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Priest DG, Ebihara T, Tulyeu J, Søndergaard JN, Sakakibara S, Sugihara F, Nakao S, Togami Y, Yoshimura J, Ito H, Onishi S, Muratsu A, Mitsuyama Y, Ogura H, Oda J, Okusaki D, Matsumoto H, Wing JB. Atypical and non-classical CD45RB lo memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19. Nat Commun 2024; 15:6811. [PMID: 39122676 PMCID: PMC11315995 DOI: 10.1038/s41467-024-50997-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Resting memory B cells can be divided into classical or atypical groups, but the heterogenous marker expression on activated memory B cells makes similar classification difficult. Here, by longitudinal analysis of mass cytometry and CITE-seq data from cohorts with COVID-19, bacterial sepsis, or BNT162b2 mRNA vaccine, we observe that resting B cell memory consist of classical CD45RB+ memory and CD45RBlo memory, of which the latter contains of two distinct groups of CD11c+ atypical and CD23+ non-classical memory cells. CD45RB levels remain stable in these cells after activation, thereby enabling the tracking of activated B cells and plasmablasts derived from either CD45RB+ or CD45RBlo memory B cells. Moreover, in both COVID-19 patients and mRNA vaccination, CD45RBlo B cells formed the majority of SARS-CoV2 specific memory B cells and correlated with serum antibodies, while CD45RB+ memory are activated by bacterial sepsis. Our results thus identify that stably expressed CD45RB levels can be exploited to trace resting memory B cells and their activated progeny, and suggest that atypical and non-classical CD45RBlo memory B cells contribute to SARS-CoV-2 infection and vaccination.
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Affiliation(s)
- David G Priest
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan
| | - Takeshi Ebihara
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Janyerkye Tulyeu
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Jonas N Søndergaard
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shuhei Sakakibara
- Laboratory of Immune Regulation, IFReC, Osaka University, Suita, Osaka, 563-0793, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, 532-0003, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center and Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
- Research Institute for Microbial Disease, Osaka University, Suita, Osaka, 563-0793, Japan
| | - Shunichiro Nakao
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yuki Togami
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jumpei Yoshimura
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ito
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shinya Onishi
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Arisa Muratsu
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Yumi Mitsuyama
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
- Division of Trauma and Surgical Critical Care, Osaka General Medical Center, Osaka, 558-8558, Japan
| | - Hiroshi Ogura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Jun Oda
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Daisuke Okusaki
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan
- Laboratory of Human Immunology (Single Cell Genomics), WPI-IFReC, Osaka University, Suita, 565-0871, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, 565-0871, Japan
| | - Hisatake Matsumoto
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Department of Traumatology and Acute Critical Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.
| | - James B Wing
- Laboratory of Human Single Cell Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Osaka, 563-0793, Japan.
- Human Single Cell Immunology Team, Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Osaka, Japan.
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Hendriks SH, Heidt S, Krop J, IJsselsteijn ME, Eggermont J, Kers J, Reinders ME, Koning F, van Kooten C. IDO + Endothelial Cells in Glomeruli of Kidney Transplantation Patients With Glomerulitis. Transplant Direct 2024; 10:e1674. [PMID: 38988690 PMCID: PMC11230740 DOI: 10.1097/txd.0000000000001674] [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: 04/11/2023] [Revised: 05/14/2024] [Indexed: 07/12/2024] Open
Abstract
Background Kidney transplantation is the preferred treatment option for patients with end-stage renal disease. However, long-term graft survival remains a challenge. The enzyme indoleamine 2,3 dioxygenase (IDO) has been reported to have immunomodulatory effects with IDO transcripts being elevated in both antibody-mediated rejection and T cell-mediated rejection. Methods A metal-conjugated antibody panel for the staining of kidney biopsies was developed, allowing the visualization of 41 structural and immune markers on a single tissue slide to gain in-depth insight into the composition and localization of the immune cell compartment. Staining was applied to week 4 and 24 protocol biopsies of 49 patients as well as on 15 indication biopsies of the TRITON study and 4 additional transplantation biopsies with glomerulitis. Results A highly distinctive and specific glomerular IDO expression was observed in biopsies from 3 of 49 patients in imaging mass cytometry. Immunohistochemistry confirmed IDO expression in glomeruli of 10 of 10 cases with glomerulitis. IDO was found to be expressed by CD31+ glomerular endothelial cells, accompanied by the presence of granzyme-B+Tbet+CD7+CD45RA+ natural killer cells and CD68+ macrophages. Furthermore, a proportion of both the immune cells and endothelial cells expressed Ki-67, indicative of cell proliferation, which was not observed in control glomeruli. Conclusions Our results show glomerular IDO expression in transplanted kidneys with glomerulitis, which is accompanied by increased numbers of natural killer cells and macrophages and likely reflects local immune activation.
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Affiliation(s)
- Sanne H. Hendriks
- Department of Immunology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Sebastiaan Heidt
- Department of Immunology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Juliette Krop
- Department of Immunology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Marieke E. IJsselsteijn
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Jeroen Eggermont
- Department of LKEB Radiology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Jesper Kers
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Pathology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Marlies E.J. Reinders
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus MC Transplant Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
| | - Cees van Kooten
- Department of Internal Medicine (Nephrology) and Transplant Center, Leiden University Medical Center, Leiden University, Leiden, the Netherlands
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3
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Coleman DJ, Keane P, Chin PS, Ames L, Kellaway S, Blair H, Khan N, Griffin J, Holmes E, Maytum A, Potluri S, Strate L, Koscielniak K, Raghavan M, Bushweller J, Heidenreich O, Rabbitts T, Cockerill PN, Bonifer C. Pharmacological inhibition of RAS overcomes FLT3 inhibitor resistance in FLT3-ITD+ AML through AP-1 and RUNX1. iScience 2024; 27:109576. [PMID: 38638836 PMCID: PMC11024925 DOI: 10.1016/j.isci.2024.109576] [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: 10/23/2023] [Revised: 02/16/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
AML is characterized by mutations in genes associated with growth regulation such as internal tandem duplications (ITD) in the receptor kinase FLT3. Inhibitors targeting FLT3 (FLT3i) are being used to treat patients with FLT3-ITD+ but most relapse and become resistant. To elucidate the resistance mechanism, we compared the gene regulatory networks (GRNs) of leukemic cells from patients before and after relapse, which revealed that the GRNs of drug-responsive patients were altered by rewiring their AP-1-RUNX1 axis. Moreover, FLT3i induces the upregulation of signaling genes, and we show that multiple cytokines, including interleukin-3 (IL-3), can overcome FLT3 inhibition and send cells back into cycle. FLT3i leads to loss of AP-1 and RUNX1 chromatin binding, which is counteracted by IL-3. However, cytokine-mediated drug resistance can be overcome by a pan-RAS inhibitor. We show that cytokines instruct AML growth via the transcriptional regulators AP-1 and RUNX1 and that pan-RAS drugs bypass this barrier.
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Affiliation(s)
- Daniel J.L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn S. Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sophie Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen Blair
- Wolfson Childhood Cancer Research Centre, University of Newcastle, Newcastle upon Tyne, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - James Griffin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Elizabeth Holmes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alexander Maytum
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Lara Strate
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Kinga Koscielniak
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - John Bushweller
- School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, University of Newcastle, Newcastle upon Tyne, UK
- Princess Máxima Centrum of Pediatric Oncology, Utrecht, the Netherlands
| | - Terry Rabbitts
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Peter N. Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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4
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Schulz AR, Rademacher J, Bockhorn V, Mei HE. Harmonized analysis of PBMC by mass cytometry. Methods Cell Biol 2024; 186:107-130. [PMID: 38705596 DOI: 10.1016/bs.mcb.2024.02.015] [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] [Indexed: 05/07/2024]
Abstract
Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.
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Affiliation(s)
- Axel R Schulz
- Deutsches Rheuma-Forschungszentrum Berlin, A Leibniz Institute, Berlin, Germany
| | - Judith Rademacher
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Department of Gastroenterology, Infectiology and Rheumatology (Including Nutrition Medicine), Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vera Bockhorn
- Deutsches Rheuma-Forschungszentrum Berlin, A Leibniz Institute, Berlin, Germany
| | - Henrik E Mei
- Deutsches Rheuma-Forschungszentrum Berlin, A Leibniz Institute, Berlin, Germany.
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5
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Kellaway SG, Potluri S, Keane P, Blair HJ, Ames L, Worker A, Chin PS, Ptasinska A, Derevyanko PK, Adamo A, Coleman DJL, Khan N, Assi SA, Krippner-Heidenreich A, Raghavan M, Cockerill PN, Heidenreich O, Bonifer C. Leukemic stem cells activate lineage inappropriate signalling pathways to promote their growth. Nat Commun 2024; 15:1359. [PMID: 38355578 PMCID: PMC10867020 DOI: 10.1038/s41467-024-45691-4] [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: 05/02/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Acute Myeloid Leukemia (AML) is caused by multiple mutations which dysregulate growth and differentiation of myeloid cells. Cells adopt different gene regulatory networks specific to individual mutations, maintaining a rapidly proliferating blast cell population with fatal consequences for the patient if not treated. The most common treatment option is still chemotherapy which targets such cells. However, patients harbour a population of quiescent leukemic stem cells (LSCs) which can emerge from quiescence to trigger relapse after therapy. The processes that allow such cells to re-grow remain unknown. Here, we examine the well characterised t(8;21) AML sub-type as a model to address this question. Using four primary AML samples and a novel t(8;21) patient-derived xenograft model, we show that t(8;21) LSCs aberrantly activate the VEGF and IL-5 signalling pathways. Both pathways operate within a regulatory circuit consisting of the driver oncoprotein RUNX1::ETO and an AP-1/GATA2 axis allowing LSCs to re-enter the cell cycle while preserving self-renewal capacity.
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Affiliation(s)
- Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
- Blood Cancer and Stem Cells, Centre for Cancer Sciences, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Helen J Blair
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Alice Worker
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Assunta Adamo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Naeem Khan
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Olaf Heidenreich
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Princess Maxima Center of Pediatric Oncology, Utrecht, Netherlands
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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6
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Milross L, Hunter B, McDonald D, Merces G, Thomson A, Hilkens CMU, Wills J, Rees P, Jiwa K, Cooper N, Majo J, Ashwin H, Duncan CJA, Kaye PM, Bayraktar OA, Filby A, Fisher AJ. Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19. EBioMedicine 2024; 99:104945. [PMID: 38142637 PMCID: PMC10788437 DOI: 10.1016/j.ebiom.2023.104945] [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: 05/18/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
BACKGROUND Lung damage in severe COVID-19 is highly heterogeneous however studies with dedicated spatial distinction of discrete temporal phases of diffuse alveolar damage (DAD) and alternate lung injury patterns are lacking. Existing studies have also not accounted for progressive airspace obliteration in cellularity estimates. We used an imaging mass cytometry (IMC) analysis with an airspace correction step to more accurately identify the cellular immune response that underpins the heterogeneity of severe COVID-19 lung disease. METHODS Lung tissue was obtained at post-mortem from severe COVID-19 deaths. Pathologist-selected regions of interest (ROIs) were chosen by light microscopy representing the patho-evolutionary spectrum of DAD and alternate disease phenotypes were selected for comparison. Architecturally normal SARS-CoV-2-positive lung tissue and tissue from SARS-CoV-2-negative donors served as controls. ROIs were stained for 40 cellular protein markers and ablated using IMC before segmented cells were classified. Cell populations corrected by ROI airspace and their spatial relationships were compared across lung injury patterns. FINDINGS Forty patients (32M:8F, age: 22-98), 345 ROIs and >900k single cells were analysed. DAD progression was marked by airspace obliteration and significant increases in mononuclear phagocytes (MnPs), T and B lymphocytes and significant decreases in alveolar epithelial and endothelial cells. Neutrophil populations proved stable overall although several interferon-responding subsets demonstrated expansion. Spatial analysis revealed immune cell interactions occur prior to microscopically appreciable tissue injury. INTERPRETATION The immunopathogenesis of severe DAD in COVID-19 lung disease is characterised by sustained increases in MnPs and lymphocytes with key interactions occurring even prior to lung injury is established. FUNDING UK Research and Innovation/Medical Research Council through the UK Coronavirus Immunology Consortium, Barbour Foundation, General Sir John Monash Foundation, Newcastle University, JGW Patterson Foundation, Wellcome Trust.
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Affiliation(s)
- Luke Milross
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - Bethany Hunter
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - David McDonald
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - George Merces
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amanda Thomson
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Catharien M U Hilkens
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
| | - John Wills
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Paul Rees
- Department of Biomedical Engineering, Swansea University, Wales, UK; Imaging Platform, Broad Institute of MIT and Harvard, 415 Main Street, Boston, Cambridge, MA, USA
| | - Kasim Jiwa
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nigel Cooper
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Joaquim Majo
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Helen Ashwin
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Christopher J A Duncan
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Paul M Kaye
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | | | - Andrew Filby
- Newcastle University Biosciences Institute, Newcastle upon Tyne, UK; Innovation Methodology and Application Research Theme, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Andrew J Fisher
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK; Institute of Transplantation, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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7
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Hunter B, Nicorescu I, Foster E, McDonald D, Hulme G, Fuller A, Thomson A, Goldsborough T, Hilkens CMU, Majo J, Milross L, Fisher A, Bankhead P, Wills J, Rees P, Filby A, Merces G. OPTIMAL: An OPTimized Imaging Mass cytometry AnaLysis framework for benchmarking segmentation and data exploration. Cytometry A 2024; 105:36-53. [PMID: 37750225 PMCID: PMC10952805 DOI: 10.1002/cyto.a.24803] [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: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023]
Abstract
Analysis of imaging mass cytometry (IMC) data and other low-resolution multiplexed tissue imaging technologies is often confounded by poor single-cell segmentation and suboptimal approaches for data visualization and exploration. This can lead to inaccurate identification of cell phenotypes, states, or spatial relationships compared to reference data from single-cell suspension technologies. To this end we have developed the "OPTimized Imaging Mass cytometry AnaLysis (OPTIMAL)" framework to benchmark any approaches for cell segmentation, parameter transformation, batch effect correction, data visualization/clustering, and spatial neighborhood analysis. Using a panel of 27 metal-tagged antibodies recognizing well-characterized phenotypic and functional markers to stain the same Formalin-Fixed Paraffin Embedded (FFPE) human tonsil sample tissue microarray over 12 temporally distinct batches we tested several cell segmentation models, a range of different arcsinh cofactor parameter transformation values, 5 different dimensionality reduction algorithms, and 2 clustering methods. Finally, we assessed the optimal approach for performing neighborhood analysis. We found that single-cell segmentation was improved by the use of an Ilastik-derived probability map but that issues with poor segmentation were only really evident after clustering and cell type/state identification and not always evident when using "classical" bivariate data display techniques. The optimal arcsinh cofactor for parameter transformation was 1 as it maximized the statistical separation between negative and positive signal distributions and a simple Z-score normalization step after arcsinh transformation eliminated batch effects. Of the five different dimensionality reduction approaches tested, PacMap gave the best data structure with FLOWSOM clustering out-performing phenograph in terms of cell type identification. We also found that neighborhood analysis was influenced by the method used for finding neighboring cells with a "disc" pixel expansion outperforming a "bounding box" approach combined with the need for filtering objects based on size and image-edge location. Importantly, OPTIMAL can be used to assess and integrate with any existing approach to IMC data analysis and, as it creates .FCS files from the segmentation output and allows for single-cell exploration to be conducted using a wide variety of accessible software and algorithms familiar to conventional flow cytometrists.
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Affiliation(s)
- Bethany Hunter
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Ioana Nicorescu
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Emma Foster
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - David McDonald
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Gillian Hulme
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fuller
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Amanda Thomson
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | | | - Catharien M. U. Hilkens
- Translational and Clinical Research Institute, Immunity and Inflammation Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Joaquim Majo
- Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Luke Milross
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew Fisher
- Transplantation and Regenerative Medicine, Newcastle University Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Peter Bankhead
- Centre for Genomic and Experimental Medicine, CRUK Scotland Centre, and Edinburgh PathologyUniversity of EdinburghEdinburghUK
| | - John Wills
- Department of Veterinary MedicineCambridge UniversityCambridgeUK
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
| | - Paul Rees
- Department of Biomedical EngineeringSwansea UniversitySwansea, WalesUK
- Imaging PlatformBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Andrew Filby
- Flow Cytometry Core Facility, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - George Merces
- Biosciences Institute, Innovation, Methodology and Application (IMA) Research Theme, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Image Analysis Unit, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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8
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Vietsch EE, Latifi D, Verheij M, van der Oost EW, de Wilde RF, Haen R, van den Boom AL, Koerkamp BG, Doornebosch PG, van Verschuer VM, Ooms AH, Mohammad F, Willemsen M, Aerts JG, Krog RT, de Miranda NF, van den Bosch TP, Mueller YM, Katsikis PD, van Eijck CH. B cell immune profiles in dysbiotic vermiform appendixes of pancreatic cancer patients. Front Immunol 2023; 14:1230306. [PMID: 38022530 PMCID: PMC10667699 DOI: 10.3389/fimmu.2023.1230306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest solid tumors and is resistant to immunotherapy. B cells play an essential role in PDAC progression and immune responses, both locally and systemically. Moreover, increasing evidence suggests that microbial compositions inside the tumor, as well as in the oral cavity and the gut, are important factors in shaping the PDAC immune landscape. However, the gut-associated lymphoid tissue (GALT) has not previously been explored in PDAC patients. In this study, we analyzed healthy vermiform appendix (VA) from 20 patients with PDAC and 32 patients with colon diseases by gene expression immune profiling, flow cytometry analysis, and microbiome sequencing. We show that the VA GALT of PDAC patients exhibits markers of increased inflammation and cytotoxic cell activity. In contrast, B cell function is decreased in PDAC VA GALT based on gene expression profiling; B cells express significantly fewer MHC class II surface receptors, whereas plasma cells express the immune checkpoint molecule HLA-G. Additionally, the vermiform appendix microbiome of PDAC patients is enriched with Klebsiella pneumoniae, Bifidobacterium animalis, and Adlercreutzia equolifaciens, while certain commensals are depleted. Our findings may suggest impaired B cell function within the GALT of PDAC patients, which could potentially be linked to microbial dysbiosis. Additional investigations are imperative to validate our observations and explore these potential targets of future therapies.
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Affiliation(s)
- Eveline E. Vietsch
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Diba Latifi
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Maaike Verheij
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | | | | | - Roel Haen
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Anne Loes van den Boom
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Department of Surgery, Reinier de Graaf Hospital, Delft, Netherlands
| | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | | | | | - Ariadne H.A.G. Ooms
- Department of Pathology, Pathan BV, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Farzana Mohammad
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Marcella Willemsen
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Joachim G.J.V. Aerts
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Ricki T. Krog
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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9
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Yousuf S, Qiu M, Voith von Voithenberg L, Hulkkonen J, Macinkovic I, Schulz AR, Hartmann D, Mueller F, Mijatovic M, Ibberson D, AlHalabi KT, Hetzer J, Anders S, Brüne B, Mei HE, Imbusch CD, Brors B, Heikenwälder M, Gaida MM, Büchler MW, Weigert A, Hackert T, Roth S. Spatially Resolved Multi-Omics Single-Cell Analyses Inform Mechanisms of Immune Dysfunction in Pancreatic Cancer. Gastroenterology 2023; 165:891-908.e14. [PMID: 37263303 DOI: 10.1053/j.gastro.2023.05.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND & AIMS As pancreatic ductal adenocarcinoma (PDAC) continues to be recalcitrant to therapeutic interventions, including poor response to immunotherapy, albeit effective in other solid malignancies, a more nuanced understanding of the immune microenvironment in PDAC is urgently needed. We aimed to unveil a detailed view of the immune micromilieu in PDAC using a spatially resolved multimodal single-cell approach. METHODS We applied single-cell RNA sequencing, spatial transcriptomics, multiplex immunohistochemistry, and mass cytometry to profile the immune compartment in treatment-naïve PDAC tumors and matched adjacent normal pancreatic tissue, as well as in the systemic circulation. We determined prognostic associations of immune signatures and performed a meta-analysis of the immune microenvironment in PDAC and lung adenocarcinoma on single-cell level. RESULTS We provided a spatially resolved fine map of the immune landscape in PDAC. We substantiated the exhausted phenotype of CD8 T cells and immunosuppressive features of myeloid cells, and highlighted immune subsets with potentially underappreciated roles in PDAC that diverged from immune populations within adjacent normal areas, particularly CD4 T cell subsets and natural killer T cells that are terminally exhausted and acquire a regulatory phenotype. Differential analysis of immune phenotypes in PDAC and lung adenocarcinoma revealed the presence of extraordinarily immunosuppressive subtypes in PDAC, along with a distinctive immune checkpoint composition. CONCLUSIONS Our study sheds light on the multilayered immune dysfunction in PDAC and presents a holistic view of the immune landscape in PDAC and lung adenocarcinoma, providing a comprehensive resource for functional studies and the exploration of therapeutically actionable targets in PDAC.
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Affiliation(s)
- Suhail Yousuf
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Mengjie Qiu
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Johannes Hulkkonen
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Igor Macinkovic
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | | | - Domenic Hartmann
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian Mueller
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Margarete Mijatovic
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Karam T AlHalabi
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jenny Hetzer
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Simon Anders
- BioQuant Center, Heidelberg University, Heidelberg, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe-University Frankfurt, Frankfurt, Germany; German Cancer Consortium, Partner Site Frankfurt, Germany
| | - Henrik E Mei
- German Rheumatism Research Center, Berlin, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center, Heidelberg, Germany
| | - Matthias M Gaida
- Institute of Pathology, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany; Research Center for Immunotherapy, University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany; Joint Unit Immunopathology, Institute of Pathology, University Medical Center, Johannes Gutenberg University and Translational Oncology, University Medical Center Mainz, Mainz, Germany
| | - Markus W Büchler
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Goethe-University Frankfurt, Frankfurt, Germany; German Cancer Consortium, Partner Site Frankfurt, Germany
| | - Thilo Hackert
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Susanne Roth
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany.
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10
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Wang XQ, Danenberg E, Huang CS, Egle D, Callari M, Bermejo B, Dugo M, Zamagni C, Thill M, Anton A, Zambelli S, Russo S, Ciruelos EM, Greil R, Győrffy B, Semiglazov V, Colleoni M, Kelly CM, Mariani G, Del Mastro L, Biasi O, Seitz RS, Valagussa P, Viale G, Gianni L, Bianchini G, Ali HR. Spatial predictors of immunotherapy response in triple-negative breast cancer. Nature 2023; 621:868-876. [PMID: 37674077 PMCID: PMC10533410 DOI: 10.1038/s41586-023-06498-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/28/2023] [Indexed: 09/08/2023]
Abstract
Immune checkpoint blockade (ICB) benefits some patients with triple-negative breast cancer, but what distinguishes responders from non-responders is unclear1. Because ICB targets cell-cell interactions2, we investigated the impact of multicellular spatial organization on response, and explored how ICB remodels the tumour microenvironment. We show that cell phenotype, activation state and spatial location are intimately linked, influence ICB effect and differ in sensitive versus resistant tumours early on-treatment. We used imaging mass cytometry3 to profile the in situ expression of 43 proteins in tumours from patients in a randomized trial of neoadjuvant ICB, sampled at three timepoints (baseline, n = 243; early on-treatment, n = 207; post-treatment, n = 210). Multivariate modelling showed that the fractions of proliferating CD8+TCF1+T cells and MHCII+ cancer cells were dominant predictors of response, followed by cancer-immune interactions with B cells and granzyme B+ T cells. On-treatment, responsive tumours contained abundant granzyme B+ T cells, whereas resistant tumours were characterized by CD15+ cancer cells. Response was best predicted by combining tissue features before and on-treatment, pointing to a role for early biopsies in guiding adaptive therapy. Our findings show that multicellular spatial organization is a major determinant of ICB effect and suggest that its systematic enumeration in situ could help realize precision immuno-oncology.
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Affiliation(s)
- Xiao Qian Wang
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Esther Danenberg
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Chiun-Sheng Huang
- National Taiwan University Hospital, College of Medicine, National Taiwan University and Taiwan Breast Cancer Consortium, Taipei, Taiwan
| | - Daniel Egle
- Department of Gynecology, Brust Gesundheit Zentrum Tirol, Medical University Innsbruck, Innsbruck, Austria
| | | | - Begoña Bermejo
- Medical Oncology, Hospital Clínico Universitario de Valencia, Biomedical Research Institute INCLIVA, Valencia, Spain
- Medicine Department, Universidad de Valencia, Valencia, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
| | | | - Claudio Zamagni
- IRCCS Azienda Ospedaliero-universitaria di Bologna, Bologna, Italy
| | - Marc Thill
- Department of Gynecology and Gynecological Oncology, Agaplesion Markus Krankenhaus, Frankfurt am Main, Germany
| | - Anton Anton
- Hospital Universitario Miguel Servet, Zaragoza, Spain
| | | | - Stefania Russo
- Department of Oncology, Azienda Sanitaria Universitaria Friuli Centrale, Udine, Italy
| | | | - Richard Greil
- 3rd Medical Department, Paracelsus Medical University Salzburg, Salzburg, Austria
- Salzburg Cancer Research Institute-CCCIT, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- Cancer Biomarker Research Group, Research Centre for Natural Sciences, Institute of Enzymology, Budapest, Hungary
| | | | | | - Catherine M Kelly
- Mater Private Hospital, Dublin and Cancer Trials Ireland Breast Group, Dublin, Ireland
| | | | - Lucia Del Mastro
- IRCCS Ospedale Policlinico San Martino, UO Clinica di Oncologia Medica, Genoa, Italy
- Dipartimento di Medicina Interna e Specialità Mediche (Di.M.I.), Università di Genova, Genoa, Italy
| | - Olivia Biasi
- IEO, Istituto Europeo di Oncologia, IRCCS, Milan, Italy
| | | | | | - Giuseppe Viale
- IEO, Istituto Europeo di Oncologia, IRCCS, Milan, Italy
- University of Milan, Milan, Italy
| | | | | | - H Raza Ali
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Department of Histopathology, Addenbrookes Hospital, Cambridge, UK.
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11
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Okamoto M, Sasai M, Kuratani A, Okuzaki D, Arai M, Wing JB, Sakaguchi S, Yamamoto M. A genetic method specifically delineates Th1-type Treg cells and their roles in tumor immunity. Cell Rep 2023; 42:112813. [PMID: 37440410 DOI: 10.1016/j.celrep.2023.112813] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 04/06/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Regulatory T (Treg) cells expressing the transcription factor (TF) Foxp3 also express other TFs shared by T helper (Th) subsets under certain conditions. Here, to determine the roles of T-bet-expressing Treg cells, we generate a mouse strain, called VeDTR, in which T-bet/Foxp3 double-positive cells are engineered to be specifically labeled and depleted by a combination of Cre- and Flp-recombinase-dependent gene expression control. Characterization of T-bet+Foxp3+ cells using VeDTR mice reveals high resistance under oxidative stress, which is involved in accumulation of T-bet+Foxp3+ cells in tumor tissues. Moreover, short-term depletion of T-bet+Foxp3+ cells leads to anti-tumor immunity but not autoimmunity, whereas that of whole Treg cells does both. Although ablation of T-bet+Foxp3+ cells during Toxoplasma infection slightly enhances Th1 immune responses, it does not affect the course of the infection. Collectively, the intersectional genetic method reveals the specific roles of T-bet+Foxp3+ cells in suppressing tumor immunity.
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Affiliation(s)
- Masaaki Okamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ayumi Kuratani
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaya Arai
- Laboratory of Experimental Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - James B Wing
- Laboratory of Human Immunology (Single Cell Immunology), WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; Human Immunology Team, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shimon Sakaguchi
- Laboratory of Experimental Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan; Department of Immunoparasitology, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
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12
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Gullotta GS, De Feo D, Friebel E, Semerano A, Scotti GM, Bergamaschi A, Butti E, Brambilla E, Genchi A, Capotondo A, Gallizioli M, Coviello S, Piccoli M, Vigo T, Della Valle P, Ronchi P, Comi G, D'Angelo A, Maugeri N, Roveri L, Uccelli A, Becher B, Martino G, Bacigaluppi M. Age-induced alterations of granulopoiesis generate atypical neutrophils that aggravate stroke pathology. Nat Immunol 2023; 24:925-940. [PMID: 37188941 DOI: 10.1038/s41590-023-01505-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Aging accounts for increased risk and dismal outcome of ischemic stroke. Here, we investigated the impact of age-related changes in the immune system on stroke. Upon experimental stroke, compared with young mice, aged mice had increased neutrophil clogging of the ischemic brain microcirculation, leading to worse no-reflow and outcomes. Aged mice showed an enhanced granulopoietic response to stroke that led to the accumulation of CD101+CD62Llo mature and CD177hiCD101loCD62Llo and CD177loCD101loCD62Lhi immature atypical neutrophils in the blood, endowed with increased oxidative stress, phagocytosis and procoagulant features. Production of CXCL3 by CD62Llo neutrophils of the aged had a key role in the development and pathogenicity of aging-associated neutrophils. Hematopoietic stem cell rejuvenation reverted aging-associated neutropoiesis and improved stroke outcome. In elderly patients with ischemic stroke, single-cell proteome profile of blood leukocytes identified CD62Llo neutrophil subsets associated with worse reperfusion and outcome. Our results unveil how stroke in aging leads to a dysregulated emergency granulopoiesis impacting neurological outcome.
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Affiliation(s)
- Giorgia Serena Gullotta
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Donatella De Feo
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Aurora Semerano
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | | | - Andrea Bergamaschi
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Erica Butti
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Elena Brambilla
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Angela Genchi
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | - Alessia Capotondo
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Mattia Gallizioli
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | | | - Marco Piccoli
- Laboratory of Stem Cells for Tissue Engineering, IRCCS, Policlinico San Donato, Milan, Italy
| | - Tiziana Vigo
- IRCCS, Ospedale Policlinico San Martino, Genova, Italy
| | - Patrizia Della Valle
- Coagulation Service and Thrombosis Research Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Paola Ronchi
- Division of Regenerative Medicine, Stem Cells and Gene Therapy, Telethon Institute for Gene Therapy (HSR-TIGET), IRCCS San Raffaele Hospital, Milan, Italy
| | - Giancarlo Comi
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | - Armando D'Angelo
- Coagulation Service and Thrombosis Research Unit, IRCCS San Raffaele Hospital, Milan, Italy
| | - Norma Maugeri
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
| | - Luisa Roveri
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | - Antonio Uccelli
- IRCCS, Ospedale Policlinico San Martino, Genova, Italy
- Department of Neurology, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genova, Genoa, Italy
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Gianvito Martino
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy
| | - Marco Bacigaluppi
- Neuroimmunology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Hospital and Vita-Salute San Raffaele University, Milan, Italy.
- Neurology Department, IRCCS San Raffaele Hospital, Milan, Italy.
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13
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Bruce-Tagoe TA, Danquah MK. Bioaffinity Nanoprobes for Foodborne Pathogen Sensing. MICROMACHINES 2023; 14:1122. [PMID: 37374709 DOI: 10.3390/mi14061122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Bioaffinity nanoprobes are a type of biosensor that utilize the specific binding properties of biological molecules, such as antibodies, enzymes, and nucleic acids, for the detection of foodborne pathogens. These probes serve as nanosensors and can provide highly specific and sensitive detection of pathogens in food samples, making them an attractive option for food safety testing. The advantages of bioaffinity nanoprobes include their ability to detect low levels of pathogens, rapid analysis time, and cost-effectiveness. However, limitations include the need for specialized equipment and the potential for cross-reactivity with other biological molecules. Current research efforts focus on optimizing the performance of bioaffinity probes and expanding their application in the food industry. This article discusses relevant analytical methods, such as surface plasmon resonance (SPR) analysis, Fluorescence Resonance Energy Transfer (FRET) measurements, circular dichroism, and flow cytometry, that are used to evaluate the efficacy of bioaffinity nanoprobes. Additionally, it discusses advances in the development and application of biosensors in monitoring foodborne pathogens.
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Affiliation(s)
- Tracy Ann Bruce-Tagoe
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga 615 McCallie Ave, Chattanooga, TN 37403, USA
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14
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Gong Y, Zeng M, Zhu Y, Li S, Zhao W, Zhang C, Zhao T, Wang K, Yang J, Bai J. Flow Cytometry with Anti-Diffraction Light Sheet (ADLS) by Spatial Light Modulation. MICROMACHINES 2023; 14:679. [PMID: 36985086 PMCID: PMC10054044 DOI: 10.3390/mi14030679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Flow cytometry is a widespread and powerful technique whose resolution is determined by its capacity to accurately distinguish fluorescently positive populations from negative ones. However, most informative results are discarded while performing the measurements of conventional flow cytometry, e.g., the cell size, shape, morphology, and distribution or location of labeled exosomes within the unpurified biological samples. Herein, we propose a novel approach using an anti-diffraction light sheet with anisotroic feature to excite fluorescent tags. Constituted by an anti-diffraction Bessel-Gaussian beam array, the light sheet is 12 μm wide, 12 μm high, and has a thickness of ~0.8 μm. The intensity profile of the excited fluorescent signal can, therefore, reflect the size and allow samples in the range from O (100 nm) to 10 μm (e.g., blood cells) to be transported via hydrodynamic focusing in a microfluidic chip. The sampling rate is 500 kHz, which provides a capability of high throughput without sacrificing the spatial resolution. Consequently, the proposed anti-diffraction light sheet flow cytometry (ADLSFC) can obtain more informative results than the conventional methodologies, and is able to provide multiple characteristics (e.g., the size and distribution of fluorescent signal) helping to distinguish the target samples from the complex backgrounds.
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Affiliation(s)
- Yanyan Gong
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Ming Zeng
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Yueqiang Zhu
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Shangyu Li
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Wei Zhao
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Ce Zhang
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Tianyun Zhao
- School of Automation, Northwestern Polytechnical University, Xi’an 710072, China
| | - Kaige Wang
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
| | - Jiangcun Yang
- Department of Transfusion Medicine, Shaanxi Provincial People’s Hospital, Xi’an 710068, China
| | - Jintao Bai
- State Key Laboratory of Photon-Technology in Western China Energy, International Collaborative Center on Photoelectric Technology and Nano Functional Materials, Institute of Photonics & Photon Technology, Northwest University, Xi’an 710127, China
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15
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Nuñez NG, Berner F, Friebel E, Unger S, Wyss N, Gomez JM, Purde MT, Niederer R, Porsch M, Lichtensteiger C, Kramer R, Erdmann M, Schmitt C, Heinzerling L, Abdou MT, Karbach J, Schadendorf D, Zimmer L, Ugurel S, Klümper N, Hölzel M, Power L, Kreutmair S, Capone M, Madonna G, Cevhertas L, Heider A, Amaral T, Hasan Ali O, Bomze D, Dimitriou F, Diem S, Ascierto PA, Dummer R, Jäger E, Driessen C, Levesque MP, van de Veen W, Joerger M, Früh M, Becher B, Flatz L. Immune signatures predict development of autoimmune toxicity in patients with cancer treated with immune checkpoint inhibitors. MED 2023; 4:113-129.e7. [PMID: 36693381 DOI: 10.1016/j.medj.2022.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are among the most promising treatment options for melanoma and non-small cell lung cancer (NSCLC). While ICIs can induce effective anti-tumor responses, they may also drive serious immune-related adverse events (irAEs). Identifying biomarkers to predict which patients will suffer from irAEs would enable more accurate clinical risk-benefit analysis for ICI treatment and may also shed light on common or distinct mechanisms underpinning treatment success and irAEs. METHODS In this prospective multi-center study, we combined a multi-omics approach including unbiased single-cell profiling of over 300 peripheral blood mononuclear cell (PBMC) samples and high-throughput proteomics analysis of over 500 serum samples to characterize the systemic immune compartment of patients with melanoma or NSCLC before and during treatment with ICIs. FINDINGS When we combined the parameters obtained from the multi-omics profiling of patient blood and serum, we identified potential predictive biomarkers for ICI-induced irAEs. Specifically, an early increase in CXCL9/CXCL10/CXCL11 and interferon-γ (IFN-γ) 1 to 2 weeks after the start of therapy are likely indicators of heightened risk of developing irAEs. In addition, an early expansion of Ki-67+ regulatory T cells (Tregs) and Ki-67+ CD8+ T cells is also likely to be associated with increased risk of irAEs. CONCLUSIONS We suggest that the combination of these cellular and proteomic biomarkers may help to predict which patients are likely to benefit most from ICI therapy and those requiring intensive monitoring for irAEs. FUNDING This work was primarily funded by the European Research Council, the Swiss National Science Foundation, the Swiss Cancer League, and the Forschungsförderung of the Kantonsspital St. Gallen.
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Affiliation(s)
- Nicolas Gonzalo Nuñez
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Fiamma Berner
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nina Wyss
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland; Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Julia Martinez Gomez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mette-Triin Purde
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Rebekka Niederer
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland; Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Maximilian Porsch
- Department of Radiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Christa Lichtensteiger
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Rafaela Kramer
- Department of Dermatology, Uniklinikum Erlangen, Deutsches Zentrum Immuntherapie (DZI), Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Michael Erdmann
- Department of Dermatology, Uniklinikum Erlangen, Deutsches Zentrum Immuntherapie (DZI), Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany
| | - Christina Schmitt
- Department of Dermatology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Lucie Heinzerling
- Department of Dermatology, Uniklinikum Erlangen, Deutsches Zentrum Immuntherapie (DZI), Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen, Germany; Department of Dermatology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Marie-Therese Abdou
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland
| | - Julia Karbach
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen and German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen, Germany
| | - Niklas Klümper
- Institute for Experimental Oncology, University Hospital Bonn, Bonn, Germany; Center for Integrated Oncology Cologne/Bonn, University Hospital Bonn, Bonn, Germany; Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Michael Hölzel
- Institute for Experimental Oncology, University Hospital Bonn, Bonn, Germany; Center for Integrated Oncology Cologne/Bonn, University Hospital Bonn, Bonn, Germany
| | - Laura Power
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefanie Kreutmair
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mariaelena Capone
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Gabriele Madonna
- Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Lacin Cevhertas
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Department of Medical Immunology, Institute of Health Sciences, Bursa Uludag University, Bursa, Turkey
| | - Anja Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Teresa Amaral
- Skin Cancer Center, Department of Dermatology, University Hospital Tübingen, Tübingen, Germany; iFIT Cluster of Excellence (EXC 2180), University of Tübingen, Tübingen, Germany
| | - Omar Hasan Ali
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland; Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - David Bomze
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Florentia Dimitriou
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stefan Diem
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | | | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Elke Jäger
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Christoph Driessen
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Mitchell Paul Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Markus Joerger
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Martin Früh
- Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Lukas Flatz
- Institute of Immunobiology, Medical Research Center, Kantonsspital St. Gallen, St.Gallen, Switzerland; Department of Dermatology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Medical Oncology and Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Universitäts-Hautklinik, University of Tübingen, 72016 Tübingen, Germany.
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16
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Arnett LP, Rana R, Chung WWY, Li X, Abtahi M, Majonis D, Bassan J, Nitz M, Winnik MA. Reagents for Mass Cytometry. Chem Rev 2023; 123:1166-1205. [PMID: 36696538 DOI: 10.1021/acs.chemrev.2c00350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm2 spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.
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Affiliation(s)
- Loryn P Arnett
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Rahul Rana
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Wilson Wai-Yip Chung
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Xiaochong Li
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mahtab Abtahi
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Daniel Majonis
- Standard BioTools Canada Inc. (formerly Fluidigm Canada Inc.), 1380 Rodick Road, Suite 400, Markham, OntarioL3R 4G5, Canada
| | - Jay Bassan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, OntarioM5S 3H6, Canada.,Department of Chemical Engineering and Applied Chemistry, 200 College Street, Toronto, OntarioM5S 3E5, Canada
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17
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Wang W, Xu Y, Wang L, Zhu Z, Aodeng S, Chen H, Cai M, Huang Z, Han J, Wang L, Lin Y, Hu Y, Zhou L, Wang X, Zha Y, Jiang W, Gao Z, He W, Lv W, Zhang J. Single-cell profiling identifies mechanisms of inflammatory heterogeneity in chronic rhinosinusitis. Nat Immunol 2022; 23:1484-1494. [PMID: 36138182 DOI: 10.1038/s41590-022-01312-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/10/2022] [Indexed: 02/06/2023]
Abstract
The heterogeneous cellular microenvironment of human airway chronic inflammatory diseases, including chronic rhinosinusitis (CRS) and asthma, is still poorly understood. Here, we performed single-cell RNA sequencing (scRNA-seq) on the nasal mucosa of healthy individuals and patients with three subtypes of CRS and identified disease-specific cell subsets and molecules that specifically contribute to the pathogenesis of CRS subtypes. As such, ALOX15+ macrophages contributed to the type 2 immunity-driven pathogenesis of one subtype of CRS, eosinophilic CRS with nasal polyps (eCRSwNP), by secreting chemokines that recruited eosinophils, monocytes and T helper 2 (TH2) cells. An inhibitor of ALOX15 reduced the release of proinflammatory chemokines in human macrophages and inhibited the overactivation of type 2 immunity in a mouse model of eosinophilic rhinosinusitis. Our findings advance the understanding of the heterogeneous immune microenvironment and the pathogenesis of CRS subtypes and identify potential therapeutic approaches for the treatment of CRS and potentially other type 2 immunity-mediated diseases.
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Affiliation(s)
- Weiqing Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yi Xu
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China
| | - Lun Wang
- Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Zhenzhen Zhu
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Surita Aodeng
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hui Chen
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China
| | - Menghua Cai
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China
| | | | - Jinbo Han
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Lei Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuxi Lin
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yu Hu
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China
| | - Liangrui Zhou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaowei Wang
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yang Zha
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Weihong Jiang
- Department of Otolaryngology Head and Neck Surgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiqiang Gao
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei He
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China.
| | - Wei Lv
- Department of Otolaryngology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Jianmin Zhang
- Department of Immunology, CAMS Key Laboratory of T Cell and Immunotherapy, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Beijing, China.
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China.
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18
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Kajihara A, Morita T, Kato Y, Konaka H, Murakami T, Yamaguchi Y, Koyama S, Takamatsu H, Nishide M, Maeda Y, Watanabe A, Nishida S, Hirano T, Shima Y, Narazaki M, Kumanogoh A. The proliferative activity levels of each immune cell population evaluated by mass cytometry are linked to the clinical phenotypes of systemic lupus erythematosus. Int Immunol 2022; 35:27-41. [PMID: 35997780 PMCID: PMC9860541 DOI: 10.1093/intimm/dxac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/19/2022] [Indexed: 01/25/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease, and many peripheral immune cell populations (ICPs) are thought to be altered according to the course of the disease. However, it is unclear which ICPs are associated with the clinical phenotypes of SLE. We analyzed peripheral blood mononuclear cells (PBMCs) of 28 SLE patients using mass cytometry and identified 30 ICPs. We determined the proliferative activity of ICPs by measuring the proportion of cells expressing specific markers and Ki-67 among CD45+ cells (Ki-67+ proportion). We observed an increased Ki-67+ proportion for many ICPs of SLE patients and examined the association between their Ki-67+ proportions and clinical findings. The Ki-67+ proportions of five ICPs [classical monocyte (cMo), effector memory CD8+ T cell (CD8Tem), CXCR5- naive B cell (CXCR5- nB), and CXCR5- IgD-CD27- B cell (CXCR5- DNB)] were identified as clinically important factors. The SLE Disease Activity Index (SLEDAI) was positively correlated with cMo and plasma cells (PC). The titer of anti-DNA antibodies was positively correlated with cMo, CXCR5- nB, and CXCR5- DNB. The C4 level was negatively correlated with CXCR5- DNB. The bioactivity of type I interferon was also positively correlated with these ICPs. Fever and renal involvement were associated with cMo. Rash was associated with CD8Tem and CXCR5- DNB. On the basis of the proliferative activity among five ICPs, SLE patients can be classified into five clusters showing different SLE phenotypes. Evaluation of the proliferative activity in each ICP can be linked to the clinical phenotypes of individual SLE patients and help in the treatment strategy.
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Affiliation(s)
| | | | - Yasuhiro Kato
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hachiro Konaka
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Department of General Medicine, Nippon Life Hospital, Public Interest Incorporated Foundation, 2-1-54 Enokojima, Osaka Nishi-ku, Osaka 550-0006, Japan
| | - Teruaki Murakami
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuta Yamaguchi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akane Watanabe
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Thermotherapeutics for Vascular Dysfunction, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sumiyuki Nishida
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toru Hirano
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Division of Rheumatology, Department of Internal Medicine, Nishinomiya Municipal Central Hospital, 8-24 Hayasidacho, Nishinomiya, Hyogo 663-8014, Japan
| | - Yoshihito Shima
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Thermotherapeutics for Vascular Dysfunction, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Narazaki
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Department of Advanced Clinical and Translational Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Center, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan,Center for Infectious Diseases for Education and Research (CiDER), Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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19
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Delgado-Gonzalez A, Laz-Ruiz JA, Cano-Cortes MV, Huang YW, Gonzalez VD, Diaz-Mochon JJ, Fantl WJ, Sanchez-Martin RM. Hybrid Fluorescent Mass-Tag Nanotrackers as Universal Reagents for Long-Term Live-Cell Barcoding. Anal Chem 2022; 94:10626-10635. [PMID: 35866879 PMCID: PMC9352147 DOI: 10.1021/acs.analchem.2c00795] [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] [Indexed: 11/29/2022]
Abstract
![]()
Barcoding and pooling cells for processing as a composite
sample
are critical to minimize technical variability in multiplex technologies.
Fluorescent cell barcoding has been established as a standard method
for multiplexing in flow cytometry analysis. In parallel, mass-tag
barcoding is routinely used to label cells for mass cytometry. Barcode
reagents currently used label intracellular proteins in fixed and
permeabilized cells and, therefore, are not suitable for studies with
live cells in long-term culture prior to analysis. In this study,
we report the development of fluorescent palladium-based hybrid-tag
nanotrackers to barcode live cells for flow and mass cytometry dual-modal
readout. We describe the preparation, physicochemical characterization,
efficiency of cell internalization, and durability of these nanotrackers
in live cells cultured over time. In addition, we demonstrate their
compatibility with standardized cytometry reagents and protocols.
Finally, we validated these nanotrackers for drug response assays
during a long-term coculture experiment with two barcoded cell lines.
This method represents a new and widely applicable advance for fluorescent
and mass-tag barcoding that is independent of protein expression levels
and can be used to label cells before long-term drug studies.
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Affiliation(s)
- Antonio Delgado-Gonzalez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain.,Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Jose Antonio Laz-Ruiz
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - M Victoria Cano-Cortes
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - Ying-Wen Huang
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Veronica D Gonzalez
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Juan Jose Diaz-Mochon
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
| | - Wendy J Fantl
- Department of Urology, Stanford University School of Medicine, Stanford, California 94305, United States.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, United States.,Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, California 94304, United States
| | - Rosario M Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Gov-ernment, PTS Granada, Avda. Ilustración 114, 18016 Granada, Spain.,Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry applied to Biomedi-cine and the Environment", Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.,Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospitals of Granada-University of Grana-da, 18012 Granada, Spain
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20
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Chaudhary R, Das SS. Application of flow cytometry in transfusion medicine: The Sanjay Gandhi Post Graduate Institute of Medical Sciences, India experience. Asian J Transfus Sci 2022; 16:159-166. [PMID: 36687536 PMCID: PMC9855202 DOI: 10.4103/ajts.ajts_61_22] [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: 05/20/2022] [Revised: 05/30/2022] [Accepted: 06/05/2022] [Indexed: 01/25/2023] Open
Abstract
The application of flow cytometry (FC) is diverse and this powerful tool in used in multiple disciplines such as molecular biology, immunology, cancer biology, virology, and infectious disease screening. FC analyzes a single cell or a particle very rapidly as they flow past single or multiple lasers while suspended in buffered solution. FC has a great impact in the field of transfusion medicine (TM) due to its ability to analyze individual cell population and cell epitopes by sensitive, reproducible, and objective methodologies. The main uses of FC in TM are detection of fetomaternal hemorrhage, diagnosis of paroxysmal nocturnal hemoglobinuria, quantification of D antigen, detection of platelet antibody, quality control of blood components, for example, residual leukocyte counts and evaluation of CD34-positive hematopoietic progenitor cells in stem cell grafts. In recent years, FC has been implemented as an alternative method for the detection and characterization of red cell autoantibodies in autoimmune hemolytic anemia. Many workers considered FC as a very good complement when aberrant expression of various erythrocyte antigens needs to be elucidated. It has been extensively used in the resolution of ABO discrepancies and chimerism study. FC has also been used successfully in various platelet immunological studies. In the recent past, FC has been used in several studies to assess the platelet storage lesions and elucidate granulocyte/monocyte integrity and immunology. FC analysis of CD34+ stem cells is now the method of choice to determine the dosage of the collected progenitor cells. The technique is vastly used to evaluate residual leukocytes in leukodepleted blood components. We conclude that flow cytometers are becoming smaller, cheaper, and more user-friendly and are available in many routine laboratories. FC represents a highly innovative technique for many common diagnostic and scientific fields in TM. Finally, it is the tool of choice to develop and optimize new cellular and immunotherapeutic trials.
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Affiliation(s)
- Rajendra Chaudhary
- Department of Transfusion Medicine, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sudipta Sekhar Das
- Department of Transfusion Medicine, Apollo Multispeciality Hospitals, Kolkata, West Bengal, India
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21
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Krop J, van der Zwan A, Ijsselsteijn ME, Kapsenberg H, Luk SJ, Hendriks SH, van der Keur C, Verleng LJ, Somarakis A, van der Meeren L, Haasnoot G, Bos M, de Miranda NF, Chuva de Sousa Lopes SM, van der Hoorn MLP, Koning F, Claas FH, Heidt S, Eikmans M. Imaging Mass cytometry reveals the prominent role of myeloid cells at the maternal-fetal interface. iScience 2022; 25:104648. [PMID: 35811852 PMCID: PMC9257341 DOI: 10.1016/j.isci.2022.104648] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/03/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022] Open
Abstract
Although the immunological complexity of the maternal-fetal interface is well appreciated, the actual interaction of maternal immune cells and fetal trophoblasts is insufficiently understood. To comprehend the composition and spatial orientation of maternal immune cells and fetal extravillous trophoblasts, we applied imaging mass cytometry on decidua basalis of the three trimesters of healthy pregnancy. Within all trimesters, we observed considerably higher frequencies of myeloid cells in the decidua than is seen with single-cell suspension techniques. Moreover, they were the most pronounced cell type in the microenvironment of other decidual cells. In first trimester, HLA-DR- macrophages represented the most abundant myeloid subcluster and these cells were frequently observed in the vicinity of trophoblasts. At term, HLA-DR+ macrophage subclusters were abundantly present and frequently observed in the microenvironment of T cells. Taken together, our results highlight the dynamic role of myeloid cells at the human maternal-fetal interface throughout gestation. Frequency of myeloid cells is underestimated after tissue digestion Myeloid cells could support NK cells with proper trophoblast invasion Myeloid cells are dynamic in their role throughout gestation
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22
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Abstract
Mass cytometry has revolutionized immunophenotyping, particularly in exploratory settings where simultaneous breadth and depth of characterization of immune populations is needed with limited samples such as in preclinical and clinical tumor immunotherapy. Mass cytometry is also a powerful tool for single-cell immunological assays, especially for complex and simultaneous characterization of diverse intratumoral immune subsets or immunotherapeutic cell populations. Through the elimination of spectral overlap seen in optical flow cytometry by replacement of fluorescent labels with metal isotopes, mass cytometry allows, on average, robust analysis of 60 individual parameters simultaneously. This is, however, associated with significantly increased complexity in the design, execution, and interpretation of mass cytometry experiments. To address the key pitfalls associated with the fragmentation, complexity, and analysis of data in mass cytometry for immunologists who are novices to these techniques, we have developed a comprehensive resource guide. Included in this review are experiment and panel design, antibody conjugations, sample staining, sample acquisition, and data pre-processing and analysis. Where feasible multiple resources for the same process are compared, allowing researchers experienced in flow cytometry but with minimal mass cytometry expertise to develop a data-driven and streamlined project workflow. It is our hope that this manuscript will prove a useful resource for both beginning and advanced users of mass cytometry.
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Affiliation(s)
- Akshay Iyer
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Anouk A. J. Hamers
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- *Correspondence: Anouk A. J. Hamers, ; Asha B. Pillai,
| | - Asha B. Pillai
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Sheila and David Fuente Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL, United States
- *Correspondence: Anouk A. J. Hamers, ; Asha B. Pillai,
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23
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Masuhiro K, Tamiya M, Fujimoto K, Koyama S, Naito Y, Osa A, Hirai T, Suzuki H, Okamoto N, Shiroyama T, Nishino K, Adachi Y, Nii T, Kinugasa-Katayama Y, Kajihara A, Morita T, Imoto S, Uematsu S, Irie T, Okuzaki D, Aoshi T, Takeda Y, Kumagai T, Hirashima T, Kumanogoh A. Bronchoalveolar lavage fluid reveals factors contributing to the efficacy of PD-1 blockade in lung cancer. JCI Insight 2022; 7:157915. [PMID: 35389889 PMCID: PMC9090256 DOI: 10.1172/jci.insight.157915] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Bronchoalveolar lavage is commonly performed to assess inflammation and identify responsible pathogens in lung diseases. Findings from bronchoalveolar lavage might be used to evaluate the immune profile of the lung tumor microenvironment (TME). To investigate whether bronchoalveolar lavage fluid (BALF) analysis can help identify patients with non–small cell lung cancer (NSCLC) who respond to immune checkpoint inhibitors (ICIs), BALF and blood were prospectively collected before initiating nivolumab. The secreted molecules, microbiome, and cellular profiles based on BALF and blood analysis of 12 patients were compared with regard to therapeutic effect. Compared with ICI nonresponders, responders showed significantly higher CXCL9 levels and a greater diversity of the lung microbiome profile in BALF, along with a greater frequency of the CD56+ subset in blood T cells, whereas no significant difference in PD-L1 expression was found in tumor cells. Antibiotic treatment in a preclinical lung cancer model significantly decreased CXCL9 in the lung TME, resulting in reduced sensitivity to anti–PD-1 antibody, which was reversed by CXCL9 induction in tumor cells. Thus, CXCL9 might be associated with the lung TME microbiome, and the balance of CXCL9 and lung TME microbiome could contribute to nivolumab sensitivity in patients with NSCLC. BALF analysis can help predict the efficacy of ICIs when performed along with currently approved examinations.
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Affiliation(s)
- Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Kosuke Fujimoto
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akio Osa
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takashi Hirai
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hidekazu Suzuki
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Norio Okamoto
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yuichi Adachi
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yumi Kinugasa-Katayama
- Department of Cellular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Akiko Kajihara
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Takuma Irie
- Division of Cancer Immunology, National Cancer Center, Tokyo, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Osaka, Japan
| | - Taiki Aoshi
- Department of Cellular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Tomonori Hirashima
- Department of Thoracic Oncology, Osaka Habikino Medical Center, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
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24
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Abstract
Recent advances in single-cell technologies have made it possible to gather increased amounts of information about even rare cell subtypes. In particular, mass cytometry is able to assess the expression of 30-50 proteins on millions of cells. Within CD4 T-cells, T-follicular helper cells (Tfh) and their regulatory counterpart, T-follicular regulatory cells (Tfr), localize to the B-cell follicle and have specialized roles in the maintenance and regulation of B-cell antibody production. The frequency of Tfh and Tfr in circulation has also been associated with ongoing antibody responses.In this chapter, we detail methods to analyze the frequency and phenotype of the populations of Tfh and Tfr found in humans by mass cytometry.
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Affiliation(s)
- James B Wing
- Laboratory of Human Immunology (Single-cell immunology), WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Shimon Sakaguchi
- Laboratory of Experimental Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan.
- Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan.
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25
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Gonzalez VD, Huang YW, Fantl WJ. Mass Cytometry for the Characterization of Individual Cell Types in Ovarian Solid Tumors. Methods Mol Biol 2022; 2424:59-94. [PMID: 34918287 PMCID: PMC10509819 DOI: 10.1007/978-1-0716-1956-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mass cytometry aka Cytometry by Time-Of-Flight (CyTOF) is one of several recently developed multiparametric single-cell technologies designed to address cellular heterogeneity within healthy and diseased tissue. Mass cytometry is an adaptation of flow cytometry in which antibodies are labeled with stable heavy metal isotopes and the readout is by time-of-flight mass spectrometry. With minimal spillover between channels, mass cytometry enables readouts of up to 60 parameters per single cell. Critically, mass cytometry can identify minority cell populations that are lost in bulk tissue analysis. Mass cytometry has been used to great effect for the study of immune cells. We have extended its use to examine single cells within disaggregated solid tissues, specifically freshly resected tubo-ovarian high-grade serous tumors. Here we detail our protocols designed to ensure the production of high-quality single-cell datasets. The methodology can be modified to accommodate the study of other solid tissues.
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Affiliation(s)
- Veronica D Gonzalez
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- 10X Genomics, Pleasanton, CA, USA
| | - Ying-Wen Huang
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wendy J Fantl
- Department of Urology, Department of Obstetrics and Gynecology, Stanford Comprehensive Cancer Institute, Stanford, CA, USA.
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26
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Zhang Y, Liu P, Majonis D, Winnik MA. Polymeric dipicolylamine based mass tags for mass cytometry. Chem Sci 2022; 13:3233-3243. [PMID: 35414868 PMCID: PMC8926288 DOI: 10.1039/d2sc00595f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
Mass cytometry is an emerging powerful bioanalytical technique for high-dimensional single-cell analysis. In this technique, cells are stained with metal-isotope-tagged antibodies and are analyzed by an inductively coupled plasma time-of-flight mass spectrometer. While there are more than 100 stable isotopes available in the m/z 75 to 209 detection range of the instrument, only about 50 parameters can be measured per cell because current reagents are metal-chelating polymers with pendant aminocarboxylate chelators that only bind hard metal ions such as the rare earths and Bi3+. Here we describe the synthesis and characterization of a new type of metal-chelating polymer with pendant dipicolylamine chelators suited to binding intermediate to soft metals such as rhenium and platinum. We introduce two different conjugation strategies, a thiol–maleimide reaction that works well for rhenium, and a DBCO-azide click reaction designed to avoid potential complications of Pt and other heavy metals interacting with thiol groups. We show that these polymers can serve as new elemental mass tags for mass cytometry. Antibody-polymer conjugates of CD20 and CD8a prepared by both coupling reactions were employed in conjunction with commercial metal-conjugated antibodies for multi-parameter single-cell immunoassays. A new type of metal-chelating polymer with pendant dipicolylamine chelators that bind rhenium and platinum has been developed for mass cytometry applications.![]()
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Affiliation(s)
- Yefeng Zhang
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
| | - Peng Liu
- Fluidigm Canada Inc. 1380 Rodick Road, Suite 400 Markham ON L3R 4G5 Canada
| | - Daniel Majonis
- Fluidigm Canada Inc. 1380 Rodick Road, Suite 400 Markham ON L3R 4G5 Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto Toronto ON M5S 3E5 Canada
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27
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Hsieh WC, Lai EY, Liu YT, Wang YF, Tzeng YS, Cui L, Lai YJ, Huang HC, Huang JH, Ni HC, Tsai DY, Liang JJ, Liao CC, Lu YT, Jiang L, Liu MT, Wang JT, Chang SY, Chen CY, Tsai HC, Chang YM, Wernig G, Li CW, Lin KI, Lin YL, Tsai HK, Huang YT, Chen SY. NK cell receptor and ligand composition influences the clearance of SARS-CoV-2. J Clin Invest 2021; 131:e146408. [PMID: 34720095 PMCID: PMC8553551 DOI: 10.1172/jci146408] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
To explore how the immune system controls clearance of SARS-CoV-2, we used a single-cell, mass cytometry-based proteomics platform to profile the immune systems of 21 patients who had recovered from SARS-CoV-2 infection without need for admission to an intensive care unit or for mechanical ventilation. We focused on receptors involved in interactions between immune cells and virus-infected cells. We found that the diversity of receptor repertoires on natural killer (NK) cells was negatively correlated with the viral clearance rate. In addition, NK subsets expressing the receptor DNAM1 were increased in patients who more rapidly recovered from infection. Ex vivo functional studies revealed that NK subpopulations with high DNAM1 expression had cytolytic activities in response to target cell stimulation. We also found that SARS-CoV-2 infection induced the expression of CD155 and nectin-4, ligands of DNAM1 and its paired coinhibitory receptor TIGIT, which counterbalanced the cytolytic activities of NK cells. Collectively, our results link the cytolytic immune responses of NK cells to the clearance of SARS-CoV-2 and show that the DNAM1 pathway modulates host-pathogen interactions during SARS-CoV-2 infection.
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Affiliation(s)
- Wan-Chen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - En-Yu Lai
- Institute of Statistical Science, and
| | - Yu-Ting Liu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yi-Fu Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Shiuan Tzeng
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Lu Cui
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, California, USA
| | - Yun-Ju Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Solomont School of Nursing, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Hsiang-Chi Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jia-Hsin Huang
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
- National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hung-Chih Ni
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Dong-Yan Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Jian-Jong Liang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chun-Che Liao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ya-Ting Lu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Laurence Jiang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Yu Chen
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsing-Chen Tsai
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Gerlinde Wernig
- Department of Pathology, Institute of Stem Cell Biology and Regenerative Medicine (ISCBRM), Stanford University School of Medicine, Stanford, California, USA
| | - Chia-Wei Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Ling Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Huai-Kuang Tsai
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Yen-Tsung Huang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- Institute of Statistical Science, and
- Department of Mathematics, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Yu Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
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28
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Distinct human Langerhans cell subsets orchestrate reciprocal functions and require different developmental regulation. Immunity 2021; 54:2305-2320.e11. [PMID: 34508661 DOI: 10.1016/j.immuni.2021.08.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022]
Abstract
Langerhans cells (LCs) play a pivotal role in skin homeostasis, and the heterogeneity of LCs has long been considered. In this study, we have identified two steady-state (LC1 and LC2) and two activated LC subsets in the epidermis of human skin and in LCs derived from CD34+ hemopoietic stem cells (HSC-LCs) by utilizing single-cell RNA sequencing and mass cytometry. Analysis of HSC-LCs at multiple time-points during differentiation revealed that EGR1 and Notch signaling were among the top pathways regulating the bifurcation of LC1 and LC2. LC1 were characterized as classical LCs, mainly related to innate immunity and antigen processing. LC2 were similar to monocytes or myeloid dendritic cells, involving in immune responses and leukocyte activation. LC1 remained stable under inflammatory microenvironment, whereas LC2 were prone to being activated and demonstrated elevated expression of immuno-suppressive molecules. We revealed distinct human LC subsets that require different developmental regulation and orchestrate reciprocal functions.
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29
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Schlecht A, Boneva S, Salie H, Killmer S, Wolf J, Hajdu RI, Auw-Haedrich C, Agostini H, Reinhard T, Schlunck G, Bengsch B, Lange CA. Imaging mass cytometry for high-dimensional tissue profiling in the eye. BMC Ophthalmol 2021; 21:338. [PMID: 34544377 PMCID: PMC8454101 DOI: 10.1186/s12886-021-02099-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Imaging mass cytometry (IMC) combines the principles of flow cytometry and mass spectrometry (MS) with laser scanning spatial resolution and offers unique advantages for the analysis of tissue samples in unprecedented detail. In contrast to conventional immunohistochemistry, which is limited in its application by the number of possible fluorochrome combinations, IMC uses isoptope-coupled antibodies that allow multiplex analysis of up to 40 markers in the same tissue section simultaneously. Methods In this report we use IMC to analyze formalin-fixed, paraffin-embedded conjunctival tissue. We performed a 18-biomarkers IMC analysis of conjunctival tissue to determine and summarize the possibilities, relevance and limitations of IMC for deciphering the biology and pathology of ocular diseases. Results Without modifying the manufacturer’s protocol, we observed positive and plausible staining for 12 of 18 biomarkers. Subsequent bioinformatical single-cell analysis and phenograph clustering identified 24 different cellular clusters with distinct expression profiles with respect to the markers used. Conclusions IMC enables highly multiplexed imaging of ocular samples at subcellular resolution. IMC is an innovative and feasible method, providing new insights into ocular disease pathogenesis that will be valuable for basic research, drug discovery and clinical diagnostics. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-021-02099-8.
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Affiliation(s)
- Anja Schlecht
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany.,Institute of Anatomy, Wuerzburg University, Wuerzburg, Germany
| | - Stefaniya Boneva
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Henrike Salie
- Faculty of Medicine, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Saskia Killmer
- Faculty of Medicine, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Julian Wolf
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Rozina Ida Hajdu
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany.,Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Claudia Auw-Haedrich
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Hansjürgen Agostini
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Thomas Reinhard
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Günther Schlunck
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Bertram Bengsch
- Faculty of Medicine, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Clemens Ak Lange
- Faculty of Medicine, Eye Center, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany.
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30
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Extended live-cell barcoding approach for multiplexed mass cytometry. Sci Rep 2021; 11:12388. [PMID: 34117319 PMCID: PMC8196040 DOI: 10.1038/s41598-021-91816-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
Sample barcoding is essential in mass cytometry analysis, since it can eliminate potential procedural variations, enhance throughput, and allow simultaneous sample processing and acquisition. Sample pooling after prior surface staining termed live-cell barcoding is more desirable than intracellular barcoding, where samples are pooled after fixation and permeabilization, since it does not depend on fixation-sensitive antigenic epitopes. In live-cell barcoding, the general approach uses two tags per sample out of a pool of antibodies paired with five palladium (Pd) isotopes in order to preserve appreciable signal-to-noise ratios and achieve higher yields after sample deconvolution. The number of samples that can be pooled in an experiment using live-cell barcoding is limited, due to weak signal intensities associated with Pd isotopes and the relatively low number of available tags. Here, we describe a novel barcoding technique utilizing 10 different tags, seven cadmium (Cd) tags and three Pd tags, with superior signal intensities that do not impinge on lanthanide detection, which enables enhanced pooling of samples with multiple experimental conditions and markedly enhances sample throughput.
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31
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Schwabenland M, Salié H, Tanevski J, Killmer S, Lago MS, Schlaak AE, Mayer L, Matschke J, Püschel K, Fitzek A, Ondruschka B, Mei HE, Boettler T, Neumann-Haefelin C, Hofmann M, Breithaupt A, Genc N, Stadelmann C, Saez-Rodriguez J, Bronsert P, Knobeloch KP, Blank T, Thimme R, Glatzel M, Prinz M, Bengsch B. Deep spatial profiling of human COVID-19 brains reveals neuroinflammation with distinct microanatomical microglia-T-cell interactions. Immunity 2021; 54:1594-1610.e11. [PMID: 34174183 PMCID: PMC8188302 DOI: 10.1016/j.immuni.2021.06.002] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/23/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022]
Abstract
COVID-19 can cause severe neurological symptoms, but the underlying pathophysiological mechanisms are unclear. Here, we interrogated the brain stems and olfactory bulbs in postmortem patients who had COVID-19 using imaging mass cytometry to understand the local immune response at a spatially resolved, high-dimensional, single-cell level and compared their immune map to non-COVID respiratory failure, multiple sclerosis, and control patients. We observed substantial immune activation in the central nervous system with pronounced neuropathology (astrocytosis, axonal damage, and blood-brain-barrier leakage) and detected viral antigen in ACE2-receptor-positive cells enriched in the vascular compartment. Microglial nodules and the perivascular compartment represented COVID-19-specific, microanatomic-immune niches with context-specific cellular interactions enriched for activated CD8+ T cells. Altered brain T-cell-microglial interactions were linked to clinical measures of systemic inflammation and disturbed hemostasis. This study identifies profound neuroinflammation with activation of innate and adaptive immune cells as correlates of COVID-19 neuropathology, with implications for potential therapeutic strategies.
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Affiliation(s)
- Marius Schwabenland
- Institute of Neuropathology and Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Henrike Salié
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Jovan Tanevski
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Saskia Killmer
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Marilyn Salvat Lago
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Alexandra Emilia Schlaak
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Lena Mayer
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Püschel
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antonia Fitzek
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henrik E Mei
- German Rheumatism Research Center Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Tobias Boettler
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Maike Hofmann
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Nafiye Genc
- Institute of Neuropathology, University of Goettingen, Goettingen, Germany
| | | | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology and Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Blank
- Institute of Neuropathology and Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marco Prinz
- Institute of Neuropathology and Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| | - Bertram Bengsch
- Faculty of Medicine, Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany; Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
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32
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Ho WJ, Danilova L, Lim SJ, Verma R, Xavier S, Leatherman JM, Sztein MB, Fertig EJ, Wang H, Jaffee E, Yarchoan M. Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma. J Immunother Cancer 2021; 8:jitc-2019-000394. [PMID: 32303615 PMCID: PMC7204805 DOI: 10.1136/jitc-2019-000394] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Background and aims Immune checkpoint inhibitors (ICIs) targeting the programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) pathway have clinical activity in hepatocellular carcinoma (HCC), but only a subset of patients respond to these therapies, highlighting a need for novel biomarkers to improve clinical benefit. HCC usually occurs in the setting of liver cirrhosis from chronic hepatitis B or C viral infection, but the effects of viral status on the tumor immune microenvironment and clinical responses to ICIs in HCC remains unclear. Methods We conducted a meta-analysis to estimate the objective response rates for PD-1/PD-L1 inhibitors in virally-infected and uninfected patients, and examined the effects of viral etiology on the tumor microenvironment using data from The Cancer Genome Atlas, as well as peripheral blood responses using an independent cohort of patients studied by mass cytometry (cytometry by time-of-flight (CyTOF)). Results Meta-analysis comparing objective response rates (ORR) between virally-infected and uninfected patients showed no clinically meaningful difference (absolute difference of ORR in virally-infected vs uninfected=−1.4%, 95% CI: −13.5% to 10.6%). There was no relationship between viral etiology on features of the tumor immune microenvironment that are known to modulate responses to PD-1/PD-L1 inhibitors, and the tumor mutational burden was similar between virally-infected and uninfected HCC. RNA sequencing of tissue-resident T cell and B cell repertoires similarly showed no effect of viral status on their diversity. CyTOF analysis of peripheral blood specimens further demonstrated similar expression of immune-related markers in response to PD-1 inhibitor therapy in virally-infected and uninfected HCC. Conclusion There is no significant effect of viral etiology on the tumor immune microenvironment in HCC, and viral status should not be used as a criterion to select patients for PD-1/PD-L1 therapy.
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Affiliation(s)
- Won Jin Ho
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ludmila Danilova
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Biostatistics and Bioinformatics, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Su Jin Lim
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rohan Verma
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephanie Xavier
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - James M Leatherman
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marcelo B Sztein
- Center for Vaccine Development, University of Maryland, Baltimore, Maryland, USA.,Molecular Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elana J Fertig
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Biostatistics and Bioinformatics, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA.,Institute for Computational Medicine, Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, MD, United States
| | - Hao Wang
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Biostatistics and Bioinformatics, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Elizabeth Jaffee
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Pancreatic Cancer Precision Medicine Program, Skip Viragh Center for Pancreatic Cancer, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mark Yarchoan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA .,Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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33
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Parajuli G, Tekguc M, Wing JB, Hashimoto A, Okuzaki D, Hirata T, Sasaki A, Itokazu T, Handa H, Sugino H, Nishikawa Y, Metwally H, Kodama Y, Tanaka S, Sabe H, Yamashita T, Sakaguchi S, Kishimoto T, Hashimoto S. Arid5a Promotes Immune Evasion by Augmenting Tryptophan Metabolism and Chemokine Expression. Cancer Immunol Res 2021; 9:862-876. [PMID: 34006522 DOI: 10.1158/2326-6066.cir-21-0014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022]
Abstract
The acquisition of mesenchymal traits leads to immune evasion in various cancers, but the underlying molecular mechanisms remain unclear. In this study, we found that the expression levels of AT-rich interaction domain-containing protein 5a (Arid5a), an RNA-binding protein, were substantially increased in mesenchymal tumor subtypes. The deletion of Arid5a in tumor cell lines enhanced antitumor immunity in immunocompetent mice, but not in immunodeficient mice, suggesting a role for Arid5a in immune evasion. Furthermore, an Arid5a-deficient tumor microenvironment was shown to have robust antitumor immunity, as manifested by suppressed infiltration of granulocytic myeloid-derived suppressor cells and regulatory T cells. In addition, infiltrated T cells were more cytotoxic and less exhausted. Mechanistically, Arid5a stabilized Ido1 and Ccl2 mRNAs and augmented their expression, resulting in enhanced tryptophan catabolism and an immunosuppressive tumor microenvironment. Thus, our findings demonstrate the role of Arid5a beyond inflammatory diseases and suggest Arid5a as a promising target for the treatment of immunotolerant malignant tumors.See related Spotlight by Van den Eynde, p. 854.
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Affiliation(s)
- Gyanu Parajuli
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Murat Tekguc
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - James B Wing
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Ari Hashimoto
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Takeshi Hirata
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
| | - Atsushi Sasaki
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan.,Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Yokohama, Japan
| | - Takahide Itokazu
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Haruka Handa
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hirokazu Sugino
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshihiro Nishikawa
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hozaifa Metwally
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Yuzo Kodama
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Hisataka Sabe
- Department of Molecular Biology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine/Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.,Department of Neuro-Medical Science, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shimon Sakaguchi
- Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Tadamitsu Kishimoto
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
| | - Shigeru Hashimoto
- Laboratory of Immune Regulation, World Premier International Immunology Frontier Research Center, Osaka University, Osaka, Japan.
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34
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Elaldi R, Hemon P, Petti L, Cosson E, Desrues B, Sudaka A, Poissonnet G, Van Obberghen-Schilling E, Pers JO, Braud VM, Anjuère F, Meghraoui-Kheddar A. High Dimensional Imaging Mass Cytometry Panel to Visualize the Tumor Immune Microenvironment Contexture. Front Immunol 2021; 12:666233. [PMID: 33936105 PMCID: PMC8085494 DOI: 10.3389/fimmu.2021.666233] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
The integrative analysis of tumor immune microenvironment (TiME) components, their interactions and their microanatomical distribution is mandatory to better understand tumor progression. Imaging Mass Cytometry (IMC) is a high dimensional tissue imaging system which allows the comprehensive and multiparametric in situ exploration of tumor microenvironments at a single cell level. We describe here the design of a 39-antibody IMC panel for the staining of formalin-fixed paraffin-embedded human tumor sections. We also provide an optimized staining procedure and details of the experimental workflow. This panel deciphers the nature of immune cells, their functions and their interactions with tumor cells and cancer-associated fibroblasts as well as with other TiME structural components known to be associated with tumor progression like nerve fibers and tumor extracellular matrix proteins. This panel represents a valuable innovative and powerful tool for fundamental and clinical studies that could be used for the identification of prognostic biomarkers and mechanisms of resistance to current immunotherapies.
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Affiliation(s)
- Roxane Elaldi
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.,Institut Universitaire de la Face et du Cou, Nice, France
| | - Patrice Hemon
- U1227, LBAI, University of Brest, INSERM, CHU de Brest, Brest, France
| | - Luciana Petti
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Estelle Cosson
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | | | - Anne Sudaka
- Centre Antoine Lacassagne, Anatomopathology Laboratory and Human Biobank, Nice, France
| | | | | | | | - Veronique M Braud
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Fabienne Anjuère
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Aïda Meghraoui-Kheddar
- Université Côte d'Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
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35
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Pfister D, Núñez NG, Pinyol R, Govaere O, Pinter M, Szydlowska M, Gupta R, Qiu M, Deczkowska A, Weiner A, Müller F, Sinha A, Friebel E, Engleitner T, Lenggenhager D, Moncsek A, Heide D, Stirm K, Kosla J, Kotsiliti E, Leone V, Dudek M, Yousuf S, Inverso D, Singh I, Teijeiro A, Castet F, Montironi C, Haber PK, Tiniakos D, Bedossa P, Cockell S, Younes R, Vacca M, Marra F, Schattenberg JM, Allison M, Bugianesi E, Ratziu V, Pressiani T, D'Alessio A, Personeni N, Rimassa L, Daly AK, Scheiner B, Pomej K, Kirstein MM, Vogel A, Peck-Radosavljevic M, Hucke F, Finkelmeier F, Waidmann O, Trojan J, Schulze K, Wege H, Koch S, Weinmann A, Bueter M, Rössler F, Siebenhüner A, De Dosso S, Mallm JP, Umansky V, Jugold M, Luedde T, Schietinger A, Schirmacher P, Emu B, Augustin HG, Billeter A, Müller-Stich B, Kikuchi H, Duda DG, Kütting F, Waldschmidt DT, Ebert MP, Rahbari N, Mei HE, Schulz AR, Ringelhan M, Malek N, Spahn S, Bitzer M, Ruiz de Galarreta M, Lujambio A, Dufour JF, Marron TU, Kaseb A, Kudo M, Huang YH, Djouder N, Wolter K, Zender L, Marche PN, Decaens T, Pinato DJ, Rad R, Mertens JC, Weber A, Unger K, Meissner F, Roth S, Jilkova ZM, Claassen M, Anstee QM, Amit I, Knolle P, Becher B, Llovet JM, Heikenwalder M. NASH limits anti-tumour surveillance in immunotherapy-treated HCC. Nature 2021. [PMID: 33762733 DOI: 10.1038/s41586-021-03362-0.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hepatocellular carcinoma (HCC) can have viral or non-viral causes1-5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment.
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Affiliation(s)
- Dominik Pfister
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Liver Disease Research, Global Drug Discovery, Novo Nordisk A/S, Malov, Denmark
| | | | - Roser Pinyol
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Matthias Pinter
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Marta Szydlowska
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Revant Gupta
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Mengjie Qiu
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | | | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Florian Müller
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ankit Sinha
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Munich, Germany.,Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Thomas Engleitner
- Center for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich, Germany
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Anja Moncsek
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Danijela Heide
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristin Stirm
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Kosla
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Eleni Kotsiliti
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Valentina Leone
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Research Unit of Radiation Cytogenetics, Helmholtz Zentrum Munich, Munich, Germany
| | - Michael Dudek
- Institute of Molecular Immunology and Experimental Oncology, Technical University Munich, Munich, Germany
| | - Suhail Yousuf
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Donato Inverso
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany.,European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Indrabahadur Singh
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Teijeiro
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Spanish National Cancer Research Centre, CNIO, Madrid, Spain
| | - Florian Castet
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Carla Montironi
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain
| | - Philipp K Haber
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Department of Pathology, Aretaeion Hospita, National and Kapodistrian University of Athens, Athens, Greece
| | - Pierre Bedossa
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Simon Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Ramy Younes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turn, Italy
| | - Michele Vacca
- University of Cambridge Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Fabio Marra
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, Florence, Italy
| | - Jörn M Schattenberg
- Metabolic Liver Research Program, I. Department of Medicine, University Medical Center Mainz, Mainz, Germany
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge Biomedical Research Centre, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastro-Hepatology, A.O. Città della Salute e della Scienza di Torino, University of Turin, Turn, Italy
| | - Vlad Ratziu
- Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, University Paris-Diderot, Paris, France
| | - Tiziana Pressiani
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy
| | - Antonio D'Alessio
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy
| | - Nicola Personeni
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Lorenza Rimassa
- Medical Oncology and Hematology Unit, Humanitas Cancer Center, Humanitas Clinical and Research Center-IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Bernhard Scheiner
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Katharina Pomej
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria.,Liver Cancer (HCC) Study Group Vienna, Medical University of Vienna, Vienna, Austria
| | - Martha M Kirstein
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,University Medical Center Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Arndt Vogel
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Markus Peck-Radosavljevic
- Department of Internal Medicine and Gastroenterology (IMuG), Hepatology, Endocrinology, Rheumatology and Nephrology including Centralized Emergency Department (ZAE), Klinikum Klagenfurt am Wörthersee, Klagenfurt, Austria
| | - Florian Hucke
- Department of Internal Medicine and Gastroenterology (IMuG), Hepatology, Endocrinology, Rheumatology and Nephrology including Centralized Emergency Department (ZAE), Klinikum Klagenfurt am Wörthersee, Klagenfurt, Austria
| | - Fabian Finkelmeier
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Oliver Waidmann
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Jörg Trojan
- Department of Gastroenterology, Hepatology and Endocrinology, University Hospital Frankfurt, Frankfurt, Germany
| | - Kornelius Schulze
- Department of Internal Medicine, Gastroenterology & Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Wege
- Department of Internal Medicine, Gastroenterology & Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Koch
- Department of Internal Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Arndt Weinmann
- Department of Internal Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marco Bueter
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Rössler
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Alexander Siebenhüner
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Sara De Dosso
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Jan-Philipp Mallm
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Viktor Umansky
- Clinical Cooperation Unit Dermato-Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Heidelberg, Germany
| | - Manfred Jugold
- Core Facility Small Animal Imaging, German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Brinda Emu
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hellmut G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center (DKFZ-ZMBH Alliance), Heidelberg, Germany.,European Center of Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Adrian Billeter
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Beat Müller-Stich
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Hiroto Kikuchi
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Dan G Duda
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Fabian Kütting
- Department of Gastroenterology and Hepatology, University of Cologne, Cologne, Germany
| | | | - Matthias Philip Ebert
- Department of Medicine II, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Nuh Rahbari
- Department of Surgery at University Hospital Mannheim, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Axel Ronald Schulz
- Mass Cytometry Lab, Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Marc Ringelhan
- Institute of Virology, Technical University Munich/Helmholtz Zentrum Munich, Munich, Germany.,Department of Internal Medicine II, University Hospital rechts der Isar, Technical University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Nisar Malek
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Stephan Spahn
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Michael Bitzer
- Medical University Hospital Department of Internal Medicine I, Tübingen, Germany
| | - Marina Ruiz de Galarreta
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amaia Lujambio
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Francois Dufour
- University Clinic for Visceral Surgery and Medicine, Inselspital, Bern, Switzerland.,Hepatology, Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Thomas U Marron
- Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Medicine, Division of Hematology/Oncology, Tisch Cancer Institute, Mount Sinai Hospital, New York, NY, USA
| | - Ahmed Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-, Sayama, Japan
| | - Yi-Hsiang Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Gastroenterology and Hepatology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Nabil Djouder
- Cancer Cell Biology Programme, Growth Factors, Nutrients and Cancer Group, Spanish National Cancer Research Centre, CNIO, Madrid, Spain
| | - Katharina Wolter
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 'Image Guided and Functionally Instructed Tumor Therapies' (iFIT), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence 'Image Guided and Functionally Instructed Tumor Therapies' (iFIT), Eberhard-Karls University of Tübingen, Tübingen, Germany.,German Consortium for Translational Cancer Research (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Tübingen, Germany
| | - Parice N Marche
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France
| | - Thomas Decaens
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France.,Service d'hépato-gastroentérologie, Pôle Digidune, CHU Grenoble Alpes, Grenoble, France
| | - David J Pinato
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK.,Division of Oncology, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), Technical University Munich, Munich, Germany.,Department of Medicine II, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Munich, Germany
| | - Joachim C Mertens
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland.,Institute of Molecular Cancer Research (IMCR), University of Zurich, Zurich, Switzerland
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum Munich, Munich, Germany
| | - Felix Meissner
- Experimental Systems Immunology Laboratory, Max-Planck Institute of Biochemistry, Munich, Germany
| | - Susanne Roth
- Department of General, Visceral and Transplantation Surgery, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Zuzana Macek Jilkova
- Université Grenoble Alpes, Grenoble, France.,Institute for Advanced Biosciences, Research Center UGA/Inserm U 1209/CNRS 5309, Grenoble, France.,Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Manfred Claassen
- Internal Medicine I, University Hospital Tübingen, Faculty of Medicine, University of Tübingen, Tübingen, Germany.,Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Quentin M Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.,Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle, UK
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Percy Knolle
- Institute of Molecular Immunology and Experimental Oncology, Technical University Munich, Munich, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Josep M Llovet
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Liver Unit, Universitat de Barcelona, Barcelona, Spain. .,Mount Sinai Liver Cancer Program, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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36
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NASH limits anti-tumour surveillance in immunotherapy-treated HCC. Nature 2021; 592:450-456. [PMID: 33762733 PMCID: PMC8046670 DOI: 10.1038/s41586-021-03362-0] [Citation(s) in RCA: 658] [Impact Index Per Article: 219.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) can have viral or non-viral causes1–5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH–HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH–HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH–HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment. In hepatocellular carcinoma driven by non-alcoholic steatohepatitis, aberrant T cell activation and impaired immune surveillance seem to make hepatocellular carcinoma less responsive to anti-PD1 or anti-PDL1 immunotherapy.
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37
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Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol 2021; 39:186-197. [PMID: 32868913 PMCID: PMC7878201 DOI: 10.1038/s41587-020-0651-8] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Cellular metabolism regulates immune cell activation, differentiation and effector functions, but current metabolic approaches lack single-cell resolution and simultaneous characterization of cellular phenotype. In this study, we developed an approach to characterize the metabolic regulome of single cells together with their phenotypic identity. The method, termed single-cell metabolic regulome profiling (scMEP), quantifies proteins that regulate metabolic pathway activity using high-dimensional antibody-based technologies. We employed mass cytometry (cytometry by time of flight, CyTOF) to benchmark scMEP against bulk metabolic assays by reconstructing the metabolic remodeling of in vitro-activated naive and memory CD8+ T cells. We applied the approach to clinical samples and identified tissue-restricted, metabolically repressed cytotoxic T cells in human colorectal carcinoma. Combining our method with multiplexed ion beam imaging by time of flight (MIBI-TOF), we uncovered the spatial organization of metabolic programs in human tissues, which indicated exclusion of metabolically repressed immune cells from the tumor-immune boundary. Overall, our approach enables robust approximation of metabolic and functional states in individual cells.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Erin McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - David R Glass
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sanne G S Verberk
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - William Graf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Van Valen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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38
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Yordanova IA, Ebner F, Schulz AR, Steinfelder S, Rosche B, Bolze A, Paul F, Mei HE, Hartmann S. The Worm-Specific Immune Response in Multiple Sclerosis Patients Receiving Controlled Trichuris suis Ova Immunotherapy. Life (Basel) 2021; 11:life11020101. [PMID: 33572978 PMCID: PMC7912101 DOI: 10.3390/life11020101] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Considering their potent immunomodulatory properties, therapeutic applications of Trichuris suis ova (TSO) are studied as potential alternative treatment of autoimmune disorders like multiple sclerosis (MS), rheumatoid arthritis (RA), or inflammatory bowel disease (IBD). Clinical phase 1 and 2 studies have demonstrated TSO treatment to be safe and well tolerated in MS patients, however, they reported only modest clinical efficacy. We therefore addressed the cellular and humoral immune responses directed against parasite antigens in individual MS patients receiving controlled TSO treatment (2500 TSO p.o. every 2 weeks for 12 month). Peripheral blood mononuclear cells (PBMC) of MS patients treated with TSO (n = 5) or placebo (n = 6) were analyzed. A continuous increase of serum IgG and IgE antibodies specific for T. suis excretory/secretory antigens was observed up to 12 months post-treatment. This was consistent with mass cytometry analysis identifying an increase of activated HLA-DRhigh plasmablast frequencies in TSO-treated patients. While stable and comparable frequencies of total CD4+ and CD8+ T cells were detected in placebo and TSO-treated patients over time, we observed an increase of activated HLA-DR+CD4+ T cells in TSO-treated patients only. Frequencies of Gata3+ Th2 cells and Th1/Th2 ratios remained stable during TSO treatment, while Foxp3+ Treg frequencies varied greatly between individuals. Using a T. suis antigen-specific T cell expansion assay, we also detected patient-to-patient variation of antigen-specific T cell recall responses and cytokine production. In summary, MS patients receiving TSO treatment established a T. suis-specific T- and B-cell response, however, with varying degrees of T cell responses and cellular functionality across individuals, which might account for the overall miscellaneous clinical efficacy in the studied patients.
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Affiliation(s)
- Ivet A. Yordanova
- Institute of Immunology, Center for Infection Medicine, Freie Universität Berlin, D-14163 Berlin, Germany; (I.A.Y.); (F.E.)
| | - Friederike Ebner
- Institute of Immunology, Center for Infection Medicine, Freie Universität Berlin, D-14163 Berlin, Germany; (I.A.Y.); (F.E.)
| | - Axel Ronald Schulz
- German Rheumatism Research Center Berlin (DRFZ), a Leibniz Institute, D-10117 Berlin, Germany; (A.R.S.); (H.E.M.)
| | | | - Berit Rosche
- Department of Neurology and Experimental Neurology, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany;
- Clinical and Experimental Multiple Sclerosis Research Center, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany;
| | - Anna Bolze
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany;
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Friedemann Paul
- Clinical and Experimental Multiple Sclerosis Research Center, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany;
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany;
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine, Charité—Universitätsmedizin Berlin, D-10117 Berlin, Germany
| | - Henrik E. Mei
- German Rheumatism Research Center Berlin (DRFZ), a Leibniz Institute, D-10117 Berlin, Germany; (A.R.S.); (H.E.M.)
| | - Susanne Hartmann
- Institute of Immunology, Center for Infection Medicine, Freie Universität Berlin, D-14163 Berlin, Germany; (I.A.Y.); (F.E.)
- Correspondence:
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39
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Devine RD, Alkhalaileh HS, Lyberger JM, Behbehani GK. Alternative methods of viability determination in single cell mass cytometry. Cytometry A 2021; 99:1042-1053. [PMID: 33476084 DOI: 10.1002/cyto.a.24308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 11/12/2022]
Abstract
The identification and discrimination of viable cells is important to understand how experimental variables may influence biochemical processes such as cell metabolism, cell cycle, and signaling pathways. Cisplatin is commonly used as a viability stain in mass cytometry studies, however, recent work by Mei et al. has demonstrated that cisplatin can also be used to label antibodies, complicating the simultaneous use of the platinum measurement channels for both antibody and viability staining. This study demonstrates that other metal salts (hafnium chloride, niobium chloride, and zirconium chloride) can serve as substitutes for cisplatin in viability staining. These stains yield similar fractions of live and dead cells and stain the same dead cells in parallel high parameter analyses. In addition, this study demonstrates how a variety of protein antigen viability markers (pRb, Ki-67, Histone H1, cleaved PARP, and GAPDH) can be used to discriminate live and dead cell populations, without the need for a separate viability staining step. As few as two of these protein antigen viability markers can help identify live and dead cell populations in fixed samples and can identify the same viable cells in high dimensional analyses with or without use of viability stain information. This study demonstrates several alternative approaches to mass cytometry viability assessment that can facilitate use of platinum isotopes for antibody staining and enables identification of live and dead cell populations in samples for which a separate viability stain is not practical.
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Affiliation(s)
- Raymond D Devine
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Hussam S Alkhalaileh
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Justin M Lyberger
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Gregory K Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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40
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Delgado-Gonzalez A, Sanchez-Martin RM. Mass Cytometry Tags: Where Chemistry Meets Single-Cell Analysis. Anal Chem 2021; 93:657-664. [PMID: 33320535 DOI: 10.1021/acs.analchem.0c03560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass cytometry is a highly multiparametric proteomic technology that allows the measurement and quantification of nearly 50 markers with single-cell resolution. Mass cytometry reagents are probes tagged with metal isotopes of defined mass and act as reporters. Metals are detected using inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS). Many different types of mass-tag reagents have been developed to afford myriad applications. We have classified these compounds into polymer-based mass-tag reagents, nonpolymer-based mass-tag reagents, and inorganic nanoparticles. Metal-chelating polymers (MCPs) are widely used to profile and quantify cellular biomarkers; however, both the range of metals that can be detected and the metal signals have to be improved. Several strategies such as the inclusion of chelating agents or highly branched polymers may overcome these issues. Biocompatible materials such as polystyrene and inorganic nanoparticles are also of profound interest in mass cytometry. While polystyrene allows the inclusion of a wide variety of metals, the high metal content of inorganic nanoparticles offers an excellent opportunity to increase the signal from the metals to detect low-abundance biomarkers. Nonpolymer-based mass-tag reagents offer multiple applications: cell detection, cell cycle property determination, biomarker detection, and mass-tag cellular barcoding (MCB). Recent developments have been achieved in live cell barcoding by targeting proteins (CD45, b2m, and CD298), by using small and nonpolar probes or by ratiometric barcoding. From this perspective, the principal applications, strengths, and shortcomings of mass-tag reagents are highlighted, summarized, and discussed, with special emphasis on mass-tag reagents for MCB. Thereafter, the future perspectives of mass-tag reagents are discussed considering the current state-of-the-art technologies.
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Affiliation(s)
- Antonio Delgado-Gonzalez
- Department of Medicinal and Organic Chemistry, Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain.,GENYO, Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research, P.T. Ciencias de la Salud 114, 18016 Granada, Spain
| | - Rosario M Sanchez-Martin
- Department of Medicinal and Organic Chemistry, Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment", Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071 Granada, Spain.,GENYO, Pfizer-University of Granada-Junta de Andalucia Centre for Genomics and Oncological Research, P.T. Ciencias de la Salud 114, 18016 Granada, Spain
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41
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Romero-Olmedo AJ, Schulz AR, Huber M, Brehm CU, Chang HD, Chiarolla CM, Bopp T, Skevaki C, Berberich-Siebelt F, Radbruch A, Mei HE, Lohoff M. Deep phenotypical characterization of human CD3 + CD56 + T cells by mass cytometry. Eur J Immunol 2020; 51:672-681. [PMID: 33231295 DOI: 10.1002/eji.202048941] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/25/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022]
Abstract
CD56+ T cells are a group of pro-inflammatory CD3+ lymphocytes with characteristics of natural killer cells, being involved in antimicrobial immune defense. Here, we performed deep phenotypic profiling of CD3+ CD56+ cells in peripheral blood of normal human donors and individuals sensitized to birch-pollen or/and house dust mite by high-dimensional mass cytometry combined with manual and computational data analysis. A co-regulation between major conventional T-cell subsets and their respective CD3+ CD56+ cell counterparts appeared restricted to CD8+ , MAIT, and TCRγδ+ T-cell compartments. Interestingly, we find a co-regulation of several CD3+ CD56+ cell subsets in allergic but not in healthy individuals. Moreover, using FlowSOM, we distinguished a variety of CD56+ T-cell phenotypes demonstrating a hitherto underestimated heterogeneity among these cells. The novel CD3+ CD56+ subset description comprises phenotypes superimposed with naive, memory, type 1, 2, and 17 differentiation stages, in part represented by a phenotypical continuum. Frequencies of two out of 19 CD3+ CD56+ FlowSOM clusters were significantly diminished in allergic individuals, demonstrating less frequent presence of cells with cytolytic, presumably protective, capacity in these donors consistent with defective expansion or their recruitment to the affected tissue. Our results contribute to defining specific cell populations to be targeted during therapy for allergic conditions.
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Affiliation(s)
- Addi J Romero-Olmedo
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg, Germany
| | - Axel R Schulz
- German Rheumatism Research Center Berlin (DRFZ), Leibniz Institute, Berlin, Germany
| | - Magdalena Huber
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg, Germany
| | - Corinna U Brehm
- Comprehensive Biobank Marburg - CBBMR, Member of the DZL, Philipps-University Marburg, Marburg, Germany.,Institute for Pathology, University Hospital Marburg, Philipps-University Marburg, Marburg, Germany
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin (DRFZ), Leibniz Institute, Berlin, Germany
| | - Cristina M Chiarolla
- Institute of Pathology, Julius-Maximilian University of Wuerzburg, Wuerzburg, Germany
| | - Tobias Bopp
- Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | | | - Andreas Radbruch
- German Rheumatism Research Center Berlin (DRFZ), Leibniz Institute, Berlin, Germany
| | - Henrik E Mei
- German Rheumatism Research Center Berlin (DRFZ), Leibniz Institute, Berlin, Germany
| | - Michael Lohoff
- Institute for Medical Microbiology and Hospital Hygiene, University of Marburg, Marburg, Germany
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Fernández‐Zapata C, Leman JKH, Priller J, Böttcher C. The use and limitations of single-cell mass cytometry for studying human microglia function. Brain Pathol 2020; 30:1178-1191. [PMID: 33058349 PMCID: PMC8018011 DOI: 10.1111/bpa.12909] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 08/23/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Microglia, the resident innate immune cells of the central nervous system (CNS), play an important role in brain development and homoeostasis, as well as in neuroinflammatory, neurodegenerative and psychiatric diseases. Studies in animal models have been used to determine the origin and development of microglia, and how these cells alter their transcriptional and phenotypic signatures during CNS pathology. However, little is known about their human counterparts. Recent studies in human brain samples have harnessed the power of multiplexed single-cell technologies such as single-cell RNA sequencing (scRNA-seq) and mass cytometry (cytometry by time-of-flight [CyTOF]) to provide a comprehensive molecular view of human microglia in healthy and diseased brains. CyTOF is a powerful tool to study high-dimensional protein expression of human microglia (huMG) at the single-cell level. This technology widens the possibilities of high-throughput quantification (of over 60 targeted molecules) at a single-cell resolution. CyTOF can be combined with scRNA-seq for comprehensive analysis, as it allows single-cell analysis of post-translational modifications of proteins, which provides insights into cell signalling dynamics in targeted cells. In addition, imaging mass cytometry (IMC) has recently become commercially available, and will be useful for analysing multiple cell types in human brain sections. IMC leverages mass spectrometry to acquire spatial data of cell-cell interactions on tissue sections, using (theoretically) over 40 markers at the same time. In this review, we summarise recent studies of huMG using CyTOF and IMC analyses. The uses and limitations as well as future directions of these technologies are discussed.
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Affiliation(s)
- Camila Fernández‐Zapata
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
| | - Julia K. H. Leman
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE)BerlinGermany
- UK Dementia Research Institute (DRI)University of EdinburghEdinburghUK
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
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Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, De Domenico E, Wendisch D, Grasshoff M, Kapellos TS, Beckstette M, Pecht T, Saglam A, Dietrich O, Mei HE, Schulz AR, Conrad C, Kunkel D, Vafadarnejad E, Xu CJ, Horne A, Herbert M, Drews A, Thibeault C, Pfeiffer M, Hippenstiel S, Hocke A, Müller-Redetzky H, Heim KM, Machleidt F, Uhrig A, Bosquillon de Jarcy L, Jürgens L, Stegemann M, Glösenkamp CR, Volk HD, Goffinet C, Landthaler M, Wyler E, Georg P, Schneider M, Dang-Heine C, Neuwinger N, Kappert K, Tauber R, Corman V, Raabe J, Kaiser KM, Vinh MT, Rieke G, Meisel C, Ulas T, Becker M, Geffers R, Witzenrath M, Drosten C, Suttorp N, von Kalle C, Kurth F, Händler K, Schultze JL, Aschenbrenner AC, Li Y, Nattermann J, Sawitzki B, Saliba AE, Sander LE. Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. Cell 2020; 182:1419-1440.e23. [PMID: 32810438 PMCID: PMC7405822 DOI: 10.1016/j.cell.2020.08.001] [Citation(s) in RCA: 947] [Impact Index Per Article: 236.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19.
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Affiliation(s)
| | - Nico Reusch
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Daniela Paclik
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kevin Baßler
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Stephan Schlickeiser
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH) Berlin, Germany
| | - Bowen Zhang
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Benjamin Krämer
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Tobias Krammer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Lorenzo Bonaguro
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Elena De Domenico
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Daniel Wendisch
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Grasshoff
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | | | - Michael Beckstette
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Tal Pecht
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Adem Saglam
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Oliver Dietrich
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany
| | - Axel R Schulz
- Mass Cytometry Lab, DRFZ Berlin, a Leibniz Institute, Berlin, Germany
| | - Claudia Conrad
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Désirée Kunkel
- Flow and Mass Cytometry Core Facility, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Ehsan Vafadarnejad
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arik Horne
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Miriam Herbert
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany
| | - Anna Drews
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Pfeiffer
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Andreas Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Holger Müller-Redetzky
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Katrin-Moira Heim
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Machleidt
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Uhrig
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Miriam Stegemann
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph R Glösenkamp
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Hans-Dieter Volk
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; BIH Center for Regenerative Therapies, Charité, Universitätsmedizin Berlin, and Berlin Institute of Health (BIH) Berlin, Germany; Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Philipp Georg
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Maria Schneider
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Chantip Dang-Heine
- Clinical Study Center (CSC), Charité, Universitätsmedizin Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nick Neuwinger
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Kai Kappert
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Rudolf Tauber
- Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany; Institute of Laboratory Medicine, Clinical Chemistry, and Pathobiochemistry, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Corman
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Raabe
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Kim Melanie Kaiser
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Michael To Vinh
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Gereon Rieke
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Christian Meisel
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Immunology, Labor Berlin-Charité Vivantes, Berlin, Germany
| | - Thomas Ulas
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Matthias Becker
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Robert Geffers
- Genome Analytics, Helmholtz-Center for Infection Research (HZI), Braunschweig, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Christian Drosten
- Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany; German Center for Infection Research (DZIF)
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
| | - Christof von Kalle
- Clinical Study Center (CSC), Charité, Universitätsmedizin Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; I. Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Kristian Händler
- German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, Bonn, Germany.
| | - Anna C Aschenbrenner
- Life and Medical Sciences (LIMES) Institute, University of Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany; German Center for Infection Research (DZIF)
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL)
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Ascenzi P, Bettinelli M, Boffi A, Botta M, De Simone G, Luchinat C, Marengo E, Mei H, Aime S. Rare earth elements (REE) in biology and medicine. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2020. [DOI: 10.1007/s12210-020-00930-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractThis survey reports on topics that were presented at the workshop on “Challenges with Rare Earth Elements. The Periodic Table at work for new Science & Technology” hold at the Academia dei Lincei in November 2019. The herein reported materials refer to presentations dealing with studies and applications of rare earth elements (REE) in several areas of Biology and Medicine. All together they show the tremendous impact REE have in relevant fields of living systems and highlight, on one hand, the still existing knowledge gap for an in-depth understanding of their function in natural systems as well as the very important role they already have in providing innovative scientific and technological solutions in a number of bio-medical areas and in fields related to the assessment of the origin of food and on their manufacturing processes. On the basis of the to-date achievements one expects that new initiatives will bring, in a not too far future, to a dramatic increase of our understanding of the REE involvement in living organisms as well as a ramp-up in the exploitation of the peculiar properties of REE for the design of novel applications in diagnostic procedures and in the set-up of powerful medical devices. This scenario calls the governmental authorities for new responsibilities to guarantee a continuous availability of REE to industry and research labs together with providing support to activities devoted to their recovery/recycling.
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45
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Abstract
Immune responses to infectious agents are initiated when a pathogen or its components bind to pattern recognition receptors (PRRs). PRR binding sets off a cascade of events that activates immune responses. We now show that, in addition to activating immune responses, PRR signaling also initiates an immunosuppressive response, probably to limit inflammation. The importance of the current findings is that blockade of immunomodulatory signaling, which is mediated by the upregulation of the CD47 molecule, can lead to enhanced immune responses to any pathogen that triggers PRR signaling. Since most or all pathogens trigger PRRs, CD47 blockade could be used to speed up and strengthen both innate and adaptive immune responses when medically indicated. Such immunotherapy could be done without a requirement for knowing the HLA type of the individual, the specific antigens of the pathogen, or, in the case of bacterial infections, the antimicrobial resistance profile. It is well understood that the adaptive immune response to infectious agents includes a modulating suppressive component as well as an activating component. We now show that the very early innate response also has an immunosuppressive component. Infected cells upregulate the CD47 “don’t eat me” signal, which slows the phagocytic uptake of dying and viable cells as well as downstream antigen-presenting cell (APC) functions. A CD47 mimic that acts as an essential virulence factor is encoded by all poxviruses, but CD47 expression on infected cells was found to be upregulated even by pathogens, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that encode no mimic. CD47 upregulation was revealed to be a host response induced by the stimulation of both endosomal and cytosolic pathogen recognition receptors (PRRs). Furthermore, proinflammatory cytokines, including those found in the plasma of hepatitis C patients, upregulated CD47 on uninfected dendritic cells, thereby linking innate modulation with downstream adaptive immune responses. Indeed, results from antibody-mediated CD47 blockade experiments as well as CD47 knockout mice revealed an immunosuppressive role for CD47 during infections with lymphocytic choriomeningitis virus and Mycobacterium tuberculosis. Since CD47 blockade operates at the level of pattern recognition receptors rather than at a pathogen or antigen-specific level, these findings identify CD47 as a novel potential immunotherapeutic target for the enhancement of immune responses to a broad range of infectious agents.
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46
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Friebel E, Kapolou K, Unger S, Núñez NG, Utz S, Rushing EJ, Regli L, Weller M, Greter M, Tugues S, Neidert MC, Becher B. Single-Cell Mapping of Human Brain Cancer Reveals Tumor-Specific Instruction of Tissue-Invading Leukocytes. Cell 2020; 181:1626-1642.e20. [PMID: 32470397 DOI: 10.1016/j.cell.2020.04.055] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/11/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022]
Abstract
Brain malignancies can either originate from within the CNS (gliomas) or invade from other locations in the body (metastases). A highly immunosuppressive tumor microenvironment (TME) influences brain tumor outgrowth. Whether the TME is predominantly shaped by the CNS micromilieu or by the malignancy itself is unknown, as is the diversity, origin, and function of CNS tumor-associated macrophages (TAMs). Here, we have mapped the leukocyte landscape of brain tumors using high-dimensional single-cell profiling (CyTOF). The heterogeneous composition of tissue-resident and invading immune cells within the TME alone permitted a clear distinction between gliomas and brain metastases (BrM). The glioma TME presented predominantly with tissue-resident, reactive microglia, whereas tissue-invading leukocytes accumulated in BrM. Tissue-invading TAMs showed a distinctive signature trajectory, revealing tumor-driven instruction along with contrasting lymphocyte activation and exhaustion. Defining the specific immunological signature of brain tumors can facilitate the rational design of targeted immunotherapy strategies.
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Affiliation(s)
- Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Konstantina Kapolou
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Nicolás Gonzalo Núñez
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Sebastian Utz
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Elisabeth Jane Rushing
- Department of Neuropathology, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Luca Regli
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Melanie Greter
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Sonia Tugues
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Marian Christoph Neidert
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland; Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich 8091, Switzerland
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland.
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47
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Michlmayr D, Kim EY, Rahman AH, Raghunathan R, Kim-Schulze S, Che Y, Kalayci S, Gümüş ZH, Kuan G, Balmaseda A, Kasarskis A, Wolinsky SM, Suaréz-Fariñas M, Harris E. Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. Cell Rep 2020; 31:107569. [PMID: 32348760 PMCID: PMC7308490 DOI: 10.1016/j.celrep.2020.107569] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/18/2019] [Accepted: 04/03/2020] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) is an emerging, mosquito-borne flavivirus responsible for recent epidemics across the Americas, and it is closely related to dengue virus (DENV). Here, we study samples from 46 DENV-naive and 43 DENV-immune patients with RT-PCR-confirmed ZIKV infection at early-acute, late-acute, and convalescent time points from our pediatric cohort study in Nicaragua. We analyze the samples via RNA sequencing (RNA-seq), CyTOF, and multiplex cytokine/chemokine Luminex to generate a comprehensive, innate immune profile during ZIKV infection. Immunophenotyping and analysis of cytokines/chemokines reveal that CD14+ monocytes play a key role during ZIKV infection. Further, we identify CD169 (Siglec-1) on CD14+ monocytes as a potential biomarker of acute ZIKV infection. Strikingly distinct transcriptomic and immunophenotypic signatures are observed at all three time points. Interestingly, pre-existing dengue immunity has minimal impact on the innate immune response to Zika. Finally, this comprehensive immune profiling and network analysis of ZIKV infection in children serves as a valuable resource.
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Affiliation(s)
- Daniela Michlmayr
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rohit Raghunathan
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Che
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mayte Suaréz-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
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48
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Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC. Multiplexed single-cell morphometry for hematopathology diagnostics. Nat Med 2020; 26:408-417. [PMID: 32161403 PMCID: PMC7301910 DOI: 10.1038/s41591-020-0783-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/30/2020] [Indexed: 01/13/2023]
Abstract
The diagnosis of lymphomas and leukemias requires hematopathologists to integrate microscopically visible cellular morphology with antibody-identified cell surface molecule expression. To merge these into one high-throughput, highly multiplexed, single-cell assay, we quantify cell morphological features by their underlying, antibody-measurable molecular components, which empowers mass cytometers to 'see' like pathologists. When applied to 71 diverse clinical samples, single-cell morphometric profiling reveals robust and distinct patterns of 'morphometric' markers for each major cell type. Individually, lamin B1 highlights acute leukemias, lamin A/C helps distinguish normal from neoplastic mature T cells, and VAMP-7 recapitulates light-cytometric side scatter. Combined with machine learning, morphometric markers form intuitive visualizations of normal and neoplastic cellular distribution and differentiation. When recalibrated for myelomonocytic blast enumeration, this approach is superior to flow cytometry and comparable to expert microscopy, bypassing years of specialized training. The contextualization of traditional surface markers on independent morphometric frameworks permits more sensitive and automated diagnosis of complex hematopoietic diseases.
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Affiliation(s)
- Albert G Tsai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - David R Glass
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | - Marisa Juntilla
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Jean S Oak
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Robert S Ohgami
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Immunology Graduate Program, Stanford University, Stanford, CA, USA.
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49
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Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol 2020; 16:87-99. [PMID: 31892734 PMCID: PMC7232872 DOI: 10.1038/s41584-019-0338-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
The cellular complexity and functional diversity of the human immune system necessitate the use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as rheumatic diseases, as well as other autoimmune and inflammatory disorders. Proteomic technologies that use elemental (heavy metal) reporter ions, such as mass cytometry (also known as CyTOF) and analogous high-dimensional imaging approaches (including multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC)), have been developed from their low-dimensional counterparts, flow cytometry and immunohistochemistry, to meet this need. A growing number of studies have been published that use these technologies to identify functional biomarkers and therapeutic targets in rheumatic diseases, but the full potential of their application to rheumatic disease research has yet to be fulfilled. This Review introduces the underlying technologies for high-dimensional immune monitoring and discusses aspects necessary for their successful implementation, including study design principles, analytical tools and future developments for the field of rheumatology.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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50
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Eccles JD, Turner RB, Kirk NA, Muehling LM, Borish L, Steinke JW, Payne SC, Wright PW, Thacker D, Lahtinen SJ, Lehtinen MJ, Heymann PW, Woodfolk JA. T-bet+ Memory B Cells Link to Local Cross-Reactive IgG upon Human Rhinovirus Infection. Cell Rep 2020; 30:351-366.e7. [PMID: 31940481 PMCID: PMC6994188 DOI: 10.1016/j.celrep.2019.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/01/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023] Open
Abstract
Human rhinoviruses cause the common cold and exacerbate chronic respiratory diseases. Although infection elicits neutralizing antibodies, these do not persist or cross-protect across multiple rhinovirus strains. To analyze rhinovirus-specific B cell responses in humans, we developed techniques using intact RV-A16 and RV-A39 for high-throughput high-dimensional single-cell analysis, with parallel assessment of antibody isotypes in an experimental infection model. Our approach identified T-bet+ B cells binding both viruses that account for ∼5% of CXCR5- memory B cells. These B cells infiltrate nasal tissue and expand in the blood after infection. Their rapid secretion of heterotypic immunoglobulin G (IgG) in vitro, but not IgA, matches the nasal antibody profile post-infection. By contrast, CXCR5+ memory B cells binding a single virus are clonally distinct, absent in nasal tissue, and secrete homotypic IgG and IgA, mirroring the systemic response. Temporal and spatial functions of dichotomous memory B cells might explain the ability to resolve infection while rendering the host susceptible to re-infection.
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Affiliation(s)
- Jacob D Eccles
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ronald B Turner
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Nicole A Kirk
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Lyndsey M Muehling
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Larry Borish
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - John W Steinke
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Spencer C Payne
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Otolaryngology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Paul W Wright
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Deborah Thacker
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Sampo J Lahtinen
- DuPont Nutrition & Biosciences, Global Health and Nutrition Science, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Markus J Lehtinen
- DuPont Nutrition & Biosciences, Global Health and Nutrition Science, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Peter W Heymann
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Judith A Woodfolk
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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