age. This raises the possibility of employing adjuvants to enhance immunogenicity and protection. Early IFNγ production is a hallmark of effective vaccine immunogenicity in adults serving as a biomarker that may predict effective adjuvanticity. We utilized mass cytometry (CyTOF) to dissect the source of adjuvant-induced cytokine production in human blood mononuclear cells (BMCs) from newborns (~39-week-gestation), adults (~18-63 years old) and elders (>65 years of age) after stimulation with pattern recognition receptors agonist (PRRa) adjuvants. Dimensionality reduction analysis of CyTOF data mapped the BMC compartment, elucidated age-specific immune responses and profiled PRR-mediated activation of monocytes and DCs upon adjuvant stimulation. Furthermore, we demonstrated PRRa adjuvants mediated innate IFNγ induction and mapped NK cells as the key source of TLR7/8 agonist (TLR7/8a) specific innate IFNγ responses. Hierarchical clustering analysis revealed age and TLR7/8a-specific accumulation of innate IFNγ producing γδ T cells. Our study demonstrates the application of mass cytometry and cutting-edge computational approaches to characterize immune responses across immunologically distinct age groups and may inform identification of the bespoke adjuvantation systems tailored to enhance immunity in distinct vulnerable populations.
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Affiliation(s)
- Simone S Schüller
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Neonatal Directorate, Child and Adolescent Health Service, Perth, Australia
| | - Soumik Barman
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Dheeraj Soni
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Sanofi, Cambridge, MA, USA
| | - John Daley
- Dana Farber CyTOF Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lindsey R Baden
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT & Harvard, Cambridge, MA, USA.
| | - David J Dowling
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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2
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Choudhury AD, Kwak L, Cheung A, Allaire KM, Marquez J, Yang DD, Tripathi A, Kilar JM, Flynn M, Maynard B, Reichel R, Pace AF, Chen BK, Van Allen EM, Kilbridge K, Wei XX, McGregor BA, Pomerantz MM, Bhatt RS, Sweeney CJ, Bubley GJ, Jacene HA, Taplin ME, Huang FW, Harshman LC, Fong L. Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer. Cancer Immunol Res 2024; 12:704-718. [PMID: 38552171 PMCID: PMC11148544 DOI: 10.1158/2326-6066.cir-22-0306] [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: 04/26/2022] [Revised: 08/15/2023] [Accepted: 03/08/2024] [Indexed: 06/05/2024]
Abstract
The checkpoint immunotherapeutic pembrolizumab induces responses in a small minority of patients with metastatic castration-resistant prostate cancer (mCRPC). Radium-223 (R223) may increase immunogenicity of bone metastases and increase pembrolizumab (P) activity. In a randomized phase II study, we assessed the effect of R223+P compared with R223 on tumor immune infiltration, safety, and clinical outcomes in patients with mCRPC. The primary endpoint was differences in CD4+ and CD8+ T-cell infiltrate in 8-week versus baseline bone metastasis biopsies; secondary endpoints were safety, radiographic progression-free survival (rPFS), and overall survival (OS). Of the 42 treated patients (29 R223+P, 13 R223), 18 R223+P and 8 R223 patients had evaluable paired tumor biopsies. Median fold-change of CD4+ T cells was -0.7 (range: -9.3 to 4.7) with R223+P and 0.1 (-11.1 to 3.7) with R223 (P = 0.66); for CD8+ T cells, median fold-change was -0.6 (-7.4 to 5.3) with R223+P and -1.3 (-3.1 to 4.8) with R223 (P = 0.66). Median rPFS and OS was 6.1 (95% confidence interval: 2.7-11.0) and 16.9 months [12.7-not reached (NR)], respectively, with R223+P and 5.7 (2.6-NR) and 16.0 (9.0-NR), respectively, with R223. Although R223+P was well tolerated with no unexpected toxicity, the combination did not improve efficacy. High-dimensional flow cytometry demonstrated minimal immune modulation with R223, whereas R223+P induced CTLA-4 expression on circulating CD4+ T cells. Clinical responders possessed lower circulating frequencies of Ki67+ T and myeloid cells at baseline and higher circulating frequencies of TIM-3+ T and myeloid cells by week 9. Although R223+P did not induce T-cell infiltration into the tumor microenvironment, exhaustion of induced peripheral T-cell immune responses may dampen the combination's clinical activity.
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Affiliation(s)
- Atish D Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Lucia Kwak
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alexander Cheung
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Kathryn M Allaire
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Jaqueline Marquez
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - David D Yang
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | - Rebecca Reichel
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Brandon K Chen
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Eliezer M Van Allen
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kerry Kilbridge
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Xiao X Wei
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Bradley A McGregor
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mark M Pomerantz
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Rupal S Bhatt
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Glenn J Bubley
- Harvard Medical School, Boston, Massachusetts
- Beth-Israel Deaconess Medical Center, Boston, Massachusetts
| | - Heather A Jacene
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Franklin W Huang
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | - Lawrence Fong
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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3
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Sbierski-Kind J, Schlickeiser S, Feldmann S, Ober V, Grüner E, Pleimelding C, Gilberg L, Brand I, Weigl N, Ahmed MIM, Ibarra G, Ruzicka M, Benesch C, Pernpruner A, Valdinoci E, Hoelscher M, Adorjan K, Stubbe HC, Pritsch M, Seybold U, Roider J. Persistent immune abnormalities discriminate post-COVID syndrome from convalescence. Infection 2024; 52:1087-1097. [PMID: 38326527 PMCID: PMC11142964 DOI: 10.1007/s15010-023-02164-y] [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: 11/13/2023] [Accepted: 12/19/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Innate lymphoid cells (ILCs) are key organizers of tissue immune responses and regulate tissue development, repair, and pathology. Persistent clinical sequelae beyond 12 weeks following acute COVID-19 disease, named post-COVID syndrome (PCS), are increasingly recognized in convalescent individuals. ILCs have been associated with the severity of COVID-19 symptoms but their role in the development of PCS remains poorly defined. METHODS AND RESULTS Here, we used multiparametric immune phenotyping, finding expanded circulating ILC precursors (ILCPs) and concurrent decreased group 2 innate lymphoid cells (ILC2s) in PCS patients compared to well-matched convalescent control groups at > 3 months after infection or healthy controls. Patients with PCS showed elevated expression of chemokines and cytokines associated with trafficking of immune cells (CCL19/MIP-3b, FLT3-ligand), endothelial inflammation and repair (CXCL1, EGF, RANTES, IL-1RA, PDGF-AA). CONCLUSION These results define immunological parameters associated with PCS and might help find biomarkers and disease-relevant therapeutic strategies.
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Affiliation(s)
- Julia Sbierski-Kind
- Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Internal Medicine IV, Division of Diabetology, Endocrinology and Nephrology, University Hospital, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
- The M3 Research Center, University Clinic Tübingen (UKT), Medical Faculty, Otfried-Müllerstr. 37, Tübingen, Germany
| | - Stephan Schlickeiser
- Charité, Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt- Universität Zu Berlin, Institute of Medical Immunology, Augustenburger Platz 1, 13353, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117, Berlin, Germany
| | - Svenja Feldmann
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Veronica Ober
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eva Grüner
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Claire Pleimelding
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Leonard Gilberg
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Brand
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Nikolas Weigl
- Department of Medicine IV, Division of Clinical Pharmacology, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mohamed I M Ahmed
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gerardo Ibarra
- The M3 Research Center, University Clinic Tübingen (UKT), Medical Faculty, Otfried-Müllerstr. 37, Tübingen, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Ruzicka
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine III, LMU University Hospital, LMU Munich, Munich, Germany
| | - Christopher Benesch
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine II, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna Pernpruner
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine II, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elisabeth Valdinoci
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine II, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Hoelscher
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kristina Adorjan
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans Christian Stubbe
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Medicine II, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Pritsch
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Seybold
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julia Roider
- Department of Infectious Diseases, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany.
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4
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Reyes JGA, Ni D, Santner-Nanan B, Pinget GV, Kraftova L, Ashhurst TM, Marsh-Wakefield F, Wishart CL, Tan J, Hsu P, King NJC, Macia L, Nanan R. A unique human cord blood CD8 +CD45RA +CD27 +CD161 + T-cell subset identified by flow cytometric data analysis using Seurat. Immunology 2024. [PMID: 38798051 DOI: 10.1111/imm.13803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T-cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.
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Affiliation(s)
- Julen Gabirel Araneta Reyes
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Duan Ni
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Brigitte Santner-Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Gabriela Veronica Pinget
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucie Kraftova
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Thomas Myles Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Felix Marsh-Wakefield
- Liver Injury and Cancer Program, Centenary Institute, Sydney, New South Wales, Australia
- Human Cancer and Viral Immunology Laboratory, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire Leana Wishart
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Jian Tan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Hsu
- Kids Research, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas Jonathan Cole King
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Nano, The University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ralph Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
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5
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von Lersner A, Fernandes F, Ozawa PM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A. Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. ACS NANO 2024; 18:10464-10484. [PMID: 38578701 PMCID: PMC11025123 DOI: 10.1021/acsnano.3c11561] [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: 11/20/2023] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
Mammalian cells release a heterogeneous array of extracellular vesicles (EVs) that contribute to intercellular communication by means of the cargo that they carry. To resolve EV heterogeneity and determine if cargo is partitioned into select EV populations, we developed a method named "EV Fingerprinting" that discerns distinct vesicle populations using dimensional reduction of multiparametric data collected by quantitative single-EV flow cytometry. EV populations were found to be discernible by a combination of membrane order and EV size, both of which were obtained through multiparametric analysis of fluorescent features from the lipophilic dye Di-8-ANEPPS incorporated into the lipid bilayer. Molecular perturbation of EV secretion and biogenesis through respective ablation of the small GTPase Rab27a and overexpression of the EV-associated tetraspanin CD63 revealed distinct and selective alterations in EV populations, as well as cargo distribution. While Rab27a disproportionately affects all small EV populations with high membrane order, the overexpression of CD63 selectively increased the production of one small EV population of intermediate membrane order. Multiplexing experiments subsequently revealed that EV cargos have a distinct, nonrandom distribution with CD63 and CD81 selectively partitioning into smaller vs larger EVs, respectively. These studies not only present a method to probe EV biogenesis but also reveal how the selective partitioning of cargo contributes to EV heterogeneity.
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Affiliation(s)
- Ariana
K. von Lersner
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
| | - Fabiane Fernandes
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Institute
of Applied Biosciences and Chemistry, Hogeschool
Arnhem en Nijmegen University of Applied Sciences, Nijmegen 6525 EM, Gelderland, Netherlands
| | - Patricia Midori
Murobushi Ozawa
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Marques Jackson
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
| | - Matthieu Masureel
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Hoangdung Ho
- Department
of Structural Biology, Genentech, San Francisco, California 94080, United States
| | - Sierra M. Lima
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Tatyana Vagner
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Bong Hwan Sung
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Mohamed Wehbe
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kai Franze
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
- KNIME
GmbH, Konstanz 78467, Germany
| | - Heather Pua
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - John T. Wilson
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Jonathan M. Irish
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Alissa M. Weaver
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Cell and Developmental Biology, Vanderbilt
University School of Medicine, Nashville, Tennessee 37232, United States
| | - Dolores Di Vizio
- Department
of Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Andries Zijlstra
- Program in
Cancer Biology, Vanderbilt University, Nashville, Tennessee 37232, United
States
- Department
of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- The
Center
for EV Research, Vanderbilt University, Nashville, Tennessee 37232, United States
- Department
of Research Pathology, Genentech, San Francisco, California 94080, United States
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6
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Spiteri AG, Pilkington KR, Wishart CL, Macia L, King NJC. High-Dimensional Methods of Single-Cell Microglial Profiling to Enhance Understanding of Neuropathological Disease. Curr Protoc 2024; 4:e985. [PMID: 38439574 DOI: 10.1002/cpz1.985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Microglia are the innate myeloid cells of the central nervous system (CNS) parenchyma, functionally implicated in almost every defined neuroinflammatory and neurodegenerative disorder. Current understanding of disease pathogenesis for many neuropathologies is limited and/or lacks reliable diagnostic markers, vaccines, and treatments. With the increasing aging of society and rise in neurogenerative diseases, improving our understanding of their pathogenesis is essential. Analysis of microglia from murine disease models provides an investigative tool to unravel disease processes. In many neuropathologies, bone-marrow-derived monocytes are recruited to the CNS, adopting a phenotype similar to that of microglia. This significantly confounds the accurate identification of cell-type-specific functions and downstream therapeutic targeting. The increased capacity to analyze more phenotypic markers using spectral-cytometry-based technologies allows improved separation of microglia from monocyte-derived cells. Full-spectrum profiling enables enhanced marker resolution, time-efficient analysis of >40 fluorescence parameters, and extraction of cellular autofluorescence parameters. Coupling this system with additional cytometric technologies, including cell sorting and high-parameter imaging, can improve the understanding of microglial phenotypes in disease. To this end, we provide detailed, step-by-step protocols for the analysis of murine brain tissue by high-parameter ex vivo cytometric analysis using the Aurora spectral cytometer (Cytek), including best practices for unmixing and autofluorescence extraction, cell sorting for single-cell RNA analysis, and imaging mass cytometry. Together, this provides a toolkit for researchers to comprehensively investigate microglial disease processes at protein, RNA, and spatial levels for the identification of therapeutic targets in neuropathology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing the mouse brain into a single-cell suspension for microglia isolation Basic Protocol 2: Staining single-cell mouse brain suspensions for microglial phenotyping by spectral cytometry Basic Protocol 3: Flow cytometric sorting of mouse microglia for ex vivo analysis Basic Protocol 4: Processing the mouse brain for imaging mass cytometry for spatial microglia analysis.
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Affiliation(s)
- Alanna G Spiteri
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | | | - Claire L Wishart
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas J C King
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, Australia
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7
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Aminov S, Giricz O, Melnekoff DT, Sica RA, Polishchuk V, Papazoglu C, Yates B, Wang HW, Sahu S, Wang Y, Gordon-Mitchell S, Leshchenko VV, Schinke C, Pradhan K, Aluri S, Sohn M, Barta SK, Agarwal B, Goldfinger M, Mantzaris I, Shastri A, Matsui W, Steidl U, Brody JD, Shah NN, Parekh S, Verma A. Immunotherapy-resistant acute lymphoblastic leukemia cells exhibit reduced CD19 and CD22 expression and BTK pathway dependency. J Clin Invest 2024; 134:e175199. [PMID: 38376944 PMCID: PMC11014656 DOI: 10.1172/jci175199] [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: 09/05/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
While therapies targeting CD19 by antibodies, chimeric antigen receptor T cells (CAR-T), and T cell engagers have improved the response rates in B cell malignancies, the emergence of resistant cell populations with low CD19 expression can lead to relapsed disease. We developed an in vitro model of adaptive resistance facilitated by chronic exposure of leukemia cells to a CD19 immunotoxin. Single-cell RNA-Seq (scRNA-Seq) showed an increase in transcriptionally distinct CD19lo populations among resistant cells. Mass cytometry demonstrated that CD22 was also decreased in these CD19lo-resistant cells. An assay for transposase-accessible chromatin with sequencing (ATAC-Seq) showed decreased chromatin accessibility at promoters of both CD19 and CD22 in the resistant cell populations. Combined loss of both CD19 and CD22 antigens was validated in samples from pediatric and young adult patients with B cell acute lymphoblastic leukemia (B-ALL) that relapsed after CD19 CAR-T-targeted therapy. Functionally, resistant cells were characterized by slower growth and lower basal levels of MEK activation. CD19lo resistant cells exhibited preserved B cell receptor signaling and were more sensitive to both Bruton's tyrosine kinase (BTK) and MEK inhibition. These data demonstrate that resistance to CD19 immunotherapies can result in decreased expression of both CD19 and CD22 and can result in dependency on BTK pathways.
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Affiliation(s)
- Sarah Aminov
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Orsi Giricz
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - David T. Melnekoff
- Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - R. Alejandro Sica
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Veronika Polishchuk
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Cristian Papazoglu
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Bonnie Yates
- Pediatric Oncology Branch, Center for Cancer Research and
| | - Hao-Wei Wang
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Srabani Sahu
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Yanhua Wang
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Shanisha Gordon-Mitchell
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Violetta V. Leshchenko
- Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carolina Schinke
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Kith Pradhan
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Srinivas Aluri
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Moah Sohn
- Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stefan K. Barta
- Department of Medicine, Division of Hematology/Oncology, Hospital of University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Mendel Goldfinger
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Ioannis Mantzaris
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Aditi Shastri
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - William Matsui
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ulrich Steidl
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
| | - Joshua D. Brody
- Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nirali N. Shah
- Pediatric Oncology Branch, Center for Cancer Research and
| | - Samir Parekh
- Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amit Verma
- Department of Oncology, Blood Cancer Institute, Montefiore Einstein Comprehensive Cancer Center, Bronx, New York, USA
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8
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Saul D, Doolittle ML, Rowsey JL, Froemming MN, Kosinsky RL, Vos SJ, Ruan M, LeBrasseur N, Chandra A, Pignolo R, Passos JF, Farr JN, Monroe DG, Khosla S. Osteochondroprogenitor cells and neutrophils expressing p21 and senescence markers modulate fracture repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578420. [PMID: 38370844 PMCID: PMC10871229 DOI: 10.1101/2024.02.01.578420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Cells expressing features of senescence, including upregulation of p21 and p16, appear transiently following tissue injury, yet the properties of these cells or how they contrast with age-induced senescent cells remains unclear. Here, we used skeletal injury as a model and identified the rapid appearance following fracture of p21+ cells expressing senescence markers, mainly as osteochondroprogenitors (OCHs) and neutrophils. Targeted genetic clearance of p21+ cells suppressed senescence-associated signatures within the fracture callus and accelerated fracture healing. By contrast, p21+ cell clearance did not alter bone loss due to aging; conversely, p16+ cell clearance, known to alleviate skeletal aging, did not affect fracture healing. Following fracture, p21+ neutrophils were enriched in signaling pathways known to induce paracrine stromal senescence, while p21+ OCHs were highly enriched in senescence-associated secretory phenotype factors known to impair bone formation. Further analysis revealed an injury-specific stem cell-like OCH subset that was p21+ and highly inflammatory, with a similar inflammatory mesenchymal population (fibro-adipogenic progenitors) evident following muscle injury. Thus, intercommunicating senescent-like neutrophils and mesenchymal progenitor cells are key regulators of tissue repair in bone and potentially across tissues. Moreover, our findings establish contextual roles of p21+ vs p16+ senescent/senescent-like cells that may be leveraged for therapeutic opportunities.
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9
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Soto M, Filbert EL, Yang H, Starzinski S, Starzinski A, Gin M, Chen B, Le P, Li T, Bol B, Cheung A, Zhang L, Hsu FJ, Ko A, Fong L, Keenan BP. Neoadjuvant CD40 Agonism Remodels the Tumor Immune Microenvironment in Locally Advanced Esophageal/Gastroesophageal Junction Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:200-212. [PMID: 38181044 PMCID: PMC10809910 DOI: 10.1158/2767-9764.crc-23-0550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
Sotigalimab is an agonistic anti-CD40 mAb that can modulate antitumor immune responses. In a phase II clinical trial of sotigalimab combined with neoadjuvant chemoradiation (CRT) in locally advanced esophageal/gastroesophageal junction (E/GEJ) cancer with the primary outcome of efficacy as measured by pathologic complete response (pCR) rate, the combination induced pCR in 38% of treated patients. We investigated the mechanism of action of sotigalimab in samples obtained from this clinical trial. Tumor biopsies and peripheral blood samples were collected at baseline, following an initial dose of sotigalimab, and at the time of surgery after CRT completion from six patients. High dimensional single-cell techniques were used, including combined single-cell RNA-sequencing and proteomics (CITEseq) and multiplexed ion beam imaging, to analyze immune responses. Sotigalimab dramatically remodeled the immune compartment in the periphery and within the tumor microenvironment (TME), increasing expression of molecules related to antigen processing and presentation and altering metabolic pathways in myeloid cells. Concomitant with these changes in myeloid cells, sotigalimab treatment primed new T cell clonotypes and increased the density and activation of T cells with enhanced cytotoxic function. Sotigalimab treatment also induced a decrease in the frequency of Tregs in the TME. These findings indicate that a single dose of sotigalimab leads to enhanced antigen presentation that can activate T cells and induce new T cell clones. This restructuring of the TME provides elements which are critical to the development of effective antitumor immune responses and improved clinical outcomes.
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Affiliation(s)
- Maira Soto
- Pyxis Oncology, Inc., Boston, Massachusetts
- Apexigen America, Inc, San Carlos, California (now a fully owned subsidiary of Pyxis Oncology, Inc.)
| | - Erin L. Filbert
- Apexigen America, Inc, San Carlos, California (now a fully owned subsidiary of Pyxis Oncology, Inc.)
| | - Hai Yang
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Stephanie Starzinski
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Alec Starzinski
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Marissa Gin
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Brandon Chen
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Phi Le
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Tony Li
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Brandon Bol
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Alexander Cheung
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Li Zhang
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
- Division of Hematology/Oncology, University of California, San Francisco, California
| | - Frank J. Hsu
- Pyxis Oncology, Inc., Boston, Massachusetts
- Apexigen America, Inc, San Carlos, California (now a fully owned subsidiary of Pyxis Oncology, Inc.)
| | - Andrew Ko
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology/Oncology, University of California, San Francisco, California
| | - Lawrence Fong
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology/Oncology, University of California, San Francisco, California
| | - Bridget P. Keenan
- Cancer Immunotherapy Program, University of California, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Division of Hematology/Oncology, University of California, San Francisco, California
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10
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Chen G, Chong H, Zhang P, Wen D, Du J, Gao C, Zeng S, Zeng L, Deng J, Zhang K, Zhang A. An integrative model with HLA-DR, CD64, and PD-1 for the diagnostic and prognostic evaluation of sepsis. Immun Inflamm Dis 2024; 12:e1138. [PMID: 38270311 PMCID: PMC10777881 DOI: 10.1002/iid3.1138] [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: 03/28/2023] [Revised: 12/12/2023] [Accepted: 12/16/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection and progressive immunosuppression with high mortality. HLA-DR, CD64, and PD-1 were assumed to be useful biomarkers for sepsis prediction. However, the ability of a combination of these biomarkers has not been clarified. METHODS An observational case-control study was conducted that included 30 sepsis patients, 30 critically ill patients without sepsis admitted to the intensive care unit (ICU), and 32 healthy individuals. The levels of HLA-DR, CD64, and PD-1 expression in peripheral blood immune cells and subsets was assayed on Days 1, 3, and 5, and the clinical information of patients was collected. We compared these biomarkers between groups and evaluated the predictive validity of single and combined biomarkers on sepsis mortality. RESULTS The results indicate that PD-1 expression on CD4- CD8- T (PD-1+ CD4- CD8- T) (19.19% ± 10.78% vs. 9.88% ± 1.79%, p = .004) cells and neutrophil CD64 index (nCD64 index) (9.15 ± 5.46 vs. 5.33 ± 2.34, p = .001) of sepsis patients were significantly increased, and HLA-DR expression on monocytes (mHLA-DR+ ) was significantly reduced (13.26% ± 8.06% vs. 30.17% ± 21.42%, p = 2.54 × 10-4 ) compared with nonsepsis critically ill patients on the first day. Importantly, the expression of PD-1+ CD4- CD8- T (OR = 0.622, 95% CI = 0.423-0.916, p = .016) and mHLA-DR+ (OR = 1.146, 95% CI = 1.014-1.295, p = .029) were significantly associated with sepsis mortality. For sepsis diagnosis, the mHLA-DR+ , PD-1+ CD4- CD8- T, and nCD64 index showed the moderate individual performance, and combinations of the three biomarkers achieved greater diagnostic value (AUC = 0.899, 95% CI = 0.792-0.962). When adding PCT into the combined model, the AUC increased to 0.936 (95% CI = 0.840-0.983). For sepsis mortality, combinations of PD-1+ CD4- CD8- T and mHLA-DR+ , have a good ability to predict the prognosis of sepsis patients, with an AUC = 0.921 (95% CI = 0.762-0.987). CONCLUSION These findings indicate that the combinations of HLA-DR, CD64, and PD-1 outperformed each of the single indicator in diagnosis and predicting prognosis of sepsis.
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Affiliation(s)
- Guosheng Chen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
- Department of EmergencyThe Affiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Huimin Chong
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Peng Zhang
- Yubei District Hospital of TCMChongqingChina
| | - Dalin Wen
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Juan Du
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Chu Gao
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Shi Zeng
- Department of NeurosurgeryThe People's Hospital of Chongqing Banan DistrictChongqingChina
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Jin Deng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
- Department of EmergencyThe Affiliated Hospital of Guizhou Medical UniversityGuiyangChina
| | - Kejun Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Anqiang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping HospitalArmy Medical University (Third Military Medical University)ChongqingChina
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11
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Bewersdorf JP, Shallis RM, Sharon E, Park S, Ramaswamy R, Roe CE, Irish JM, Caldwell A, Wei W, Yacoub A, Madanat YF, Zeidner JF, Altman JK, Odenike O, Yerrabothala S, Kovacsovics T, Podoltsev NA, Halene S, Little RF, Piekarz R, Gore SD, Kim TK, Zeidan AM. A multicenter phase Ib trial of the histone deacetylase inhibitor entinostat in combination with pembrolizumab in patients with myelodysplastic syndromes/neoplasms or acute myeloid leukemia refractory to hypomethylating agents. Ann Hematol 2024; 103:105-116. [PMID: 38036712 DOI: 10.1007/s00277-023-05552-4] [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: 09/28/2023] [Accepted: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Patients with myelodysplastic syndromes/neoplasms (MDS) or acute myeloid leukemia (AML) with hypomethylating agent failure have a poor prognosis. Myeloid-derived suppressor cells (MDSCs) can contribute to MDS progression and mediate resistance to anti-PD1 therapy. As histone deacetylase inhibitors (HDACi) decrease MDSCs in preclinical models, we conducted an investigator-initiated, NCI-Cancer Therapy Evaluation Program-sponsored, multicenter, dose escalation, and expansion phase Ib trial (NCT02936752) of the HDACi entinostat and the anti-PD1 antibody pembrolizumab. Twenty-eight patients (25 MDS and 3 AML) were enrolled. During dose escalation (n=13 patients), there was one dose-limiting toxicity (DLT) on dose level (DL) 1 (G5 pneumonia/bronchoalveolar hemorrhage) and two DLTs at DL 2 (G3 pharyngeal mucositis and G3 anorexia). Per the 3 + 3 dose escalation design, DL 1 (entinostat 8 mg PO days 1 and 15 + pembrolizumab 200 mg IV day 1 every 21 days) was expanded and another 15 patients were enrolled. Hematologic adverse events (AEs) were common. The most common non-hematologic ≥G3 AEs were infection (32%), hypoxia/respiratory failure (11%), and dyspnea (11%). There were no protocol-defined responses among the 28 patients enrolled. Two patients achieved a marrow complete remission (mCR). Using a systems immunology approach with mass cytometry and machine learning analysis, mCR patients had increased classical monocytes and macrophages but there was no significant change of MDSCs. In conclusion, combining entinostat with pembrolizumab in patients with advanced MDS and AML was associated with limited clinical efficacy and substantial toxicity. Absence of an effect on MDSCs could be a potential explanation for the limited efficacy of this combination. ClinicalTrial.gov Identifier: NCT02936752.
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Affiliation(s)
- Jan Philipp Bewersdorf
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Rory M Shallis
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Elad Sharon
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Silvia Park
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rahul Ramaswamy
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA
| | - Anne Caldwell
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Wei Wei
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Abdulraheem Yacoub
- The Division of Hematologic Malignancies and Cellular Therapeutics (HMCT), The University of Kansas Cancer Center, Westwood, KS, USA
| | - Yazan F Madanat
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua F Zeidner
- Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jessica K Altman
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | | | | | | | - Nikolai A Podoltsev
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Richard F Little
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Richard Piekarz
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Steven D Gore
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA
| | - Tae Kon Kim
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Center for Immunobiology, Vanderbilt University, Nashville, TN, USA.
| | - Amer M Zeidan
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
- Hematology Section, Department of Internal Medicine, Yale School of Medicine, Yale University, 333 Cedar Street, PO Box 208028, New Haven, CT, 06520-8028, USA.
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12
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Alinger JB, Mace EM, Porter JR, Mah-Som AY, Daugherty AL, Li S, Throm AA, Pingel JT, Saucier N, Yao A, Chinn IK, Lupski JR, Ehlayel M, Keller M, Bowman GR, Cooper MA, Orange JS, French AR. Human PLCG2 haploinsufficiency results in a novel natural killer cell immunodeficiency. J Allergy Clin Immunol 2024; 153:216-229. [PMID: 37714437 DOI: 10.1016/j.jaci.2023.09.002] [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: 02/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND Although most individuals effectively control herpesvirus infections, some suffer from severe and/or recurrent infections. A subset of these patients possess defects in natural killer (NK) cells, lymphocytes that recognize and lyse herpesvirus-infected cells; however, the genetic etiology is rarely diagnosed. PLCG2 encodes a signaling protein in NK-cell and B-cell signaling. Dominant-negative or gain-of-function variants in PLCG2 cause cold urticaria, antibody deficiency, and autoinflammation. However, loss-of-function variants and haploinsufficiency have not been reported to date. OBJECTIVES The investigators aimed to identify the genetic cause of NK-cell immunodeficiency in 2 families and herein describe the functional consequences of 2 novel loss-of-function variants in PLCG2. METHODS The investigators employed whole-exome sequencing in conjunction with mass cytometry, microscopy, functional assays, and a mouse model of PLCG2 haploinsufficiency to investigate 2 families with NK-cell immunodeficiency. RESULTS The investigators identified novel heterozygous variants in PLCG2 in 2 families with severe and/or recurrent herpesvirus infections. In vitro studies demonstrated that these variants were loss of function due to haploinsufficiency with impaired NK-cell calcium flux and cytotoxicity. In contrast to previous PLCG2 variants, B-cell function remained intact. Plcg2+/- mice also displayed impaired NK-cell function with preserved B-cell function, phenocopying human disease. CONCLUSIONS PLCG2 haploinsufficiency represents a distinct syndrome from previous variants characterized by NK-cell immunodeficiency with herpesvirus susceptibility, expanding the spectrum of PLCG2-related disease.
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Affiliation(s)
- Joshua B Alinger
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Emily M Mace
- Departments of Pediatrics, Baylor College of Medicine, Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Justin R Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Mo
| | - Annelise Y Mah-Som
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Allyssa L Daugherty
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Stephanie Li
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Allison A Throm
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Jeanette T Pingel
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Nermina Saucier
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Albert Yao
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Ivan K Chinn
- Departments of Pediatrics, Baylor College of Medicine, Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex
| | - James R Lupski
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex
| | | | | | - Greg R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Mo
| | - Megan A Cooper
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo
| | - Jordan S Orange
- Departments of Pediatrics, Baylor College of Medicine, Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Center for Human Immunobiology, Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY
| | - Anthony R French
- Division of Rheumatology, Department of Pediatrics, St Louis Children's Hospital, Washington University School of Medicine, St Louis, Mo.
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13
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Zivanovic N, Öner D, Abraham Y, McGinley J, Drysdale SB, Wildenbeest JG, Crabbe M, Vanhoof G, Thys K, Thwaites RS, Robinson H, Bont L, Openshaw PJM, Martinón‐Torres F, Pollard AJ, Aerssens J. Single-cell immune profiling reveals markers of emergency myelopoiesis that distinguish severe from mild respiratory syncytial virus disease in infants. Clin Transl Med 2023; 13:e1507. [PMID: 38115705 PMCID: PMC10731116 DOI: 10.1002/ctm2.1507] [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: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023] Open
Abstract
Whereas most infants infected with respiratory syncytial virus (RSV) show no or only mild symptoms, an estimated 3 million children under five are hospitalized annually due to RSV disease. This study aimed to investigate biological mechanisms and associated biomarkers underlying RSV disease heterogeneity in young infants, enabling the potential to objectively categorize RSV-infected infants according to their medical needs. Immunophenotypic and functional profiling demonstrated the emergence of immature and progenitor-like neutrophils, proliferative monocytes (HLA-DRLow , Ki67+), impaired antigen-presenting function, downregulation of T cell response and low abundance of HLA-DRLow B cells in severe RSV disease. HLA-DRLow monocytes were found as a hallmark of RSV-infected infants requiring hospitalization. Complementary transcriptomics identified genes associated with disease severity and pointed to the emergency myelopoiesis response. These results shed new light on mechanisms underlying the pathogenesis and development of severe RSV disease and identified potential new candidate biomarkers for patient stratification.
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Affiliation(s)
- Nevena Zivanovic
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Deniz Öner
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Yann Abraham
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Joseph McGinley
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Simon B. Drysdale
- Centre for Neonatal and Paediatric Infection, Institute for Infection and Immunity, St George's, University of LondonLondonUK
| | - Joanne G. Wildenbeest
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Marjolein Crabbe
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Greet Vanhoof
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Kim Thys
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
| | - Ryan S. Thwaites
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Hannah Robinson
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Louis Bont
- Department of Pediatric Infectious Diseases and ImmunologyWilhelmina Children's Hospital, University Medical Center UtrechtUtrechtThe Netherlands
| | - Peter J. M. Openshaw
- Department of Respiratory MedicineNational Heart and Lung Institute, Imperial College LondonLondonUK
| | - Federico Martinón‐Torres
- Pediatrics DepartmentTranslational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de CompostelaGaliciaSpain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, University of Santiago de CompostelaGaliciaSpain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadridSpain
| | | | - Andrew J. Pollard
- Department of PaediatricsOxford Vaccine Group, NIHR Oxford Biomedical Research Centre, University of OxfordLondonUK
| | - Jeroen Aerssens
- Discovery Sciences & Translational Biomarkers Infectious DiseasesJanssen Research and DevelopmentBeerseBelgium
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14
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Kverneland A, Thorsen S, Granhøj J, Hansen F, Konge M, Ellebæk E, Donia M, Svane I. Supervised clustering of peripheral immune cells associated with clinical response to checkpoint inhibitor therapy in patients with advanced melanoma. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 20:100396. [PMID: 37810199 PMCID: PMC10558712 DOI: 10.1016/j.iotech.2023.100396] [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] [Indexed: 10/10/2023]
Abstract
Background and purpose Immune therapy with checkpoint inhibitors (CPIs) is a highly successful therapy in many cancers including metastatic melanoma. Still, many patients do not respond well to therapy and there are no blood-borne biomarkers available to assess the clinical outcome. Materials and methods To investigate cellular changes after CPI therapy, we carried out flow cytometry-based immune monitoring in a cohort of 90 metastatic melanoma patients before and after CPI therapy using the FlowSOM algorithm. To evaluate associations to the clinical outcome with therapy, we divided the patients based on progression-free survival. Results We found significant associations with CPI therapy in both peripheral blood mononuclear cell and T-cell subsets, but with the most pronounced effects in the latter. Particularly CD4+ effector memory T-cell subsets were associated with response with a positive correlation between CD27+HLA-DR+CD4+ effector memory T cells in a univariate (odds ratio: 1.07 [95% confidence interval 1.02-1.12]) and multivariate regression model (odds ratio: 1.08 [95% confidence interval 1.03-1.14]). We also found a trend towards stronger accumulation of CD57+CD8+ T cells in non-responding patients. Conclusion Our results show significant associations between immune monitoring and clinical outcome of therapy that could be evaluated as biomarkers in a clinical setting.
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Affiliation(s)
- A.H. Kverneland
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen
| | - S.U. Thorsen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - J.S. Granhøj
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
| | - F.S. Hansen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
| | - M. Konge
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
| | - E. Ellebæk
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
| | - M. Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
| | - I.M. Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev
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15
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Martinez-Navajas G, Ceron-Hernandez J, Simon I, Lupiañez P, Diaz-McLynn S, Perales S, Modlich U, Guerrero JA, Martin F, Sevivas T, Lozano ML, Rivera J, Ramos-Mejia V, Tersteeg C, Real PJ. Lentiviral gene therapy reverts GPIX expression and phenotype in Bernard-Soulier syndrome type C. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:75-92. [PMID: 37416759 PMCID: PMC10320622 DOI: 10.1016/j.omtn.2023.06.008] [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: 02/03/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Bernard-Soulier syndrome (BSS) is a rare congenital disease characterized by macrothrombocytopenia and frequent bleeding. It is caused by pathogenic variants in three genes (GP1BA, GP1BB, or GP9) that encode for the GPIbα, GPIbβ, and GPIX subunits of the GPIb-V-IX complex, the main platelet surface receptor for von Willebrand factor, being essential for platelet adhesion and aggregation. According to the affected gene, we distinguish BSS type A1 (GP1BA), type B (GP1BB), or type C (GP9). Pathogenic variants in these genes cause absent, incomplete, or dysfunctional GPIb-V-IX receptor and, consequently, a hemorrhagic phenotype. Using gene-editing tools, we generated knockout (KO) human cellular models that helped us to better understand GPIb-V-IX complex assembly. Furthermore, we developed novel lentiviral vectors capable of correcting GPIX expression, localization, and functionality in human GP9-KO megakaryoblastic cell lines. Generated GP9-KO induced pluripotent stem cells produced platelets that recapitulated the BSS phenotype: absence of GPIX on the membrane surface and large size. Importantly, gene therapy tools reverted both characteristics. Finally, hematopoietic stem cells from two unrelated BSS type C patients were transduced with the gene therapy vectors and differentiated to produce GPIX-expressing megakaryocytes and platelets with a reduced size. These results demonstrate the potential of lentiviral-based gene therapy to rescue BSS type C.
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Affiliation(s)
- Gonzalo Martinez-Navajas
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Jorge Ceron-Hernandez
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Iris Simon
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Pablo Lupiañez
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
| | - Sofia Diaz-McLynn
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
| | - Sonia Perales
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
| | - Ute Modlich
- Department of Gene and Cell Therapy, Institute of Regenerative Medicine, University of Zürich, Wagistrasse 12, 8952 Schlieren-Zürich, Switzerland
| | - Jose A. Guerrero
- Department of Haematology, University of Cambridge, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Francisco Martin
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, Avenida Ilustracion S/n, 18016 Granada, Spain
| | - Teresa Sevivas
- Serviço de Sangue, Medicina Transfusional e Imunohemoterapia Do Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Maria L. Lozano
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, U765 Murcia, Spain
| | - Jose Rivera
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, U765 Murcia, Spain
- Grupo Español de Alteraciones Plaquetarias Congénitas (GEAPC), Madrid, Spain
| | - Veronica Ramos-Mejia
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
| | - Claudia Tersteeg
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk, Belgium
| | - Pedro J. Real
- GENyO, Pfizer-Universidad de Granada-Junta de Andalucia Centre for Genomics and Oncological Research, PTS, Granada, Avenida de la Ilustracion 114, 18016 Granada, Spain
- University of Granada, Department of Biochemistry and Molecular Biology I, Faculty of Science, Avenida Fuentenueva S/n, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs.GRANADA, Granada, Spain
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16
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Ma W, Wei S, Long S, Tian EC, McLaughlin B, Jaimes M, Montoya DJ, Viswanath VR, Chien J, Zhang Q, Van Dyke JE, Chen S, Li T. Dynamic evaluation of blood immune cells predictive of response to immune checkpoint inhibitors in NSCLC by multicolor spectrum flow cytometry. Front Immunol 2023; 14:1206631. [PMID: 37638022 PMCID: PMC10449448 DOI: 10.3389/fimmu.2023.1206631] [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: 04/16/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction Immune checkpoint inhibitors (ICIs) only benefit a subset of cancer patients, underlining the need for predictive biomarkers for patient selection. Given the limitations of tumor tissue availability, flow cytometry of peripheral blood mononuclear cells (PBMCs) is considered a noninvasive method for immune monitoring. This study explores the use of spectrum flow cytometry, which allows a more comprehensive analysis of a greater number of markers using fewer immune cells, to identify potential blood immune biomarkers and monitor ICI treatment in non-small-cell lung cancer (NSCLC) patients. Methods PBMCs were collected from 14 non-small-cell lung cancer (NSCLC) patients before and after ICI treatment and 4 healthy human donors. Using spectrum flow cytometry, 24 immune cell markers were simultaneously monitored using only 1 million PBMCs. The results were also compared with those from clinical flow cytometry and bulk RNA sequencing analysis. Results Our findings showed that the measurement of CD4+ and CD8+ T cells by spectrum flow cytometry matched well with those by clinical flow cytometry (Pearson R ranging from 0.75 to 0.95) and bulk RNA sequencing analysis (R=0.80, P=1.3 x 10-4). A lower frequency of CD4+ central memory cells before treatment was associated with a longer median progression-free survival (PFS) [Not reached (NR) vs. 5 months; hazard ratio (HR)=8.1, 95% confidence interval (CI) 1.5-42, P=0.01]. A higher frequency of CD4-CD8- double-negative (DN) T cells was associated with a longer PFS (NR vs. 4.45 months; HR=11.1, 95% CI 2.2-55.0, P=0.003). ICIs significantly changed the frequency of cytotoxic CD8+PD1+ T cells, DN T cells, CD16+CD56dim and CD16+CD56- natural killer (NK) cells, and CD14+HLDRhigh and CD11c+HLADR + monocytes. Of these immune cell subtypes, an increase in the frequency of CD16+CD56dim NK cells and CD14+HLADRhigh monocytes after treatment compared to before treatment were associated with a longer PFS (NR vs. 5 months, HR=5.4, 95% CI 1.1-25.7, P=0.03; 7.8 vs. 3.8 months, HR=5.7, 95% CI 169 1.0-31.7, P=0.04), respectively. Conclusion Our preliminary findings suggest that the use of multicolor spectrum flow cytometry helps identify potential blood immune biomarkers for ICI treatment, which warrants further validation.
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Affiliation(s)
- Weijie Ma
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine, Dartmouth, NH, United States
| | - Sixi Wei
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Siqi Long
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Eddie C. Tian
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Bridget McLaughlin
- University of California Davis, Flow cytometry Shared Resource, Davis, CA, United States
| | | | - Dennis J. Montoya
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA, United States
| | - Varun R. Viswanath
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
| | - Jeremy Chien
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, CA, United States
| | - Qianjun Zhang
- Beckman Coulter Life Sciences, San Jose, CA, United States
| | - Jonathan E. Van Dyke
- University of California Davis, Flow cytometry Shared Resource, Davis, CA, United States
| | - Shuai Chen
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, Davis, CA, United States
| | - Tianhong Li
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, University of California Davis School of Medicine, Sacramento, CA, United States
- Medical Service, Hematology and Oncology, Veterans Affairs Northern California Health Care System, Mather, CA, United States
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17
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Yamamoto T, Tsunedomi R, Nakajima M, Suzuki N, Yoshida S, Tomochika S, Xu M, Nakagami Y, Matsui H, Tokumitsu Y, Shindo Y, Watanabe Y, Iida M, Takeda S, Hazama S, Tanabe T, Ioka T, Hoshii Y, Kiyota A, Takizawa H, Kawakami Y, Ueno T, Nagano H. IL-6 Levels Correlate with Prognosis and Immunosuppressive Stromal Cells in Patients with Colorectal Cancer. Ann Surg Oncol 2023; 30:5267-5277. [PMID: 37222942 DOI: 10.1245/s10434-023-13527-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 04/05/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND The prognosis for patients with colorectal cancer (CRC) is determined by tumor characteristics as well as the host immune response. This study investigated the relationship between an immunosuppressive state and patient prognosis by evaluating the systemic and tumor microenvironment (TME) interleukin (IL)-6 levels. METHODS Preoperative serum IL-6 levels were measured using an electrochemiluminescence assay. Expression of IL-6 in tumor and stromal cells was evaluated immunohistochemically in 209 patients with resected CRC. Single-cell analysis of tumor-infiltrating immune cells was performed using mass cytometry in 10 additional cases. RESULTS Elevated serum IL-6 levels were associated with elevated stromal IL-6 levels and a poor prognosis for patients with CRC. High IL-6 expression in stromal cells was associated with low-density subsets of CD3+ and CD4+ T cells as well as FOXP3+ cells. Mass cytometry analysis showed that IL-6+ cells among tumor-infiltrating immune cells were composed primarily of myeloid cells and rarely of lymphoid cells. In the high-IL-6-expression group, the percentages of myeloid-derived suppressor cells (MDSCs) and CD4+FOXP3highCD45RA- effector regulatory T cells (eTreg) were significantly higher than in the low-IL-6-expression group. Furthermore, the proportion of IL-10+ cells in MDSCs and that of IL-10+ or CTLA-4+ cells in eTregs correlated with IL-6 levels. CONCLUSION Elevated serum IL-6 levels were associated with stromal IL-6 levels in CRC. High IL-6 expression in tumor-infiltrating immune cells also was associated with accumulation of immunosuppressive cells in the TME.
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Affiliation(s)
- Tsunenori Yamamoto
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Masao Nakajima
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Nobuaki Suzuki
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shin Yoshida
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shinobu Tomochika
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Ming Xu
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yuki Nakagami
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
- Department of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Hiroto Matsui
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yukio Tokumitsu
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yoshitaro Shindo
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yusaku Watanabe
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Michihisa Iida
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shigeru Takeda
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shoichi Hazama
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Tsuyoshi Tanabe
- Department of Public Health and Preventive Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Tatsuya Ioka
- Oncology Center, Yamaguchi University Hospital, Ube, Yamaguchi, Japan
| | - Yoshinobu Hoshii
- Department of Diagnostic Pathology, Yamaguchi University Hospital, Ube, Yamaguchi, Japan
| | - Akifumi Kiyota
- Center for Medical Sciences, Kumamoto University International Research, Kumamoto, Kumamoto, Japan
| | - Hitoshi Takizawa
- Center for Medical Sciences, Kumamoto University International Research, Kumamoto, Kumamoto, Japan
| | - Yutaka Kawakami
- Division of Cellular Signaling, Institute for Advanced Medical Research, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Tomio Ueno
- Department of Digestive Surgery, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan.
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18
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Doolittle ML, Saul D, Kaur J, Rowsey JL, Vos SJ, Pavelko KD, Farr JN, Monroe DG, Khosla S. Multiparametric senescent cell phenotyping reveals targets of senolytic therapy in the aged murine skeleton. Nat Commun 2023; 14:4587. [PMID: 37524694 PMCID: PMC10390564 DOI: 10.1038/s41467-023-40393-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Senescence drives organismal aging, yet the deep characterization of senescent cells in vivo remains incomplete. Here, we apply mass cytometry by time-of-flight using carefully validated antibodies to analyze senescent cells at single-cell resolution. We use multiple criteria to identify senescent mesenchymal cells that are growth-arrested and resistant to apoptosis. These p16 + Ki67-BCL-2+ cells are highly enriched for senescence-associated secretory phenotype and DNA damage markers, are strongly associated with age, and their percentages are increased in late osteoblasts/osteocytes and CD24high osteolineage cells. Moreover, both late osteoblasts/osteocytes and CD24high osteolineage cells are robustly cleared by genetic and pharmacologic senolytic therapies in aged mice. Following isolation, CD24+ skeletal cells exhibit growth arrest, senescence-associated β-galactosidase positivity, and impaired osteogenesis in vitro. These studies thus provide an approach using multiplexed protein profiling to define senescent mesenchymal cells in vivo and identify specific skeletal cell populations cleared by senolytics.
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Affiliation(s)
- Madison L Doolittle
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Dominik Saul
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
- Department for Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Tübingen, Germany
| | - Japneet Kaur
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jennifer L Rowsey
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Stephanie J Vos
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kevin D Pavelko
- Department of Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joshua N Farr
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - David G Monroe
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sundeep Khosla
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA.
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA.
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19
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Tan Y, Wang Y, Souza-Moreira L, Wang C, Murray ABP, Salkhordeh M, Florian M, McIntyre L, Stewart DJ, Mei SHJ. Mesenchymal stem cells induce dynamic immunomodulation of airway and systemic immune cells in vivo but do not improve survival for mice with H1N1 virus-induced acute lung injury. Front Bioeng Biotechnol 2023; 11:1203387. [PMID: 37362215 PMCID: PMC10285296 DOI: 10.3389/fbioe.2023.1203387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Influenza A virus (IAV)-induced acute lung injury (ALI) is characterized by pronounced proinflammatory activation and respiratory lung dysfunction. In this study, we performed deep immune profiling on airway and circulating immune cells to examine the effect of immunomodulation and therapeutic outcomes of mesenchymal stem cells (MSCs) therapy in mice with IAV-induced ALI. Methods: Animals were inoculated intranasally with H1N1 IAV, followed by intravenous administration of vehicle, or human clinical-grade, bone marrow-derived MSCs 24-h later, and monitored for six days to evaluate the survival. In another set of animals, bronchoalveolar lavage (BAL) fluid and whole blood were collected three days after infection for flow or mass cytometry (CyTOF) immune profiling analysis. Results: Immune cell population and phenotypic shifts in blood were mapped by CyTOF. Increases were observed in granulocytes and myeloid-derived cells in blood from vehicle-treated animals. While MSC treatment accentuated changes in these populations, naïve B, antibody-secreting B cells, and T cells were decreased in MSC-treated animals at day 3. Compared to sham animals, IAV infection induced a significant 5.5-fold increase in BAL total cell counts, including CD4+ and CD8+ T cells, CD19+ B cells, CD11b + Ly6G + neutrophils, and CD11b + Ly6C + monocytes. MSC treatment significantly decreased BAL total cell counts in IAV-infected mice, specifically the number of infiltrating CD4+ T cells and CD11b + Ly6G + neutrophils. In contrast, there were increases in CD8+ T cells, B cells, and monocytes in the alveolar space in MSC-treated animals. Phenotypic immune cell profiling of blood and BAL revealed a significantly higher proportion of the monocyte population with the M2 phenotype (CD206) in MSC-treated animals; however, this failed to confer protective effects in the survival of infected mice or reduce viral titer in the lung. Further investigation revealed that MSCs were susceptible to IAV infection, leading to increased cell death and potentially affecting their efficacy. Conclusion: These findings provided in vivo evidence that MSCs promote the selective recruitment of immune cells to the site of infection during IAV infection, with reductions in proinflammatory phenotypes. However, MSCs offered no survival benefit in IAV-infected animals, possibly due to MSCs' H1N1 IAV susceptibility and subsequent cell death.
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Affiliation(s)
- Yuan Tan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Yan Wang
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Luciana Souza-Moreira
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Chi Wang
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Aidan B. P. Murray
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Mahmoud Salkhordeh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Maria Florian
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lauralyn McIntyre
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Duncan J. Stewart
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Shirley H. J. Mei
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
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20
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Kumar A, Taghi Khani A, Duault C, Aramburo S, Sanchez Ortiz A, Lee SJ, Chan A, McDonald T, Huang M, Lacayo NJ, Sakamoto KM, Yu J, Hurtz C, Carroll M, Tasian SK, Ghoda L, Marcucci G, Gu Z, Rosen ST, Armenian S, Izraeli S, Chen CW, Caligiuri MA, Forman SJ, Maecker HT, Swaminathan S. Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia. J Immunother Cancer 2023; 11:jitc-2022-006649. [PMID: 37217248 DOI: 10.1136/jitc-2022-006649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Type I interferons (IFN-Is), secreted by hematopoietic cells, drive immune surveillance of solid tumors. However, the mechanisms of suppression of IFN-I-driven immune responses in hematopoietic malignancies including B-cell acute lymphoblastic leukemia (B-ALL) are unknown. METHODS Using high-dimensional cytometry, we delineate the defects in IFN-I production and IFN-I-driven immune responses in high-grade primary human and mouse B-ALLs. We develop natural killer (NK) cells as therapies to counter the intrinsic suppression of IFN-I production in B-ALL. RESULTS We find that high expression of IFN-I signaling genes predicts favorable clinical outcome in patients with B-ALL, underscoring the importance of the IFN-I pathway in this malignancy. We show that human and mouse B-ALL microenvironments harbor an intrinsic defect in paracrine (plasmacytoid dendritic cell) and/or autocrine (B-cell) IFN-I production and IFN-I-driven immune responses. Reduced IFN-I production is sufficient for suppressing the immune system and promoting leukemia development in mice prone to MYC-driven B-ALL. Among anti-leukemia immune subsets, suppression of IFN-I production most markedly lowers the transcription of IL-15 and reduces NK-cell number and effector maturation in B-ALL microenvironments. Adoptive transfer of healthy NK cells significantly prolongs survival of overt ALL-bearing transgenic mice. Administration of IFN-Is to B-ALL-prone mice reduces leukemia progression and increases the frequencies of total NK and NK-cell effectors in circulation. Ex vivo treatment of malignant and non-malignant immune cells in primary mouse B-ALL microenvironments with IFN-Is fully restores proximal IFN-I signaling and partially restores IL-15 production. In B-ALL patients, the suppression of IL-15 is the most severe in difficult-to-treat subtypes with MYC overexpression. MYC overexpression promotes sensitivity of B-ALL to NK cell-mediated killing. To counter the suppressed IFN-I-induced IL-15 production in MYChigh human B-ALL, we CRISPRa-engineered a novel human NK-cell line that secretes IL-15. CRISPRa IL-15-secreting human NK cells kill high-grade human B-ALL in vitro and block leukemia progression in vivo more effectively than NK cells that do not produce IL-15. CONCLUSION We find that restoration of the intrinsically suppressed IFN-I production in B-ALL underlies the therapeutic efficacy of IL-15-producing NK cells and that such NK cells represent an attractive therapeutic solution for the problem of drugging MYC in high-grade B-ALL.
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Affiliation(s)
- Anil Kumar
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Adeleh Taghi Khani
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Caroline Duault
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA
| | - Soraya Aramburo
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Ashly Sanchez Ortiz
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Sung June Lee
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Anthony Chan
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Tinisha McDonald
- The Hematopoietic Tissue Biorepository/Research Pathology Shared Resources, City of Hope, Duarte, California, USA
| | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Norman J Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Christian Hurtz
- Department of Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Martin Carroll
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah K Tasian
- Department of Pediatrics, Division of Oncology, The Children's Hospital, Philadelphia, Pennsylvania, USA
| | - Lucy Ghoda
- Hematological Malignancies Translational Science, City of Hope, Duarte, California, USA
| | - Guido Marcucci
- The Hematopoietic Tissue Biorepository/Research Pathology Shared Resources, City of Hope, Duarte, California, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
- Hematological Malignancies Translational Science, City of Hope, Duarte, California, USA
| | - Zhaohui Gu
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Steven T Rosen
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Saro Armenian
- Department of Pediatrics, City of Hope, Duarte, California, USA
| | - Shai Izraeli
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
- Hematology-Oncology Department, Tel Aviv University, Tel Aviv, Israel
| | - Chun-Wei Chen
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Michael A Caligiuri
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Stephen J Forman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA
| | - Srividya Swaminathan
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
- Department of Pediatrics, City of Hope, Duarte, California, USA
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21
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Anagnostou T, Yang ZZ, Jalali S, Kim HJ, Larson DP, Tang X, Yu Y, Pritchett JC, Bisneto JV, Price-Troska TL, Mondello P, Novak AJ, Ansell SM. Characterization of immune exhaustion and suppression in the tumor microenvironment of splenic marginal zone lymphoma. Leukemia 2023:10.1038/s41375-023-01911-2. [PMID: 37117318 DOI: 10.1038/s41375-023-01911-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023]
Abstract
The role of the tumor microenvironment (TME) and intratumoral T cells in splenic marginal zone lymphoma (sMZL) is largely unknown. In the present study, we evaluated 36 sMZL spleen specimens by single cell analysis to gain a better understanding of the TME in sMZL. Using mass cytometry (CyTOF), we observed that the TME in sMZL is distinct from that of control non-malignant reactive spleen (rSP). We found that the number of TFH cells varied greatly in sMZL, ICOS+ TFH cells were more abundant in sMZL than rSP, and TFH cells positively correlated with increased numbers of memory B cells. Treg cell analysis revealed that TIGIT+ Treg cells are enriched in sMZL and correlate with suppression of TH17 and TH22 cells. Intratumoral CD8+ T cells were comprised of subsets of short-lived, exhausted and late-stage differentiated cells, thereby functionally impaired. We observed that T-cell exhaustion was present in sMZL and TIM-3 expression on PD-1low cells identified cells with severe immune dysfunction. Gene expression profiling by CITE-seq analysis validated this finding. Taken together, our data suggest that the TME as a whole, and T-cell population specifically, are heterogenous in sMZL and immune exhaustion is one of the major factors impairing T-cell function.
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Affiliation(s)
- Theodora Anagnostou
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhi-Zhang Yang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Shahrzad Jalali
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Hyo Jin Kim
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Xinyi Tang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yue Yu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Joshua C Pritchett
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Patrizia Mondello
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stephen M Ansell
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, MN, USA.
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22
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Sülzen H, Began J, Dhillon A, Kereïche S, Pompach P, Votrubova J, Zahedifard F, Šubrtova A, Šafner M, Hubalek M, Thompson M, Zoltner M, Zoll S. Cryo-EM structures of Trypanosoma brucei gambiense ISG65 with human complement C3 and C3b and their roles in alternative pathway restriction. Nat Commun 2023; 14:2403. [PMID: 37105991 PMCID: PMC10140031 DOI: 10.1038/s41467-023-37988-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
African Trypanosomes have developed elaborate mechanisms to escape the adaptive immune response, but little is known about complement evasion particularly at the early stage of infection. Here we show that ISG65 of the human-infective parasite Trypanosoma brucei gambiense is a receptor for human complement factor C3 and its activation fragments and that it takes over a role in selective inhibition of the alternative pathway C5 convertase and thus abrogation of the terminal pathway. No deposition of C4b, as part of the classical and lectin pathway convertases, was detected on trypanosomes. We present the cryo-electron microscopy (EM) structures of native C3 and C3b in complex with ISG65 which reveal a set of modes of complement interaction. Based on these findings, we propose a model for receptor-ligand interactions as they occur at the plasma membrane of blood-stage trypanosomes and may facilitate innate immune escape of the parasite.
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Affiliation(s)
- Hagen Sülzen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- Faculty of Science, Charles University, Albertov 6, 12800, Prague 2, Czech Republic
| | - Jakub Began
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- Department of Immunobiology, University of Lausanne, Chemin des Boveresses 155, 1066, Epalinges, Switzerland
| | - Arun Dhillon
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereïche
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Albertov 4, 12800, Prague, Czech Republic
| | - Petr Pompach
- Institute of Biotechnology of the Czech Academy of Sciences, 25250, Vestec, Czech Republic
| | - Jitka Votrubova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Farnaz Zahedifard
- Department of Parasitology, Faculty of Science, Charles University Prague, Biocev, 25250, Vestec, Czech Republic
| | - Adriana Šubrtova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Marie Šafner
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
| | - Maaike Thompson
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic
- University of Antwerp, Antwerp, Belgium
- Agidens, Industrial Machinery Manufacturing, Zwijndrecht, Antwerp, Belgium
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University Prague, Biocev, 25250, Vestec, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000, Prague, Czech Republic.
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23
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Ioannidis LJ, Studniberg SI, Eriksson EM, Suwarto S, Denis D, Liao Y, Shi W, Garnham AL, Sasmono RT, Hansen DS. Integrated systems immunology approach identifies impaired effector T cell memory responses as a feature of progression to severe dengue fever. J Biomed Sci 2023; 30:24. [PMID: 37055751 PMCID: PMC10103532 DOI: 10.1186/s12929-023-00916-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/02/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Typical symptoms of uncomplicated dengue fever (DF) include headache, muscle pains, rash, cough, and vomiting. A proportion of cases progress to severe dengue hemorrhagic fever (DHF), associated with increased vascular permeability, thrombocytopenia, and hemorrhages. Progression to severe dengue is difficult to diagnose at the onset of fever, which complicates patient triage, posing a socio-economic burden on health systems. METHODS To identify parameters associated with protection and susceptibility to DHF, we pursued a systems immunology approach integrating plasma chemokine profiling, high-dimensional mass cytometry and peripheral blood mononuclear cell (PBMC) transcriptomic analysis at the onset of fever in a prospective study conducted in Indonesia. RESULTS After a secondary infection, progression to uncomplicated dengue featured transcriptional profiles associated with increased cell proliferation and metabolism, and an expansion of ICOS+CD4+ and CD8+ effector memory T cells. These responses were virtually absent in cases progressing to severe DHF, that instead mounted an innate-like response, characterised by inflammatory transcriptional profiles, high circulating levels of inflammatory chemokines and with high frequencies of CD4low non-classical monocytes predicting increased odds of severe disease. CONCLUSIONS Our results suggests that effector memory T cell activation might play an important role ameliorating severe disease symptoms during a secondary dengue infection, and in the absence of that response, a strong innate inflammatory response is required to control viral replication. Our research also identified discrete cell populations predicting increased odds of severe disease, with potential diagnostic value.
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Affiliation(s)
- Lisa J Ioannidis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephanie I Studniberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Emily M Eriksson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Suhendro Suwarto
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo National Hospital (RSCM), Jakarta, Indonesia
| | - Dionisius Denis
- Eijkman Research Center for Molecular Biology, Jakarta, Indonesia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - R Tedjo Sasmono
- Eijkman Research Center for Molecular Biology, Jakarta, Indonesia
| | - Diana S Hansen
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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24
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Paterson CW, Gutierrez MB, Coopersmith CM, Ford ML. Impact of chronic alcohol exposure on conventional and regulatory murine T cell subsets. Front Immunol 2023; 14:1142614. [PMID: 37006296 PMCID: PMC10063870 DOI: 10.3389/fimmu.2023.1142614] [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: 01/11/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction Chronic alcohol use poses significant negative consequences to public health and, among its many biologic effects, is associated with significant T cell dysregulation within the adaptive immune system that has yet to be fully characterized. Novel, automated strategies for high dimensional flow cytometric analysis of the immune system are rapidly improving researchers' ability to detect and characterize rare cell types. Methods Using a murine model of chronic alcohol ingestion in conjunction with viSNE and CITRUS analysis tools, we performed a machine-driven, exploratory analysis comparing rare splenic subpopulations within the conventional CD4+, regulatory CD4+ and CD8+ T cell compartments between alcohol- and water-fed animals. Results While there were no differences in the absolute numbers of bulk CD3+ T cells, bulk CD4+ T cells, bulk CD8+ T cells, Foxp3- CD4+ conventional T cells (Tconv) or Foxp3+ CD4+ regulatory T cells (Treg), we identified populations of naïve Helios+ CD4+Tconv and naïve CD103+ CD8+ splenic T cells that were decreased in chronically alcohol exposed mice versus water-fed controls. In addition, we identified increased CD69+ Treg and decreased CD103+ effector regulatory T cell (eTreg) subsets in conjunction with increased frequency of a population that may represent a transitional phenotype between central regulatory T cell (cTreg) and eTreg. Discussion These data provide further resolution into the character of decreased naïve T cell populations known to be present in alcohol exposed mice, as well as describe alterations in effector regulatory T cell phenotypes associated with the pathogenesis of chronic alcohol-induced immune dysfunction.
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Affiliation(s)
- Cameron W. Paterson
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Medical Corps, United States Navy, Navy Reserve Officer Training Corps (NROTC), Atlanta, GA, United States
- Emory Critical Care Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Melissa B. Gutierrez
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Critical Care Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Craig M. Coopersmith
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
| | - Mandy L. Ford
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, United States
- Emory Transplant Center, Emory University School of Medicine, Atlanta, GA, United States
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25
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Wanjalla CN, Gabriel CL, Fuseini H, Bailin SS, Mashayekhi M, Simmons J, Warren CM, Glass DR, Oakes J, Gangula R, Wilfong E, Priest S, Temu T, Newell EW, Pakala S, Kalams SA, Gianella S, Smith D, Harrison DG, Mallal SA, Koethe JR. CD4 + T cells expressing CX3CR1, GPR56, with variable CD57 are associated with cardiometabolic diseases in persons with HIV. Front Immunol 2023; 14:1099356. [PMID: 36865544 PMCID: PMC9971959 DOI: 10.3389/fimmu.2023.1099356] [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: 11/15/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
Persons with HIV (PWH) on long-term antiretroviral therapy (ART) have a higher incidence and prevalence of cardiometabolic diseases attributed, in part, to persistent inflammation despite viral suppression. In addition to traditional risk factors, immune responses to co-infections such as cytomegalovirus (CMV) may play an unappreciated role in cardiometabolic comorbidities and offer new potential therapeutic targets in a subgroup of individuals. We assessed the relationship of CX3CR1+, GPR56+, and CD57+/- T cells (termed CGC+) with comorbid conditions in a cohort of 134 PWH co-infected with CMV on long-term ART. We found that PWH with cardiometabolic diseases (non-alcoholic fatty liver disease, calcified coronary arteries, or diabetes) had higher circulating CGC+CD4+ T cells compared to metabolically healthy PWH. The traditional risk factor most correlated with CGC+CD4+ T cell frequency was fasting blood glucose, as well as starch/sucrose metabolites. While unstimulated CGC+CD4+ T cells, like other memory T cells, depend on oxidative phosphorylation for energy, they exhibited higher expression of carnitine palmitoyl transferase 1A compared to other CD4+ T cell subsets, suggesting a potentially greater capacity for fatty acid β-oxidation. Lastly, we show that CMV-specific T cells against multiple viral epitopes are predominantly CGC+. Together, this study suggests that among PWH, CGC+ CD4+ T cells are frequently CMV-specific and are associated with diabetes, coronary arterial calcium, and non-alcoholic fatty liver disease. Future studies should assess whether anti-CMV therapies could reduce cardiometabolic disease risk in some individuals.
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Affiliation(s)
- Celestine N. Wanjalla
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Curtis L. Gabriel
- Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Hubaida Fuseini
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Samuel S. Bailin
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mona Mashayekhi
- Division of Endocrinology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Joshua Simmons
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Christopher M. Warren
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - David R. Glass
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jared Oakes
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rama Gangula
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Erin Wilfong
- Division of Rheumatology, Vanderbilt University Medical Center, Nashville, TN, United States
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stephen Priest
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Tecla Temu
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Evan W. Newell
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Suman Pakala
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Spyros A. Kalams
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Sara Gianella
- Department of Medicine, University of California, San Diego, CA, United States
| | - David Smith
- Department of Medicine, University of California, San Diego, CA, United States
| | - David G. Harrison
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Simon A. Mallal
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
| | - John R. Koethe
- Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, United States
- Infectious Disease Section, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
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26
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Stirm K, Leary P, Wüst D, Stark D, Joller N, Karakus U, Boyman O, Tzankov A, Müller A. Treg-selective IL-2 starvation synergizes with CD40 activation to sustain durable responses in lymphoma models. J Immunother Cancer 2023; 11:e006263. [PMID: 36822670 PMCID: PMC9950978 DOI: 10.1136/jitc-2022-006263] [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] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Roughly half of all diffuse large B-cell lymphomas (DLBCLs) are infiltrated by large numbers of regulatory T-cells (Tregs). Although the presence of 'effector' Tregs in particular is associated with an inferior prognosis in patients on standard rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) immunochemotherapy, the role of this cell type during lymphoma initiation and progression is poorly understood. METHODS Here, we use tissue microarrays containing prospectively collected DLBCL patient specimens, as well as data from publicly available cohorts to explore the mutational landscape of Treg-infiltrated DLBCL. We further take advantage of a model of MYC-driven lymphoma to mechanistically dissect the contribution of Tregs to lymphoma pathogenesis and to develop a strategy of Treg-selective interleukin-2 (IL-2) starvation to improve immune control of MYC-driven lymphoma. RESULTS We find that all genetic DLBCL subtypes, except for one characterized by co-occurring MYD88/CD79 mutations, are heavily infiltrated by Tregs. Spectral flow cytometry and scRNA-sequencing reveal the robust expression of functional and immunosuppressive markers on Tregs infiltrating MYC-driven lymphomas; notably, we find that intratumoral Tregs arise due to local conversion from naïve CD4+ precursors on tumor contact. Treg ablation in Foxp3iDTR mice, or by antibody-mediated Treg-selective blockade of IL-2 signaling, strongly reduces the lymphoma burden. We identify lymphoma B-cells as a major source of IL-2, and show that the effects of Treg depletion are reversed by the simultaneous depletion of Foxp3-negative CD4+ T-cells, but not CD8+ T-cells or natural killer (NK) cells. The inhibition of ATP hydrolyzation and adenosine production by Tregs at least partly phenocopies the effects of Treg depletion. Treg depletion further synergizes with pro-apoptotic CD40 activation to sustain durable responses. CONCLUSION The combined data implicate Tregs as a potential therapeutic target in DLBCL, especially in combination with other immunotherapies.
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Affiliation(s)
- Kristin Stirm
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Peter Leary
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Daria Wüst
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Dominique Stark
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nicole Joller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Ufuk Karakus
- Department of Immunology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich, Zurich, Switzerland
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Doolittle ML, Saul D, Kaur J, Rowsey JL, Vos SJ, Pavelko KD, Farr JN, Monroe DG, Khosla S. Multiparametric senescent cell phenotyping reveals CD24 osteolineage cells as targets of senolytic therapy in the aged murine skeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523760. [PMID: 36711531 PMCID: PMC9882155 DOI: 10.1101/2023.01.12.523760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Senescence drives organismal aging, yet the deep characterization of senescent cells in vivo remains incomplete. Here, we applied mass cytometry by time-of-flight (CyTOF) using carefully validated antibodies to analyze senescent cells at single-cell resolution. We used multiple criteria to identify senescent mesenchymal cells that were growth arrested and resistant to apoptosis (p16+/Ki67-/BCL-2+; "p16KB" cells). These cells were highly enriched for senescence-associated secretory phenotype (SASP) and DNA damage markers and were strongly associated with age. p16KB cell percentages were also increased in CD24+ osteolineage cells, which exhibited an inflammatory SASP in aged mice and were robustly cleared by both genetic and pharmacologic senolytic therapies. Following isolation, CD24+ skeletal cells exhibited growth arrest, SA-βgal positivity, and impaired osteogenesis in vitro . These studies thus provide a new approach using multiplexed protein profiling by CyTOF to define senescent mesenchymal cells in vivo and identify a highly inflammatory, senescent CD24+ osteolineage population cleared by senolytics.
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Affiliation(s)
- Madison L. Doolittle
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Dominik Saul
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department for Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Germany
| | - Japneet Kaur
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Jennifer L. Rowsey
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephanie J. Vos
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Kevin D. Pavelko
- Department of Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joshua N. Farr
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - David G. Monroe
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Sundeep Khosla
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
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28
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Lin W, Liu S, Huang Z, Li H, Lu T, Luo Y, Zhong J, Xu Z, Liu Y, Li Y, Li P, Xu Q, Cai J, Li H, Chen XL. Mass cytometry and single-cell RNA sequencing reveal immune cell characteristics of active and inactive phases of Crohn's disease. Front Med (Lausanne) 2023; 9:1064106. [PMID: 36714133 PMCID: PMC9878392 DOI: 10.3389/fmed.2022.1064106] [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: 10/07/2022] [Accepted: 12/14/2022] [Indexed: 01/13/2023] Open
Abstract
Objectives For Crohn's disease (CD), the alternation of the active phase and inactive phase may be related to humoral immunity and cellular immunity. This study aims to understand the characteristics of immune cells in patients with active CD (CDa) and inactive CD (CDin). Methods Mass cytometry (CyTOF) and single-cell RNA sequencing (scRNA-seq) data about CDa, CDin, and healthy control (HC) were included. CyTOF analysis was performed to capture gated subsets, including T cells, T regulatory (Treg) cells, B cells, innate immune cells, and natural killer (NK) cells. Differential analysis was used to identify different immune cell subsets among CDa, CDin, and HC. ScRNA-seq analysis was used to verify the results of CyTOF. CD-related signaling pathways were obtained using KEGG pathway enrichment analysis. CellChat analysis was used to infer the cell communication network among immune cell subsets. Results Compared to patients with CDin, patients with CDa had higher abundances of CD16+CD38+CD4+CXCR3+CCR6+ naive T cells, HLA-DR+CD38+IFNγ+TNF+ effector memory (EM) T cells, HLA-DR+IFNγ+ naive B cells, and CD14++CD11C+IFNγ+IL1B+ monocytes. KEGG analysis showed the similarity of pathway enrichment for the earlier four subsets, such as thermogenesis, oxidative phosphorylation, and metabolic pathways. The patients with CDin were characterized by an increased number of CD16+CD56dimCD44+HLA-DR+IL22+ NK cells. Compared to HC, patients with CDa demonstrated a low abundance of HLA-DR+CCR6+ NK cells and a high abundance of FOXP3+CD44+ EM Tregs. CellChat analysis revealed the interaction network of cell subsets amplifying in CDa compared with CDin. Conclusion Some immune subsets cells were identified for CDa and CDin. These cells may be related to the occurrence and development of CD and may provide assistance in disease diagnosis and treatment.
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Affiliation(s)
- Wenjia Lin
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shiying Liu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhuojian Huang
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haiwen Li
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Tianyu Lu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongxin Luo
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiamin Zhong
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zewen Xu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yu Liu
- Department of Medical Statistics, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yanwu Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China,Pi-Wei Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peiwu Li
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Xu
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiazhong Cai
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China,Pi-Wei Institute, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huibiao Li
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xin-lin Chen
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Xin-lin Chen,
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Glasson Y, Chépeaux LA, Dumé AS, Lafont V, Faget J, Bonnefoy N, Michaud HA. Single-cell high-dimensional imaging mass cytometry: one step beyond in oncology. Semin Immunopathol 2023; 45:17-28. [PMID: 36598557 PMCID: PMC9812013 DOI: 10.1007/s00281-022-00978-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/11/2022] [Indexed: 01/05/2023]
Abstract
Solid tumors have a dynamic ecosystem in which malignant and non-malignant (endothelial, stromal, and immune) cell types constantly interact. Importantly, the abundance, localization, and functional orientation of each cell component within the tumor microenvironment vary significantly over time and in response to treatment. Such intratumoral heterogeneity influences the tumor course and its sensitivity to treatments. Recently, high-dimensional imaging mass cytometry (IMC) has been developed to explore the tumor ecosystem at the single-cell level. In the last years, several studies demonstrated that IMC is a powerful tool to decipher the tumor complexity. In this review, we summarize the potential of this technology and how it may be useful for cancer research (from preclinical to clinical studies).
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Affiliation(s)
- Yaël Glasson
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Laure-Agnès Chépeaux
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Anne-Sophie Dumé
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | | | - Julien Faget
- IRCM, Univ Montpellier, ICM, Inserm Montpellier, France
| | - Nathalie Bonnefoy
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d’Imagerie de Masse, Inserm Montpellier, France
| | - Henri-Alexandre Michaud
- IRCM, Univ Montpellier, ICM, Plateforme de Cytométrie Et d'Imagerie de Masse, Inserm Montpellier, France.
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30
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Mysore KR, Kannanganat S, Schraw JM, Lupo PJ, Goss JA, Setchell KDR, Kheradmand F, Li XC, Shneider BL. Innate immune cell dysfunction and systemic inflammation in children with chronic liver diseases undergoing transplantation. Am J Transplant 2023; 23:26-36. [PMID: 36695617 DOI: 10.1016/j.ajt.2022.09.004] [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: 05/20/2022] [Revised: 08/19/2022] [Accepted: 09/17/2022] [Indexed: 01/12/2023]
Abstract
Advanced liver diseases (ALD) can affect immune function and compromise host defense against infections. In this study, we examined the phenotypic and functional alterations in circulating monocyte and dendritic cells (DCs) in children with ALD undergoing liver transplantation (LT). Children were stratified into 2 clusters, C1 (mild) and C2 (severe), on the basis of laboratory parameters of ALD and compared with healthy pediatric controls. Children in C2 had a significant reduction in frequencies of nonclassical monocytes and myeloid DCs. Children in C2 displayed monocyte and DC dysfunction, characterized by lower human leucocyte antigen DR expression and reduced interleukin 12 production, and had an increased incidence of infections before and after LT. Children in C2 demonstrated immune dysregulation with elevations of pro- and anti-inflammatory cytokines in plasma. Alterations of innate immune cells correlated with multiple laboratory parameters of ALD, including plasma bile acids. In vitro, monocytes cultured with specific bile acids demonstrated a dose-dependent reduction in interleukin 12 production, similar to alterations in children with ALD. In conclusion, a cohort of children with ALD undergoing LT exhibited innate immune dysfunction, which may be related to the chronic elevation of serum bile acids. Identifying at-risk patients may permit personalized management pre- and post-transplant, thereby reducing the incidence of infection-related complications.
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Affiliation(s)
- Krupa R Mysore
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; William Shearer Center for Human Immunobiology, Feigin Center, Texas Children's Hospital, Houston, Texas, USA.
| | - Sunil Kannanganat
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; William Shearer Center for Human Immunobiology, Feigin Center, Texas Children's Hospital, Houston, Texas, USA
| | - Jeremy M Schraw
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, Center for Epidemiology and Population Health, Baylor College of Medicine, Houston, Texas, USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, Center for Epidemiology and Population Health, Baylor College of Medicine, Houston, Texas, USA
| | - John A Goss
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Kenneth D R Setchell
- Department of Pathology and Laboratory Medicine, Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Farrah Kheradmand
- Department of Medicine, Pulmonary and Critical Care, Baylor College of Medicine, Houston, Texas, USA
| | - Xian C Li
- Immunobiology & Transplant Science Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Benjamin L Shneider
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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31
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Vakrakou AG, Paschalidis N, Pavlos E, Giannouli C, Karathanasis D, Tsipota X, Velonakis G, Stadelmann-Nessler C, Evangelopoulos ME, Stefanis L, Kilidireas C. Specific myeloid signatures in peripheral blood differentiate active and rare clinical phenotypes of multiple sclerosis. Front Immunol 2023; 14:1071623. [PMID: 36761741 PMCID: PMC9905713 DOI: 10.3389/fimmu.2023.1071623] [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: 10/16/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
Current understanding of Multiple Sclerosis (MS) pathophysiology implicates perturbations in adaptive cellular immune responses, predominantly T cells, in Relapsing-Remitting forms (RRMS). Nevertheless, from a clinical perspective MS is a heterogeneous disease reflecting the heterogeneity of involved biological systems. This complexity requires advanced analysis tools at the single-cell level to discover biomarkers for better patient-group stratification. We designed a novel 44-parameter mass cytometry panel to interrogate predominantly the role of effector and regulatory subpopulations of peripheral blood myeloid subsets along with B and T-cells (excluding granulocytes) in MS, assessing three different patient cohorts: RRMS, PPMS (Primary Progressive) and Tumefactive MS patients (TMS) (n=10, 8, 14 respectively). We further subgrouped our cohort into inactive or active disease stages to capture the early underlying events in disease pathophysiology. Peripheral blood analysis showed that TMS cases belonged to the spectrum of RRMS, whereas PPMS cases displayed different features. In particular, TMS patients during a relapse stage were characterized by a specific subset of CD11c+CD14+ CD33+, CD192+, CD172+-myeloid cells with an alternative phenotype of monocyte-derived macrophages (high arginase-1, CD38, HLA-DR-low and endogenous TNF-a production). Moreover, TMS patients in relapse displayed a selective CD4 T-cell lymphopenia of cells with a Th2-like polarised phenotype. PPMS patients did not display substantial differences from healthy controls, apart from a trend toward higher expansion of NK cell subsets. Importantly, we found that myeloid cell populations are reshaped under effective disease-modifying therapy predominantly with glatiramer acetate and to a lesser extent with anti-CD20, suggesting that the identified cell signature represents a specific therapeutic target in TMS. The expanded myeloid signature in TMS patients was also confirmed by flow cytometry. Serum neurofilament light-chain levels confirmed the correlation of this myeloid cell signature with indices of axonal injury. More in-depth analysis of myeloid subsets revealed an increase of a subset of highly cytolytic and terminally differentiated NK cells in PPMS patients with leptomeningeal enhancement (active-PPMS), compared to those without (inactive-PPMS). We have identified previously uncharacterized subsets of circulating myeloid cells and shown them to correlate with distinct disease forms of MS as well as with specific disease states (relapse/remission).
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Affiliation(s)
- Aigli G Vakrakou
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Department of Neuropathology, University of Göttingen Medical Center, Göttingen, Germany
| | - Nikolaos Paschalidis
- Mass Cytometry-CyTOF Laboratory, Center for Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleftherios Pavlos
- Center for Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation of the Academy of Athens, Athens, Greece.,Division of Basic Sciences, University of Crete Medical School, Heraklion, Greece
| | - Christina Giannouli
- Center for Clinical Research, Experimental Surgery and Translational Research Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Dimitris Karathanasis
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Xristina Tsipota
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Velonakis
- Research Unit of Radiology, 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Maria-Eleftheria Evangelopoulos
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Leonidas Stefanis
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Kilidireas
- Demyelinating Diseases Unit, 1st Department of Neurology, School of Medicine, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece.,Department of Neurology, Henry Dunant Hospital Center, Athens, Greece
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32
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Porpiglia E, Mai T, Kraft P, Holbrook CA, de Morree A, Gonzalez VD, Hilgendorf KI, Frésard L, Trejo A, Bhimaraju S, Jackson PK, Fantl WJ, Blau HM. Elevated CD47 is a hallmark of dysfunctional aged muscle stem cells that can be targeted to augment regeneration. Cell Stem Cell 2022; 29:1653-1668.e8. [PMID: 36384141 PMCID: PMC9746883 DOI: 10.1016/j.stem.2022.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/04/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
In aging, skeletal muscle strength and regenerative capacity decline, due in part to functional impairment of muscle stem cells (MuSCs), yet the underlying mechanisms remain elusive. Here, we capitalize on mass cytometry to identify high CD47 expression as a hallmark of dysfunctional MuSCs (CD47hi) with impaired regenerative capacity that predominate with aging. The prevalent CD47hi MuSC subset suppresses the residual functional CD47lo MuSC subset through a paracrine signaling loop, leading to impaired proliferation. We uncover that elevated CD47 levels on aged MuSCs result from increased U1 snRNA expression, which disrupts alternative polyadenylation. The deficit in aged MuSC function in regeneration can be overcome either by morpholino-mediated blockade of CD47 alternative polyadenylation or antibody blockade of thrombospondin-1/CD47 signaling, leading to improved regeneration in aged mice, with therapeutic implications. Our findings highlight a previously unrecognized age-dependent alteration in CD47 levels and function in MuSCs, which underlies reduced muscle repair in aging.
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Affiliation(s)
- Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark.
| | - Thach Mai
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peggy Kraft
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Colin A Holbrook
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Biomedicine, Aarhus University, Aarhus C 8000, Denmark; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica D Gonzalez
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keren I Hilgendorf
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Angelica Trejo
- Nolan Laboratory, Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sriram Bhimaraju
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Jackson Laboratory, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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DeBarry JD, Nural MV, Pakala SB, Nayak V, Warrenfeltz S, Humphrey J, Lapp SA, Cabrera-Mora M, Brito CFA, Jiang J, Saney CL, Hankus A, Stealey HM, DeBarry MB, Lackman N, Legall N, Lee K, Tang Y, Gupta A, Trippe ED, Bridger RR, Weatherly DB, Peterson MS, Jiang X, Tran V, Uppal K, Fonseca LL, Joyner CJ, Karpuzoglu E, Cordy RJ, Meyer EVS, Wells LL, Ory DS, Lee FEH, Tirouvanziam R, Gutiérrez JB, Ibegbu C, Lamb TJ, Pohl J, Pruett ST, Jones DP, Styczynski MP, Voit EO, Moreno A, Galinski MR, Kissinger JC. MaHPIC malaria systems biology data from Plasmodium cynomolgi sporozoite longitudinal infections in macaques. Sci Data 2022; 9:722. [PMID: 36433985 PMCID: PMC9700667 DOI: 10.1038/s41597-022-01755-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: 07/14/2022] [Accepted: 10/10/2022] [Indexed: 11/27/2022] Open
Abstract
Plasmodium cynomolgi causes zoonotic malarial infections in Southeast Asia and this parasite species is important as a model for Plasmodium vivax and Plasmodium ovale. Each of these species produces hypnozoites in the liver, which can cause relapsing infections in the blood. Here we present methods and data generated from iterative longitudinal systems biology infection experiments designed and performed by the Malaria Host-Pathogen Interaction Center (MaHPIC) to delve deeper into the biology, pathogenesis, and immune responses of P. cynomolgi in the Macaca mulatta host. Infections were initiated by sporozoite inoculation. Blood and bone marrow samples were collected at defined timepoints for biological and computational experiments and integrative analyses revolving around primary illness, relapse illness, and subsequent disease and immune response patterns. Parasitological, clinical, haematological, immune response, and -omic datasets (transcriptomics, proteomics, metabolomics, and lipidomics) including metadata and computational results have been deposited in public repositories. The scope and depth of these datasets are unprecedented in studies of malaria, and they are projected to be a F.A.I.R., reliable data resource for decades.
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Affiliation(s)
- Jeremy D DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Mustafa V Nural
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Suman B Pakala
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Vishal Nayak
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Cancer Data Science Initiatives, Frederick National Laboratory for Cancer Research, Post Office Box B, Frederick, MD, 21702, USA
| | - Susanne Warrenfeltz
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Jay Humphrey
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Stacey A Lapp
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Monica Cabrera-Mora
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Cristiana F A Brito
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Laboratório de Malária, Instituto René Rachou/Fiocruz Minas, Av. Augusto de Lima 1715, Belo Horizonte, MG, 30190 009, Brazil
| | - Jianlin Jiang
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Celia L Saney
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, 30605, USA
| | - Allison Hankus
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Senior Public Health Informaticist, MITRE Corp, Atlanta, GA, 30345, USA
| | - Hannah M Stealey
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Megan B DeBarry
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Nicolas Lackman
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Interdisciplinary Disease Ecology Across Scales Research Traineeship Program, Institute of Bioinformatics, Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
| | - Kevin Lee
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Yan Tang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Anuj Gupta
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Valted Seq, 704 Quince Orchard Rd, Gaithersburg, MD, 20878, USA
| | - Elizabeth D Trippe
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Federal Drug Administration, Silver Spring, MD, 20993, USA
| | - Robert R Bridger
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Daniel Brent Weatherly
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Mariko S Peterson
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Xuntian Jiang
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Luis L Fonseca
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Florida, Gainesville, FL, 32603, USA
| | - Chester J Joyner
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Center for Tropical and Emerging Global Disease, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Ebru Karpuzoglu
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Regina J Cordy
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Biology, Wake Forest University, Winston Salem, NC, 27103, USA
| | - Esmeralda V S Meyer
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Institutional Animal Care and Use Committee, Research Compliance and Research Integrity Office, Emory University, Atlanta, GA, 30322, USA
| | - Lance L Wells
- Complex Carbohydrate Research Center, Department of Biochemistry, University of Georgia, Athens, GA, 30602, USA
| | - Daniel S Ory
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Casma Therapeutics, Cambridge, MA, 02139, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, GA, 30322, USA
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Juan B Gutiérrez
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- Department of Mathematics, Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA
- University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Chris Ibegbu
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Tracey J Lamb
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sarah T Pruett
- Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- University of Tennessee, Knoxville, TN, 37996, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, & Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Eberhard O Voit
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Alberto Moreno
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes/Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA.
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA.
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
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Waller KJ, Saihi H, Li W, Brindley JH, De Jong A, Syn WK, Bessant C, Alazawi W. Single-cell phenotypes of peripheral blood immune cells in early and late stages of non-alcoholic fatty liver disease. Clin Mol Hepatol 2022; 29:417-432. [PMID: 36727210 PMCID: PMC10121278 DOI: 10.3350/cmh.2022.0205] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/16/2022] [Indexed: 02/03/2023] Open
Abstract
Background Immune and inflammatory cells respond to multiple pathological hits in the development of non-alcoholic steatohepatitis (NASH) and fibrosis. Relatively little is known about how their type and function change through the non-alcoholic fatty liver disease (NAFLD) spectrum. We used multi-dimensional mass cytometry and a tailored bioinformatic approach to study circulating immune cells sampled from healthy individuals and people with NAFLD. Methods Cytometry by time of flight (CyTOF) using 36 metal-conjugated antibodies was applied to peripheral blood mononuclear cells (PBMCs) from biopsy-proven NASH fibrosis (late disease), steatosis (early disease) and healthy patients. Supervised and unsupervised analyses were used, findings confirmed and mechanisms assessed using independent healthy and disease PBMC samples. Results Of 36 PBMC clusters, 21 changed between controls and disease samples. Significant differences between diseases stages with changes in T cells and myeloid cells throughout disease and B cell changes in late stages. Semi-supervised gating and re-clustering showed that disease stages were associated with fewer monocytes with active signalling and more inactive NK cells, while B and T cells bearing activation markers reduced in late stages, B cells bearing co-stimulatory molecules increased. Functionally, disease states were associated with fewer activated MAIT cells and reduced TLR-mediated cytokine production in late disease. Conclusions A range of innate and adaptive immune changes begin early in NAFLD and disease stages are associated with a functionally less active phenotype compared to controls. Further study of the immune response in NAFLD spectrum may give insight into mechanisms of disease with potential clinical application.
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Affiliation(s)
- Kathryn Jane Waller
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Hajar Saihi
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Wenhao Li
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | | | - Anja De Jong
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - Wing-Kin Syn
- Division of Gastroenterology and Hepatology, Medical University of South Carolina, Charleston, SC, USA.,Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country, Universidad del Pa S Vasco/Euskal Herriko Univertsitatea (UPV/EHU), Leioa, Spain.,Division of Gastroenterology and Hepatology, Saint Louis University School of Medicine, Missouri, USA
| | - Conrad Bessant
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London, UK.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - William Alazawi
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
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Mulder PP, Vlig M, Fasse E, Stoop MM, Pijpe A, van Zuijlen PP, Joosten I, Boekema BK, Koenen HJ. Burn-injured skin is marked by a prolonged local acute inflammatory response of innate immune cells and pro-inflammatory cytokines. Front Immunol 2022; 13:1034420. [PMID: 36451819 PMCID: PMC9703075 DOI: 10.3389/fimmu.2022.1034420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 10/10/2023] Open
Abstract
The systemic and local immune response in burn patients is often extreme and derailed. As excessive inflammation can damage healthy tissues and slow down the healing process, modulation of inflammatory responses could limit complications and improve recovery. Due to its complexity, more detailed information on the immune effects of thermal injury is needed to improve patient outcomes. We therefore characterized and quantified subsets of immune cells and mediators present in human burn wound tissue (eschar), sampled at various time points. This study shows that after burn injury, the number of immune cells were persistently increased, unlike the normal wound healing process. There was an immediate, strong increase in neutrophils and a moderate increase in monocytes/macrophages and lymphocytes, especially in the second and third week post burn. The percentage of classical (CD14highCD16-) monocytes/macrophages demonstrated a steady decrease over time, whereas the proportion of intermediate (CD14highCD16+) monocytes/macrophages slowly increased. The absolute numbers of T cells, NK cells and B cells increased up to week 3, while the fraction of γδ T cells was increased only in week 1. Secretome profiling revealed high levels of chemokines and an overall pro-inflammatory cytokine milieu in burn tissue. The local burn immune response shows similarities to the systemic immune reaction, but differs in neutrophil maturity and lymphocyte composition. Altogether, the neutrophil surges, high levels of pro-inflammatory cytokines and limited immunosuppression might be key factors that prolong the inflammation phase and delay the wound healing process in burns.
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Affiliation(s)
- Patrick P.G. Mulder
- Preclinical & Clinical Research, Association of Dutch Burn Centres (ADBC), Beverwijk, Netherlands
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marcel Vlig
- Preclinical & Clinical Research, Association of Dutch Burn Centres (ADBC), Beverwijk, Netherlands
| | - Esther Fasse
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Matthea M. Stoop
- Burn Center & Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, Netherlands
| | - Anouk Pijpe
- Preclinical & Clinical Research, Association of Dutch Burn Centres (ADBC), Beverwijk, Netherlands
- Burn Center & Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, Netherlands
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Amsterdam, Netherlands
| | - Paul P.M. van Zuijlen
- Burn Center & Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, Netherlands
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Amsterdam, Netherlands
- Paediatric Surgical Centre, Emma Children’s Hospital, Amsterdam UMC University of Amsterdam, Amsterdam, Netherlands
| | - Irma Joosten
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bouke K.H.L. Boekema
- Preclinical & Clinical Research, Association of Dutch Burn Centres (ADBC), Beverwijk, Netherlands
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hans J.P.M. Koenen
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
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Vallet N, Michonneau D, Tournier S. Toward practical transparent verifiable and long-term reproducible research using Guix. Sci Data 2022; 9:597. [PMID: 36195618 PMCID: PMC9532446 DOI: 10.1038/s41597-022-01720-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an interface between data and source code running analyses, is not addressed. Environments are usually described with software and library names associated with version labels or provided as an opaque container image. This is not enough to describe the complexity of the dependencies on which they rely to operate on. We describe this issue and illustrate how open tools like Guix can be used by any scientist to share their environment and allow peers to reproduce it. Some steps of research might not be fully reproducible, but at least, transparency for computation is technically addressable. These tools should be considered by scientists willing to promote transparency and open science.
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Affiliation(s)
- Nicolas Vallet
- Université de Paris, INSERM U976, F-75010, Paris, France.
| | - David Michonneau
- Université de Paris, INSERM U976, F-75010, Paris, France.,Hematology Transplantation, Saint Louis hospital, 1 avenue Claude Vellefaux, 75010, Paris, France
| | - Simon Tournier
- Université de Paris, INSERM US53, CNRS UAR 2030, Saint Louis Research Institute, 1 avenue Claude Vellefaux, 75010, Paris, France
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Tang X, Yang ZZ, Kim HJ, Anagnostou T, Yu Y, Wu X, Chen J, Krull JE, Wenzl K, Mondello P, Bhardwaj V, Wang J, Novak AJ, Ansell SM. Phenotype, Function, and Clinical Significance of CD26+ and CD161+Tregs in Splenic Marginal Zone Lymphoma. Clin Cancer Res 2022; 28:4322-4335. [PMID: 35686915 PMCID: PMC10443733 DOI: 10.1158/1078-0432.ccr-22-0977] [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: 03/29/2022] [Revised: 05/17/2022] [Accepted: 06/08/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Regulatory T-cells (Treg) are essential to Tregs homeostasis and modulate the antitumor immune response in patients with lymphoma. However, the biology and prognostic impact of Tregs in splenic marginal zone lymphoma (SMZL) have not been studied. EXPERIMENTAL DESIGN Biopsy specimens from 24 patients with SMZL and 12 reactive spleens (rSP) from individuals without lymphoma were analyzed by using CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), CyTOF (mass cytometry) analysis, and flow cytometry to explore the phenotype, transcriptomic profile, and clinical significance of intratumoral Tregs and their subsets. The biological characteristics and cell signaling pathways of intratumoral Treg subsets were confirmed by in vitro functional assays. RESULTS We found that Tregs are more abundant in SMZL patients' spleens than rSP, and Tregs from patients with SMZL and rSP can be separated into CD161+Treg and CD26+Treg subsets. CD161+Tregs are increased in SMZL but have dysregulated immune function. We found that CD161+Treg and CD26+Tregs have unique gene expression and phenotypic profiles and are differentially correlated with patient outcomes. Specifically, increased CD161+Tregs are significantly associated with a favorable prognosis in patients with SMZL, whereas CD26+Tregs are associated with a poor prognosis. Furthermore, activation of the IL2/STAT5 pathway contributes to the induction of CD26+Tregs and can be reversed by STAT5 inhibition. CONCLUSIONS IL2/STAT5-mediated expansion of CD26+Tregs contributes to a poor clinical outcome in SMZL and may represent a therapeutic opportunity in this disease.
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Affiliation(s)
- Xinyi Tang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Zhi-Zhang Yang
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Hyo Jin Kim
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Theodora Anagnostou
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Yue Yu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Xiaosheng Wu
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Jun Chen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Jordan E. Krull
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Kerstin Wenzl
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Patrizia Mondello
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Vaishali Bhardwaj
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Junwen Wang
- Department of Quantitative Health Sciences and Center for Individualized Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Anne J. Novak
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Stephen M. Ansell
- Division of Hematology and Internal Medicine, Mayo Clinic, Rochester, Minnesota
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Yao L, Jayasinghe RG, Lee BH, Bhasin SS, Pilcher W, Doxie DB, Gonzalez-Kozlova E, Dasari S, Fiala MA, Pita-Juarez Y, Strausbauch M, Kelly G, Thomas BE, Kumar SK, Cho HJ, Anderson E, Wendl MC, Dawson T, D'souza D, Oh ST, Cheloni G, Li Y, DiPersio JF, Rahman AH, Dhodapkar KM, Kim-Schulze S, Vij R, Vlachos IS, Mehr S, Hamilton M, Auclair D, Kourelis T, Avigan D, Dhodapkar MV, Gnjatic S, Bhasin MK, Ding L. Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis. CANCER RESEARCH COMMUNICATIONS 2022; 2:1255-1265. [PMID: 36969740 PMCID: PMC10035369 DOI: 10.1158/2767-9764.crc-22-0022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
Abstract
As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of multiple myeloma bone marrow samples from 18 patients assessed by single-cell RNA sequencing (scRNA-seq), mass cytometry (CyTOF), and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System stage 3 patients exhibited decreased CD4+ T/CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in natural killer cells of fast progressors compared with those of nonprogressors, as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in multiple myeloma using multiple single-cell technologies revealed markers associated with multiple myeloma rapid progression which will be further characterized by the full-scale immune atlas project. Significance scRNA-seq, CyTOF, and CITE-seq are increasingly used for evaluating cellular heterogeneity. Understanding their concordances is of great interest. To date, this study is the most comprehensive examination of the measurement of the immune microenvironment in multiple myeloma using the three techniques. Moreover, we identified markers predicted to be significantly associated with multiple myeloma rapid progression.
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Affiliation(s)
- Lijun Yao
- Washington University School of Medicine, Saint Louis, Missouri
| | | | - Brian H. Lee
- Icahn School of Medicine at Mt. Sinai, New York, New York
| | | | | | | | | | | | - Mark A. Fiala
- Washington University School of Medicine, Saint Louis, Missouri
| | - Yered Pita-Juarez
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | | | - Geoffrey Kelly
- Icahn School of Medicine at Mt. Sinai, New York, New York
| | | | | | - Hearn Jay Cho
- Icahn School of Medicine at Mt. Sinai, New York, New York
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | | | | | - Travis Dawson
- Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Darwin D'souza
- Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Stephen T. Oh
- Washington University School of Medicine, Saint Louis, Missouri
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Ying Li
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | - Ravi Vij
- Washington University School of Medicine, Saint Louis, Missouri
| | - Ioannis S. Vlachos
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Shaadi Mehr
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Mark Hamilton
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Daniel Auclair
- Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | | | - David Avigan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | | | - Sacha Gnjatic
- Icahn School of Medicine at Mt. Sinai, New York, New York
| | | | - Li Ding
- Washington University School of Medicine, Saint Louis, Missouri
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Bauer CJ, Findlay M, Koliamitra C, Zimmer P, Schick V, Ludwig S, Gurtner GC, Riedel B, Schier R. Preoperative exercise induces endothelial progenitor cell mobilisation in patients undergoing major surgery – A prospective randomised controlled clinical proof-of-concept trial. Heliyon 2022; 8:e10705. [PMID: 36200018 PMCID: PMC9529507 DOI: 10.1016/j.heliyon.2022.e10705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/10/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Introduction Prehabilitation is increasingly recognised as a therapeutic option to reduce postoperative complications. Investigating the beneficial effects of exercise on cellular mechanisms, we have previously shown that a single episode of exhaustive exercise effectively stimulates endothelial progenitor cells (a cell population associated with vascular maintenance, repair, angiogenesis, and neovascularization) in correlation with fewer postoperative complications, despite the ongoing debate about the appropriate cell surface marker profiles of these cells (common phenotypical definitions include CD45dim, CD133+, CD34+ and/or CD31+). In order to translate these findings into clinical application, a feasible prehabilitation programme achieving both functional and cellular benefits in a suitable timeframe to expedite surgery is necessary. Objective The objective of this study was to test the hypothesis that a four-week prehabilitation programme of vigorous-intensity interval exercise training is feasible, increases physical capacity (primary outcome) and the circulatory number of endothelial progenitor cells within peripheral blood. Methods In this unblinded, parallel-group, randomised controlled proof-of-concept clinical trial (German Clinical Trial Register number: DRKS00000527) conducted between 01st December 2014 and 30th November 2016, fifteen female adult patients scheduled for incontinence surgery with abdominal laparotomy at the University Hospital Cologne were allocated to either an exercise (n = 8, exclusion of 1 patient, analysed n = 7) or non-exercise group (n = 7, exclusion of 1 patient, analysed n = 6). The exercise group's intervention consisted of a vigorous-intensity interval training for four weeks preoperatively. Cardiopulmonary Exercise Testing accompanied by peripheral blood collection was performed before and after the (non-)training phase. Cellular investigations were conducted by flow cytometry and cluster-based analyses. Results Vigorous-intensity interval training over four weeks was feasible in the exercise group (successful completion by 8 out of 8 patients without any harms), with significant improvements in patients' functional capacity (increased oxygen uptake at anaerobic threshold [intervention group mean + 1.71 ± 3.20 mL/min/kg vs. control group mean −1.83 ± 2.14 mL/min/kg; p = 0.042] and peak exercise [intervention group mean + 1.71 ± 1.60 mL/min/kg vs. control group mean −1.67 ± 1.37 mL/min/kg; p = 0.002]) and a significant increase in the circulatory number of endothelial progenitor cells (proportionate CD45dim/CD14dim/CD133+/CD309+/CD34+/CD31 + subpopulation within the circulating CD45-pool [p = 0.016]). Conclusions We introduce a novel prehabilitation concept that shows effective stimulation of an endothelial progenitor cell subpopulation within four weeks of preoperative exercise, serving as a clinical cell-mediated intervention with the aim to reduce surgical complications. Funding Institutional funding. DFG (German Research Foundation, 491454339) support for the Article Processing Charge.
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Affiliation(s)
- Claus Juergen Bauer
- Department of Internal Medicine—Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Michael Findlay
- Department of Surgery, Division of Cancer Surgery, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Christina Koliamitra
- Institute for Cardiovascular Research and Sports Medicine, German Sports University Cologne, Cologne, Germany
| | - Philipp Zimmer
- Institute of Sports and Sports Medicine, TU Dortmund University, Dortmund, Germany
| | - Volker Schick
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Sebastian Ludwig
- Department of Obstetrics and Gynaecology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Geoffrey C. Gurtner
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, USA
| | - Bernhard Riedel
- Department of Anaesthetics, Perioperative Medicine and Pain Medicine, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Robert Schier
- Department of Anaesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Corresponding author.
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40
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Crowell HL, Chevrier S, Jacobs A, Sivapatham S, Bodenmiller B, Robinson MD. An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data. F1000Res 2022; 9:1263. [PMID: 36072920 PMCID: PMC9411975 DOI: 10.12688/f1000research.26073.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Mass cytometry (CyTOF) has become a method of choice for in-depth characterization of tissue heterogeneity in health and disease, and is currently implemented in multiple clinical trials, where higher quality standards must be met. Currently, preprocessing of raw files is commonly performed in independent standalone tools, which makes it difficult to reproduce. Here, we present an R pipeline based on an updated version of CATALYST that covers all preprocessing steps required for downstream mass cytometry analysis in a fully reproducible way. This new version of CATALYST is based on Bioconductor’s SingleCellExperiment class and fully unit tested. The R-based pipeline includes file concatenation, bead-based normalization, single-cell deconvolution, spillover compensation and live cell gating after debris and doublet removal. Importantly, this pipeline also includes different quality checks to assess machine sensitivity and staining performance while allowing also for batch correction. This pipeline is based on open source R packages and can be easily be adapted to different study designs. It therefore has the potential to significantly facilitate the work of CyTOF users while increasing the quality and reproducibility of data generated with this technology.
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Affiliation(s)
- Helena L. Crowell
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, 8057, Switzerland
| | - Mark D. Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich, 8057, Switzerland
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41
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Yang Z, Wang Y, Liu S, Deng W, Lomeli SH, Moriceau G, Wohlschlegel J, Piva M, Lo RS. Enhancing PD-L1 Degradation by ITCH during MAPK Inhibitor Therapy Suppresses Acquired Resistance. Cancer Discov 2022; 12:1942-1959. [PMID: 35638972 PMCID: PMC9357203 DOI: 10.1158/2159-8290.cd-21-1463] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/23/2022] [Accepted: 05/25/2022] [Indexed: 01/09/2023]
Abstract
MAPK inhibitor (MAPKi) therapy in melanoma leads to the accumulation of tumor-surface PD-L1/L2, which may evade antitumor immunity and accelerate acquired resistance. Here, we discover that the E3 ligase ITCH binds, ubiquitinates, and downregulates tumor-surface PD-L1/L2 in MAPKi-treated human melanoma cells, thereby promoting T-cell activation. During MAPKi therapy in vivo, melanoma cell-intrinsic ITCH knockdown induced tumor-surface PD-L1, reduced intratumoral cytolytic CD8+ T cells, and accelerated acquired resistance only in immune-competent mice. Conversely, tumor cell-intrinsic ITCH overexpression reduced MAPKi-elicited PD-L1 accumulation, augmented intratumoral cytolytic CD8+ T cells, and suppressed acquired resistance in BrafV600MUT, NrasMUT, or Nf1MUT melanoma and KrasMUT-driven cancers. CD8+ T-cell depletion and tumor cell-intrinsic PD-L1 overexpression nullified the phenotype of ITCH overexpression, thereby supporting an in vivo ITCH-PD-L1-T-cell regulatory axis. Moreover, we identify a small-molecular ITCH activator that suppresses acquired MAPKi resistance in vivo. Thus, MAPKi-induced PD-L1 accelerates resistance, and a PD-L1-degrading ITCH activator prolongs antitumor response. SIGNIFICANCE MAPKi induces tumor cell-surface PD-L1 accumulation, which promotes immune evasion and therapy resistance. ITCH degrades PD-L1, optimizing antitumor T-cell immunity. We propose degrading tumor cell-surface PD-L1 and/or activating tumor-intrinsic ITCH as strategies to overcome MAPKi resistance. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Weixian Deng
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Shirley H. Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Marco Piva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Roger S. Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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42
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Boss AL, Damani T, Wickman TJ, Chamley LW, James JL, Brooks AES. Full spectrum flow cytometry reveals mesenchymal heterogeneity in first trimester placentae and phenotypic convergence in culture, providing insight into the origins of placental mesenchymal stromal cells. eLife 2022; 11:76622. [PMID: 35920626 PMCID: PMC9371602 DOI: 10.7554/elife.76622] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/01/2022] [Indexed: 12/05/2022] Open
Abstract
Single-cell technologies (RNA-sequencing, flow cytometry) are critical tools to reveal how cell heterogeneity impacts developmental pathways. The placenta is a fetal exchange organ, containing a heterogeneous mix of mesenchymal cells (fibroblasts, myofibroblasts, perivascular, and progenitor cells). Placental mesenchymal stromal cells (pMSC) are also routinely isolated, for therapeutic and research purposes. However, our understanding of the diverse phenotypes of placental mesenchymal lineages, and their relationships remain unclear. We designed a 23-colour flow cytometry panel to assess mesenchymal heterogeneity in first-trimester human placentae. Four distinct mesenchymal subsets were identified; CD73+CD90+ mesenchymal cells, CD146+CD271+ perivascular cells, podoplanin+CD36+ stromal cells, and CD26+CD90+ myofibroblasts. CD73+CD90+ and podoplanin + CD36+ cells expressed markers consistent with cultured pMSCs, and were explored further. Despite their distinct ex-vivo phenotype, in culture CD73+CD90+ cells and podoplanin+CD36+ cells underwent phenotypic convergence, losing CD271 or CD36 expression respectively, and homogenously exhibiting a basic MSC phenotype (CD73+CD90+CD31-CD144-CD45-). However, some markers (CD26, CD146) were not impacted, or differentially impacted by culture in different populations. Comparisons of cultured phenotypes to pMSCs further suggested cultured pMSCs originate from podoplanin+CD36+ cells. This highlights the importance of detailed cell phenotyping to optimise therapeutic capacity, and ensure use of relevant cells in functional assays.
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Affiliation(s)
- Anna Leabourn Boss
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Tanvi Damani
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tayla J Wickman
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Larry W Chamley
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Jo L James
- Department of Obstetrics and Gynaecology, University of Auckland, Auckland, New Zealand
| | - Anna E S Brooks
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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43
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Balsamo JA, Penton KE, Zhao Z, Hayes MJ, Lima SM, Irish JM, Bachmann BO. An immunogenic cell injury module for the single-cell multiplexed activity metabolomics platform to identify promising anti-cancer natural products. J Biol Chem 2022; 298:102300. [PMID: 35931117 PMCID: PMC9424577 DOI: 10.1016/j.jbc.2022.102300] [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: 03/05/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/05/2022] Open
Abstract
Natural products constitute and significantly impact many current anti-cancer medical interventions. A subset of natural products induces injury processes in malignant cells that recruit and activate host immune cells to produce an adaptive anti-cancer immune response, a process known as immunogenic cell death. However, a challenge in the field is to delineate forms of cell death and injury that best promote durable antitumor immunity. Addressing this with a single-cell chemical biology natural product discovery platform, like multiplex activity metabolomics, would be especially valuable in human leukemia, where cancer cells are heterogeneous and may react differently to the same compounds. Herein, a new ten-color, fluorescent cell barcoding-compatible module measuring six immunogenic cell injury signaling readouts are as follows: DNA damage response (γH2AX), apoptosis (cCAS3), necroptosis (p-MLKL), mitosis (p-Histone H3), autophagy (LC3), and the unfolded protein response (p-EIF2α). A proof-of-concept screen was performed to validate functional changes in single cells induced by secondary metabolites with known mechanisms within bacterial extracts. This assay was then applied in multiplexed activity metabolomics to reveal an unexpected mammalian cell injury profile induced by the natural product narbomycin. Finally, the functional consequences of injury pathways on immunogenicity were compared with three canonical assays for immunogenic hallmarks, ATP, HMGB1, and calreticulin, to correlate secondary metabolite-induced cell injury profiles with canonical markers of immunogenic cell death. In total, this work demonstrated a new phenotypic screen for discovery of natural products that modulate injury response pathways that can contribute to cancer immunogenicity.
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Affiliation(s)
- Joseph A Balsamo
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US
| | - Kathryn E Penton
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Zhihan Zhao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sierra M Lima
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian O Bachmann
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, US; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN, USA.
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44
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Navas A, Van de Wijer L, Jacobs-Cleophas M, Schimmel-Naber AM, van Cranenbroek B, van der Heijden WA, van der Lei RJ, Vergara Z, Netea MG, van der Ven AJAM, Kapinsky M, Koenen HJPM, Joosten LAB. Comprehensive phenotyping of circulating immune cell subsets in people living with HIV. J Immunol Methods 2022; 507:113307. [PMID: 35760096 DOI: 10.1016/j.jim.2022.113307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022]
Abstract
Systemic chronic inflammation and immune dysfunction are recognized as drivers of the development of non-AIDS related comorbidities (NARCs) in people living with HIV (PLHIV). In order to lower the risk of NARCs, it is critical to elucidate what is the contribution of alterations in the composition and function of circulating immune cells to NARCs-related pathogenesis. Findings from previous immunophenotyping studies in PLHIV are highly heterogeneous and it is not fully understood to what extent phenotypic changes on immune cells play a role in the dysregulated inflammatory response observed. In this study, three flow cytometry panels were designed and standardized to phenotypically and functionally identify the main circulating immune cell subsets in PLHIV. To reduce variability, up to 10 markers out of the approximately 20 markers in each panel were used in a custom dry format DURA Innovations (LUCID product line). Intra-assay precision tests performed for the selected cell subsets showed that the three panels had a %CV below 18% for percent of positive cells and the MFI (mean fluorescent intensity) of lineage markers. Our reported pipeline for immunophenotypic analysis facilitated the discrimination of 1153 cell populations, providing an integrated overview of circulating innate and adaptative immune cells as well as the cells' functional status in terms of activation, exhaustion, and maturation. When combined with unsupervised computational techniques, this standardized immunophenotyping approach may support the discovery of novel phenotypes with clinical relevance in NARCs and demonstrate future utility in other immune-mediated diseases.
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Affiliation(s)
- Adriana Navas
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands.
| | - Lisa Van de Wijer
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands
| | - Maartje Jacobs-Cleophas
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands
| | - A Marlies Schimmel-Naber
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands
| | - Bram van Cranenbroek
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands
| | - Wouter A van der Heijden
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands
| | - Roelof J van der Lei
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Drive Indianapolis, Indiana 46268, United States
| | - Zaida Vergara
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Drive Indianapolis, Indiana 46268, United States
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Germany
| | - André J A M van der Ven
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands
| | - Michael Kapinsky
- Beckman Coulter Life Sciences, 5350 Lakeview Pkwy S Drive Indianapolis, Indiana 46268, United States
| | - Hans J P M Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud university medical center, Nijmegen, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud university medical center, Nijmegen, the Netherlands; Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.
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45
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Kim EH, Manganaro L, Schotsaert M, Brown BD, Mulder LC, Simon V. Development of an HIV reporter virus that identifies latently infected CD4 + T cells. CELL REPORTS METHODS 2022; 2:100238. [PMID: 35784650 PMCID: PMC9243624 DOI: 10.1016/j.crmeth.2022.100238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 04/23/2023]
Abstract
There is no cure for HIV infection, as the virus establishes a latent reservoir, which escapes highly active antiretroviral treatments. One major obstacle is the difficulty identifying cells that harbor latent proviruses. We devised a single-round viral vector that carries a series of versatile reporter molecules that are expressed in an LTR-dependent or LTR-independent manner and make it possible to accurately distinguish productive from latent infection. Using primary human CD4+ T cells, we show that transcriptionally silent proviruses are found in more than 50% of infected cells. The latently infected cells harbor proviruses but lack evidence for multiple spliced transcripts. LTR-silent integrations occurred to variable degrees in all CD4+ T subsets examined, with CD4+ TEM and CD4+ TREG displaying the highest frequency of latent infections. This viral vector permits the interrogation of HIV latency at single-cell resolution, revealing mechanisms of latency establishment and allowing the characterization of effective latency-reversing agents.
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Affiliation(s)
- Eun Hye Kim
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lara Manganaro
- INGM, Istituto Nazionale di Genetica Molecolare, ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian D. Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lubbertus C.F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine at Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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46
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Naeimi Kararoudi M, Likhite S, Elmas E, Yamamoto K, Schwartz M, Sorathia K, de Souza Fernandes Pereira M, Sezgin Y, Devine RD, Lyberger JM, Behbehani GK, Chakravarti N, Moriarity BS, Meyer K, Lee DA. Optimization and validation of CAR transduction into human primary NK cells using CRISPR and AAV. CELL REPORTS METHODS 2022; 2:100236. [PMID: 35784645 PMCID: PMC9243630 DOI: 10.1016/j.crmeth.2022.100236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/08/2021] [Accepted: 05/23/2022] [Indexed: 11/22/2022]
Abstract
Human primary natural killer (NK) cells are being widely advanced for cancer immunotherapy. However, methods for gene editing of these cells have suffered low transduction rates, high cell death, and loss of transgene expression after expansion. Here, we developed a highly efficient method for site-specific gene insertion in NK cells using CRISPR (Cas9/RNP) and AAVs. We compared AAV vectors designed to mediate gene insertion by different DNA repair mechanisms, homology arm lengths, and virus concentrations. We then validated the method for site-directed gene insertion of CD33-specific CARs into primary human NK cells. CAR transduction was efficient, its expression remained stable after expansion, and it improved efficacy against AML targets.
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Affiliation(s)
- Meisam Naeimi Kararoudi
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Shibi Likhite
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Ezgi Elmas
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Kenta Yamamoto
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Maura Schwartz
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Kinnari Sorathia
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | | | - Yasemin Sezgin
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Raymond D. Devine
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Justin M. Lyberger
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Gregory K. Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Nitin Chakravarti
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | | | - Kathrin Meyer
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
| | - Dean A. Lee
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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47
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Grebinoski S, Zhang Q, Cillo AR, Manne S, Xiao H, Brunazzi EA, Tabib T, Cardello C, Lian CG, Murphy GF, Lafyatis R, Wherry EJ, Das J, Workman CJ, Vignali DAA. Autoreactive CD8 + T cells are restrained by an exhaustion-like program that is maintained by LAG3. Nat Immunol 2022; 23:868-877. [PMID: 35618829 DOI: 10.1038/s41590-022-01210-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/12/2022] [Indexed: 01/02/2023]
Abstract
Impaired chronic viral and tumor clearance has been attributed to CD8+ T cell exhaustion, a differentiation state in which T cells have reduced and altered effector function that can be partially reversed upon blockade of inhibitory receptors. The role of the exhaustion program and transcriptional networks that control CD8+ T cell function and fate in autoimmunity is not clear. Here we show that intra-islet CD8+ T cells phenotypically, transcriptionally, epigenetically and metabolically possess features of canonically exhausted T cells, yet maintain important differences. This 'restrained' phenotype can be perturbed and disease accelerated by CD8+ T cell-restricted deletion of the inhibitory receptor lymphocyte activating gene 3 (LAG3). Mechanistically, LAG3-deficient CD8+ T cells have enhanced effector-like functions, trafficking to the islets, and have a diminished exhausted phenotype, highlighting a physiological role for an exhaustion program in limiting autoimmunity and implicating LAG3 as a target for autoimmune therapy.
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Affiliation(s)
- Stephanie Grebinoski
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Qianxia Zhang
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Graduate Program of Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Sasikanth Manne
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Hanxi Xiao
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,CMU-Pitt Joint Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin A Brunazzi
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Christine G Lian
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - George F Murphy
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - E John Wherry
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Parker Institute for Cancer Immunotherapy at University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jishnu Das
- Center for Systems Immunology, Departments of Immunology and Computational & Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA. .,Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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48
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Hoang Y, Gryzik S, Hoppe I, Rybak A, Schädlich M, Kadner I, Walther D, Vera J, Radbruch A, Groth D, Baumgart S, Baumgrass R. PRI: Re-Analysis of a Public Mass Cytometry Dataset Reveals Patterns of Effective Tumor Treatments. Front Immunol 2022; 13:849329. [PMID: 35592315 PMCID: PMC9110672 DOI: 10.3389/fimmu.2022.849329] [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: 01/05/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm “pattern recognition of immune cells (PRI)” to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4+T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data.
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Affiliation(s)
- Yen Hoang
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Stefanie Gryzik
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Ines Hoppe
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Alexander Rybak
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Martin Schädlich
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabelle Kadner
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Dirk Walther
- Bioinformatics, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Julio Vera
- Laboratory of Systems Tumor Immunology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Radbruch
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Department of Rheumatology and Clinical Immunology, Charité, Campus Berlin Mitte, Berlin, Germany
| | - Detlef Groth
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Sabine Baumgart
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Institute of Immunology, Core Facility Cytometry, University Hospital Jena, Jena, Germany
| | - Ria Baumgrass
- German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.,Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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49
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Guo F, Hancock B, Griffith A, Lin H, Howard K, Keegan J, Zhang F, Chicoine A, Cahill L, Ng J, Lederer J. Distinct Injury Responsive Regulatory T Cells Identified by Multi-Dimensional Phenotyping. Front Immunol 2022; 13:833100. [PMID: 35634302 PMCID: PMC9135044 DOI: 10.3389/fimmu.2022.833100] [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: 12/10/2021] [Accepted: 04/11/2022] [Indexed: 01/21/2023] Open
Abstract
CD4+ regulatory T cells (Tregs) activate and expand in response to different types of injuries, suggesting that they play a critical role in controlling the immune response to tissue and cell damage. This project used multi-dimensional profiling techniques to comprehensively characterize injury responsive Tregs in mice. We show that CD44high Tregs expand in response to injury and were highly suppressive when compared to CD44low Tregs. T cell receptor (TCR) repertoire analysis revealed that the CD44high Treg population undergo TCRαβ clonal expansion as well as increased TCR CDR3 diversity. Bulk RNA sequencing and single-cell RNA sequencing with paired TCR clonotype analysis identified unique differences between CD44high and CD44low Tregs and specific upregulation of genes in Tregs with expanded TCR clonotypes. Gene ontology analysis for molecular function of RNA sequencing data identified chemokine receptors and cell division as the most enriched functional terms in CD44high Tregs versus CD44low Tregs. Mass cytometry (CyTOF) analysis of Tregs from injured and uninjured mice verified protein expression of these genes on CD44high Tregs, with injury-induced increases in Helios, Galectin-3 and PYCARD expression. Taken together, these data indicate that injury triggers the expansion of a highly suppressive CD44high Treg population that is transcriptionally and phenotypically distinct from CD44low Tregs suggesting that they actively participate in controlling immune responses to injury and tissue damage.
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Affiliation(s)
- Fei Guo
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo, China
| | - Brandon Hancock
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Alec Griffith
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Hui Lin
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Department of Pathophysiology, School of Basic Medical Sciences, Nanchang University, Nanchang, China
| | - Kaitlyn Howard
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Joshua Keegan
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Fan Zhang
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,Department of Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Adam Chicoine
- Human Immunology Center, Brigham and Women’s Hospital, Boston, MA, United States
| | - Laura Cahill
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Julie Ng
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - James Lederer
- Department of Surgery, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States,*Correspondence: James Lederer,
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50
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Yanai H, Dunn C, Park B, Coletta C, McDevitt RA, McNeely T, Leone M, Wersto RP, Perdue KA, Beerman I. Male rat leukocyte population dynamics predict a window for intervention in aging. eLife 2022; 11:76808. [PMID: 35507394 PMCID: PMC9150891 DOI: 10.7554/elife.76808] [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: 01/05/2022] [Accepted: 05/03/2022] [Indexed: 12/03/2022] Open
Abstract
Many age-associated changes in the human hematopoietic system have been reproduced in murine models; however, such changes have not been as robustly explored in rats despite the fact these larger rodents are more physiologically similar to humans. We examined peripheral blood of male F344 rats ranging from 3 to 27 months of age and found significant age-associated changes with distinct leukocyte population shifts. We report CD25+ CD4+ population frequency is a strong predictor of healthy aging, generate a model using blood parameters, and find rats with blood profiles that diverge from chronologic age indicate debility; thus, assessments of blood composition may be useful for non-lethal disease profiling or as a surrogate measure for efficacy of aging interventions. Importantly, blood parameters and DNA methylation alterations, defined distinct juncture points during aging, supporting a non-linear aging process. Our results suggest these inflection points are important considerations for aging interventions. Overall, we present rat blood aging metrics that can serve as a resource to evaluate health and the effects of interventions in a model system physiologically more reflective of humans. Our blood contains many types of white blood cells, which play important roles in defending the body against infections and other threats to our health. The number of these cells changes with age, and this in turn contributes to many other alterations that happen in the body as we get older. For example, the immune system generally gets weaker at fighting infections and preventing other cells from developing into cancer. On top of that, the white blood cells themselves can become cancerous, resulting in several types of blood cancer that are more likely to happen in older people. Many previous studies have examined how the number of white blood cells changes with age in humans and mice. However, our understanding of this process in rats is still poor, despite the fact that the way the human body works has more in common with the rat body than the mouse body. Here, Yanai, Dunn et al. have studied samples of blood from rats between three to 27 months old. The experiments found that it is possible to accurately predict the age of healthy rats by measuring the frequency of populations of white blood cells, especially a certain type known as CD25+ CD4+ cells. If the animals had any form of illness, their predicted age deviated from their actual age. Furthermore, while some changes in the blood were gradual and continuous, others displayed distinct shifts when the rats reached specific ages. In the future, these findings may be used as a tool to help researchers diagnose illnesses in rats before the animals develop symptoms, or to more easily establish if a treatment is having a positive effect on the rats’ health. The work of Yanai, Dunn et al. also provides new insights into aging that could potentially aid the design of new screening methods to predict cancer and intervene using a model system that is more similar to humans.
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Affiliation(s)
- Hagai Yanai
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Christopher Dunn
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Bongsoo Park
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Christopher Coletta
- Computational Biology and Genomics Core, National Institute on Aging, Baltimore, United States
| | - Ross A McDevitt
- Comparative Medicine Section, National Institute on Aging, Baltimore, United States
| | - Taylor McNeely
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Michael Leone
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Robert P Wersto
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Kathy A Perdue
- Comparative Medicine Section, National Institute on Aging, Baltimore, United States
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
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