1
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Vos WAJW, Navas A, Meeder EMG, Blaauw MJT, Groenendijk AL, van Eekeren LE, Otten T, Vadaq N, Matzaraki V, van Cranenbroek B, Brinkman K, van Lunzen J, Joosten LAB, Netea MG, Blok WL, van der Ven AJAM, Koenen HJPM, Stalenhoef JE. HIV immunological non-responders are characterized by extensive immunosenescence and impaired lymphocyte cytokine production capacity. Front Immunol 2024; 15:1350065. [PMID: 38779686 PMCID: PMC11109418 DOI: 10.3389/fimmu.2024.1350065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction Immunological non-responders (INR) are people living with HIV (PLHIV) who fail to fully restore CD4+ T-cell counts despite complete viral suppression with antiretroviral therapy (ART). INR are at higher risk for non-HIV related morbidity and mortality. Previous research suggest persistent qualitative defects. Methods The 2000HIV study (clinical trials NTC03994835) enrolled 1895 PLHIV, divided in a discovery and validation cohort. PLHIV with CD4 T-cell count <350 cells/mm3 after ≥2 years of suppressive ART were defined as INR and were compared to immunological responders (IR) with CD4 T-cell count >500 cells/mm3. Logistic and rank based regression were used to analyze clinical data, extensive innate and adaptive immunophenotyping, and ex vivo monocyte and lymphocyte cytokine production after stimulation with various stimuli. Results The discovery cohort consisted of 62 INR and 1224 IR, the validation cohort of 26 INR and 243 IR. INR were older, had more advanced HIV disease before starting ART and had more frequently a history of non-AIDS related malignancy. INR had lower absolute CD4+ T-cell numbers in all subsets. Activated (HLA-DR+, CD38+) and exhausted (PD1+) subpopulations were proportionally increased in CD4 T-cells. Monocyte and granulocyte immunophenotypes were comparable. INR lymphocytes produced less IL-22, IFN-γ, IL-10 and IL-17 to stimuli. In contrast, monocyte cytokine production did not differ. The proportions of CD4+CD38+HLA-DR+ and CD4+PD1+ subpopulations showed an inversed correlation to lymphocyte cytokine production. Conclusions INR compared to IR have hyperactivated and exhausted CD4+ T-cells in combination with lymphocyte functional impairment, while innate immune responses were comparable. Our data provide a rationale to consider the use of anti-PD1 therapy in INR.
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Affiliation(s)
- Wilhelm A. J. W. Vos
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine and Infectious Diseases, OLVG, Amsterdam, Netherlands
| | - Adriana Navas
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Elise M. G. Meeder
- Department of Psychiatry, Radboudumc, Radboud University, Nijmegen, Netherlands
- Cognition and Behavior, Donders Institute for Brain, Radboud University, Nijmegen, Netherlands
| | - Marc J. T. Blaauw
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine and Infectious Diseases, Elizabeth-Tweesteden Ziekenhuis, Tilburg, Netherlands
| | - Albert L. Groenendijk
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine, ErasmusMC, Erasmus University, Rotterdam, Netherlands
- Department of Medical Microbiology and Infectious diseases, ErasmusMC, Erasmus University, Rotterdam, Netherlands
| | - Louise E. van Eekeren
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Twan Otten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Internal Medicine and Infectious Diseases, Elizabeth-Tweesteden Ziekenhuis, Tilburg, Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vasiliki Matzaraki
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Bram van Cranenbroek
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kees Brinkman
- Department of Internal Medicine and Infectious Diseases, OLVG, Amsterdam, Netherlands
| | - Jan van Lunzen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Willem L. Blok
- Department of Internal Medicine and Infectious Diseases, OLVG, Amsterdam, Netherlands
| | | | - Hans J. P. M. Koenen
- Department of Laboratory Medicine, Laboratory for Medical Immunology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janneke E. Stalenhoef
- Department of Internal Medicine and Infectious Diseases, OLVG, Amsterdam, Netherlands
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2
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Kolypetri P, Weiner HL. Monocyte regulation by gut microbial signals. Trends Microbiol 2023; 31:1044-1057. [PMID: 37271658 PMCID: PMC10524398 DOI: 10.1016/j.tim.2023.05.006] [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: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Monocytes are innate immune cells that sense environmental changes and participate in the immunoregulation of autoimmune, neurologic, cardiovascular, and metabolic diseases as well as cancer. Recent studies have suggested that the gut microbiome shapes the biology of monocytes via microbial signals at extraintestinal sites. Interestingly, in chronic diseases, communication between microbial signals and monocytes can either promote or inhibit disease activity, suggesting that some of these pathways can be harnessed for clinical therapies. In this review, we discuss the newer concepts of regulation of monocyte homeostasis and function by gut microbial signals during steady state and inflammation. We also highlight the therapeutic potential of microbial signal-based approaches for modulation in the context of various diseases.
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Affiliation(s)
- Panayota Kolypetri
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Howard L Weiner
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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3
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Ye G, Xu Z, Yang M, Wang J, Liang J, Yin J, Yang Y, Xia H, Liu Y. Clinical features and transmission risk analysis of dengue virus infections in Shenzhen, During 2014-2019. Comput Struct Biotechnol J 2023; 21:3728-3735. [PMID: 37560123 PMCID: PMC10407296 DOI: 10.1016/j.csbj.2023.07.001] [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: 09/08/2022] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 08/11/2023] Open
Abstract
UNLABELLED Dengue fever (DF) and dengue hemorrhagic fever (DHF) are among the most common tropical diseases affecting humans. To analyze the risk of clinical and transmission of DF/DHF in Shenzhen, the surveillance on patients of all-age patients with dengue virus (DENV) infections was conducted. Our findings revealed that the majority of DENV-infected patients are young to middle-aged males, and the development of the disease is accompanied by abnormal changes in the percentages of neutrophils, lymphocytes, and basophils. Demographic analysis revealed that these patients is concentrated in areas such as Futian District, which may be due to the higher mosquito density and temperature than that in other area. Subsequent, mosquito infection experiments confirmed that the effect of temperature shift on DENV proliferation and transmission. Not only that, constant temperatures can enhance the spread of DENV, even increase the risk of epidemic. Thus, the role of innate immune response should be highlighted in the prediction of severe severity of DENV-infected patients, and temperature should be taken into account in the prevention and control of DENV. INTRODUCTION Dengue fever (DF) and dengue hemorrhagic fever (DHF) are among the most common tropical diseases affecting humans, and which caused by the four dengue virus serotypes (DENV 1-4). OBJECTIVES To analyze the risk of clinical and transmission of DF/DHF in Shenzhen. METHODS The surveillance on patients of all-age patients with dengue virus (DENV) infections was conducted. RESULTS Our findings revealed that the majority of DENV-infected patients are young to middle-aged males, and the development of the disease is accompanied by abnormal changes in the percentages of neutrophils, lymphocytes, and basophils. Demographic analysis revealed that these patients is concentrated in areas such as Futian District, which may be due to the higher mosquito density and temperature than that in other area. Subsequent, mosquito infection experiments confirmed that the effect of temperature shift on DENV proliferation and transmission. Not only that, constant temperatures can enhance the spread of DENV, even increase the risk of epidemic. CONCLUSION 1. Elevated levels of neutrophils, lymphocytes, basophils, and temperature are all significant risk factors for dengue transmission and pathogenesis; 2. Temperature increasing is associated with a higher risk of dengue transmission; 3. Fluctuations in temperature around 28 °C (28 ± 5 °C) would increase dengue transmission.
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Affiliation(s)
- Guoguo Ye
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhixiang Xu
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Yang
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of Molecular Medicine and Biotherapy, Beijing 100081, China
- Advanced Research Institute of Multidisciplinary Sciences, Beijing Institute of Technology, Beijing 100081, China
| | - Jun Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| | - Jinhu Liang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Juzhen Yin
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Han Xia
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Division of Infectious Disease,The Third People's Hospital of Shenzhen, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
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4
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Psarras A, Clarke A. A cellular overview of immunometabolism in systemic lupus erythematosus. OXFORD OPEN IMMUNOLOGY 2023; 4:iqad005. [PMID: 37554724 PMCID: PMC10264559 DOI: 10.1093/oxfimm/iqad005] [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: 02/17/2023] [Revised: 04/16/2023] [Accepted: 05/02/2023] [Indexed: 08/10/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease, characterized by a breakdown of immune tolerance and the development of autoantibodies against nucleic self-antigens. Immunometabolism is a rapidly expanding scientific field investigating the metabolic programming of cells of the immune system. During the normal immune response, extensive reprogramming of cellular metabolism occurs, both to generate adenosine triphosphate and facilitate protein synthesis, and also to manage cellular stress. Major pathways upregulated include glycolysis, oxidative phosphorylation, the tricarboxylic acid cycle and the pentose phosphate pathway, among others. Metabolic reprogramming also occurs to aid resolution of inflammation. Immune cells of both patients with SLE and lupus-prone mice are characterized by metabolic abnormalities resulting in an altered functional and inflammatory state. Recent studies have described how metabolic reprogramming occurs in many cell populations in SLE, particularly CD4+ T cells, e.g. favouring a glycolytic profile by overactivation of the mechanistic target of rapamycin pathway. These advances have led to an increased understanding of the metabolic changes affecting the inflammatory profile of T and B cells, monocytes, dendritic cells and neutrophils, and how they contribute to autoimmunity and SLE pathogenesis. In the current review, we aim to summarize recent advances in the field of immunometabolism involved in SLE and how these could potentially lead to new therapeutic strategies in the future.
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Affiliation(s)
- Antonios Psarras
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
| | - Alexander Clarke
- Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, UK
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5
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Muir V, Sagadiev S, Liu S, Holder U, Armendariz AM, Suchland E, Meitlis I, Camp N, Giltiay N, Tam JM, Garner EC, Wivagg CN, Shows D, James RG, Lacy-Hulbert A, Acharya M. Transcriptomic analysis of pathways associated with ITGAV/alpha(v) integrin-dependent autophagy in human B cells. Autophagy 2023; 19:926-942. [PMID: 36016494 PMCID: PMC9980515 DOI: 10.1080/15548627.2022.2113296] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Macroautophagy/autophagy proteins have been linked with the development of immune-mediated diseases including lupus, but the mechanisms for this are unclear due to the complex roles of these proteins in multiple immune cell types. We have previously shown that a form of noncanonical autophagy induced by ITGAV/alpha(v) integrins regulates B cell activation by viral and self-antigens, in mice. Here, we investigate the involvement of this pathway in B cells from human tissues. Our data reveal that autophagy is specifically induced in the germinal center and memory B cell subpopulations of human tonsils and spleens. Transcriptomic analysis show that the induction of autophagy is related to unique aspects of activated B cells such as mitochondrial metabolism. To understand the function of ITGAV/alpha(v) integrin-dependent autophagy in human B cells, we used CRISPR-mediated knockdown of autophagy genes. Integrating data from primary B cells and knockout cells, we found that ITGAV/alpha(v)-dependent autophagy limits activation of specific pathways related to B cell responses, while promoting others. These data provide new mechanistic links for autophagy and B-cell-mediated immune dysregulation in diseases such as lupus.
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Affiliation(s)
- Virginia Muir
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Sara Sagadiev
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Shuozhi Liu
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ursula Holder
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Andrea M Armendariz
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Emmaline Suchland
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Iana Meitlis
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nathan Camp
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Natalia Giltiay
- Departments of Rheumatology, University of Washington, Seattle, WA, USA
| | - Jenny M Tam
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA
| | - Carl N Wivagg
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, USA
| | - Donna Shows
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Richard G James
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatric, University of Washington, Seattle, WA, USA.,Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Adam Lacy-Hulbert
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.,Department of Immunology, University of Washington, Seattle, WA, USA
| | - Mridu Acharya
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.,Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatric, University of Washington, Seattle, WA, USA
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6
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Liu J, Allo B, Winnik MA. Development of Multiplexed Bead-Based Immunoassays for Profiling Soluble Cytokines and CD163 Using Mass Cytometry. ACS MEASUREMENT SCIENCE AU 2022; 2:629-640. [PMID: 36573076 PMCID: PMC9783081 DOI: 10.1021/acsmeasuresciau.2c00038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/17/2023]
Abstract
Bead-based immunoassays are multiparametric analysis allowing for the simultaneous quantification of a large number of biomarkers within a single sample. Mass cytometry is an emerging cytometric technique that offers a high multiplexing capacity in a high-throughput setting but has not yet been applied to bead-based assays. In this study, we developed a multiplex bead-based immunoassay of cytokines and CD163 designed for mass cytometry (MC). A set of 11 types of lanthanide-encoded microbeads were synthesized by two-stage dispersion polymerization as classifier candidates for the assay. These beads were then decorated with different Abs on the surface to capture the target cytokines in solution. Gold nanoparticles were employed as reporters to identify the binding of target cytokines on the classifier surface. As a proof-of-concept study, we first developed four-plex and nine-plex assays of mixtures of cytokines in standard solutions. The MC signal intensities of these immunoassays were responsive to the concentration differences in the standard solutions with high detection sensitivities at low analyte concentrations. Finally, we examined a sample of peripheral blood mononuclear cells (PBMCs) with the nine-plex assay, comparing an unstimulated sample with a sample stimulated to promote cytokine secretion.
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Affiliation(s)
- Jieyi Liu
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Bedilu Allo
- Fluidigm
Canada (now Standard BioTools Canada), 1380 Rodick Road, Markham, Ontario L3R 4G5, Canada
| | - Mitchell A. Winnik
- Department
of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Department
of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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7
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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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8
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Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP. Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types. Front Immunol 2022; 13:867016. [PMID: 35419006 PMCID: PMC8995898 DOI: 10.3389/fimmu.2022.867016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/28/2022] Open
Abstract
Assessing the health and competence of the immune system is central to evaluating vaccination responses, autoimmune conditions, cancer prognosis, and treatment. With an increasing number of studies examining immune dysregulation, there is a growing need for a curated reference of variation in immune parameters in healthy individuals. We used mass cytometry (CyTOF) to profile blood from 86 humans in response to 15 ex vivo immune stimuli. We present reference ranges for cell-specific immune markers and highlight differences that appear across sex and age. We identified modules of immune features that suggest there exists an underlying structure to the immune system based on signaling pathway responses across cell types. We observed increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in females. In contrast, males exhibited stronger pSTAT1 and pTBK1 responses. These reference data are publicly available as a resource for immune profiling studies.
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Affiliation(s)
- Gabriela K. Fragiadakis
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States
- CoLabs, University of California San Francisco, San Francisco, CA, United States
- Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | | | - Deepthi Madhireddy
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Karen Sachs
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Han Chen
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - David R. McIlwain
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Matthew H. Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States
- Department of Otolaryngology – Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, United States
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Garry P. Nolan
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
- Department of Pathology, Stanford University, Stanford, CA, United States
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9
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Rudra P, Baxter R, Hsieh EWY, Ghosh D. Compositional Data Analysis using Kernels in mass cytometry data. BIOINFORMATICS ADVANCES 2022; 2:vbac003. [PMID: 35224501 PMCID: PMC8867823 DOI: 10.1093/bioadv/vbac003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/06/2021] [Accepted: 01/12/2022] [Indexed: 01/27/2023]
Abstract
MOTIVATION Cell-type abundance data arising from mass cytometry experiments are compositional in nature. Classical association tests do not apply to the compositional data due to their non-Euclidean nature. Existing methods for analysis of cell type abundance data suffer from several limitations for high-dimensional mass cytometry data, especially when the sample size is small. RESULTS We proposed a new multivariate statistical learning methodology, Compositional Data Analysis using Kernels (CODAK), based on the kernel distance covariance (KDC) framework to test the association of the cell type compositions with important predictors (categorical or continuous) such as disease status. CODAK scales well for high-dimensional data and provides satisfactory performance for small sample sizes (n < 25). We conducted simulation studies to compare the performance of the method with existing methods of analyzing cell type abundance data from mass cytometry studies. The method is also applied to a high-dimensional dataset containing different subgroups of populations including Systemic Lupus Erythematosus (SLE) patients and healthy control subjects. AVAILABILITY AND IMPLEMENTATION CODAK is implemented using R. The codes and the data used in this manuscript are available on the web at http://github.com/GhoshLab/CODAK/. CONTACT prudra@okstate.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Pratyaydipta Rudra
- Department of Statistics, Oklahoms State University, Stillwater, OK 74078, USA
- To whom correspondence should be addressed.
| | - Ryan Baxter
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatrics, Section of Allergy and Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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10
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Zhang L, Liu X, Chen X, Warden AR, Yu Y, Huang B, Ding X. SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum. Bioinformatics 2022; 38:1361-1368. [PMID: 34664638 DOI: 10.1093/bioinformatics/btab713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/20/2021] [Accepted: 10/13/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION High-dimensional mass cytometry (CyTOF), which provides both cellular signatures and inter-cluster interactions like the antagonism between immune activation and suppression, and the pro-inflammatory synergy, sheds light on the cellular and molecular basis of disease pathogenesis. However, revealing the aberrance of inter-cluster communication networks in CyTOF datasets remains a significant challenge. RESULTS Here, we developed Sample Classification and direct Association Network among Cell clusters (SCANCell) that quantifies the direct association (DA) network of cell clusters. SCANCell was applied to profile inter-cluster interaction patterns of a well-recruited systemic lupus erythematosus (SLE) cohort, including 8 healthy controls, 10 active SLE patients (APs) and 8 remission SLE patients (RPs). SCANCell identified decreased inter-cluster interactions of CD8+ T cells in APs compared with RPs, and enhanced DA of CD8+ T cells after stimulation with immunostimulatory cytokine interleukin-2 in vitro. These discoveries prove that SCANCell can uncover pathology- and drug stimulation-associated inter-cluster interactions, which potentially benefits understanding of pathogenesis and novel therapeutic strategies. AVAILABILITY AND IMPLEMENTATION The main processing scripts of SCNACell are available at https://github.com/Lxc417/SCANCell. Other codes for the following data statistics are available from the corresponding author upon request. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lulu Zhang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiao Liu
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaoxiang Chen
- Department of Rheumatology, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai 200030, China
| | - Antony R Warden
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Youyi Yu
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Baozhen Huang
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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11
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Wimmers F, Donato M, Kuo A, Ashuach T, Gupta S, Li C, Dvorak M, Foecke MH, Chang SE, Hagan T, De Jong SE, Maecker HT, van der Most R, Cheung P, Cortese M, Bosinger SE, Davis M, Rouphael N, Subramaniam S, Yosef N, Utz PJ, Khatri P, Pulendran B. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 2021; 184:3915-3935.e21. [PMID: 34174187 PMCID: PMC8316438 DOI: 10.1016/j.cell.2021.05.039] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mariko Hinton Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne E De Jong
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mark Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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12
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Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. ACTA ACUST UNITED AC 2021; 93:e71. [PMID: 32250555 DOI: 10.1002/cpcy.71] [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] [Indexed: 12/23/2022]
Abstract
This article presents a single experiment designed to introduce a trainee to multiple advanced bench and analysis techniques, including high-dimensional cytometry, profiling cell signaling networks, functional assays with primary human tissue, and single-cell analysis with machine learning tools. The trainee is expected to have only minimal laboratory experience and is not required to have any prior training in flow cytometry, immunology, or data science. This article aims to introduce the advanced research areas with a design that is robust enough that novice trainees will succeed, flexible enough to allow some project customization, and fundamental enough that the skills and knowledge gained will provide a template for future experiments. For advanced users, the updated phospho-flow protocol and the established controls, best practices, and expected outcomes presented here also provide a framework for adapting these tools in new areas with unexplored biology. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Phospho-protein stimulation and mass cytometry data collection Support Protocol: Analysis of signaling mass cytometry data.
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Affiliation(s)
- Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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13
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Marques CPC, Rodrigues VP, de Carvalho LC, Nichilatti LP, Franco MM, Patrício FJB, Magalhães M, de Andrade MS, Benatti BB. Expression of Toll-like receptors 2 and 4 in the saliva of patients with systemic lupus erythematosus and chronic periodontitis. Clin Rheumatol 2021; 40:2727-2734. [PMID: 33570702 DOI: 10.1007/s10067-020-05560-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/08/2020] [Accepted: 12/21/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the expression of salivary Toll-like receptors (TRL) 2 and 4 in patients with systemic lupus erythematosus (SLE) and chronic periodontitis (CP). METHODS A case-control study was conducted with 77 participants (42 SLE and 35 non-SLE) stratified according to CP diagnosis criteria. Periodontal parameters consisted of clinical attachment level (CAL), probing depth (PD), the visible plaque index (VPI), and the gingival bleeding index (GBI). Salivary TRL 2 and 4 expressions were determined by quantitative real-time polymerase chain reaction (RT-PCR). Statistical analysis included Mann-Whitney U test, Kruskal-Wallis test, Spearman's correlation rank, and multiple linear regression. RESULTS Patients with isolated SLE or CP had higher TLR 2 and TLR 4 expression in their saliva samples (P < 0.05). The group with both SLE and CP had lower TLR 2 and 4 expressions (P < 0.05). TLR 2 and TLR 4 showed significant negative correlations with PD, CAL, and GBI in SLE patients, and a significant positive correlation with periodontal parameters in non-SLE patients. CP was independently associated with reduction of TLR2 and TLR4 expression, even after adjusting for clinical data and current drug use. CONCLUSION Reduced TRL 2 and 4 expression in saliva was associated with the presence of CP in SLE patients. Key Points • Patients affected by isolated CP or SLE had higher TLR2 and TLR4 expression. • TLR under-expression may be associated with a worse periodontal status in SLE. • Abnormalities in TLRs expression may increase the susceptibility to periodontitis.
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Affiliation(s)
- Consuelo P C Marques
- Dentistry Graduate Program, Federal University of Maranhão, São Luís, Maranhão, Brazil.,School of Medicine, Federal University of Maranhão, Pinheiro, Maranhão, Brazil
| | - Vandilson P Rodrigues
- Dentistry Graduate Program, Federal University of Maranhão, São Luís, Maranhão, Brazil. .,Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), President Dutra Hospital of the Federal University of Maranhão, São Luís, Maranhão, Brazil.
| | | | - Louise P Nichilatti
- School of Medicine, Federal University of Maranhão, Pinheiro, Maranhão, Brazil
| | - Mayra M Franco
- Dentistry Graduate Program, Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Fernando José B Patrício
- Laboratory of Genomic Studies and Histocompatibility, President Dutra Hospital of the Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Marcelo Magalhães
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), President Dutra Hospital of the Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Marcelo S de Andrade
- Laboratory of Genomic Studies and Histocompatibility, President Dutra Hospital of the Federal University of Maranhão, São Luís, Maranhão, Brazil
| | - Bruno B Benatti
- Dentistry Graduate Program, Federal University of Maranhão, São Luís, Maranhão, Brazil
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14
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Subjects at-risk for future development of rheumatoid arthritis demonstrate a PAD4-and TLR-dependent enhanced histone H3 citrullination and proinflammatory cytokine production in CD14 hi monocytes. J Autoimmun 2020; 117:102581. [PMID: 33310262 DOI: 10.1016/j.jaut.2020.102581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022]
Abstract
The presence of anti-citrullinated protein/peptide antibodies (ACPA) and epitope spreading across the target autoantigens is a unique feature of rheumatoid arthritis (RA). ACPA are present in the peripheral blood for several years prior to the onset of arthritis and clinical classification of RA. ACPA recognize multiple citrullinated proteins, including histone H3 (H3). Intracellular citrullination of H3 in neutrophils and T cells is known to regulate immune cell function by promoting neutrophil extracellular trap formation and citrullinated autoantigen release as well as regulating the Th2/Th17 T cell phenotypic balance. However, the roles of H3 citrullination in other immune cells are not fully elucidated. We aimed to explore H3 citrullination and cytokine/metabolomic signatures in peripheral blood immune cells from subjects prior to and after the onset of RA, at baseline and in response to ex vivo toll-like receptor (TLR) stimulation. Here, we analyzed 13 ACPA (+) subjects without arthritis but at-risk for future development of RA, 14 early RA patients, and 13 healthy controls. We found significantly elevated H3 citrullination in CD14hi monocytes, as well as CD1c+ dendritic cells and CD66+ granulocytes. Unsupervised analysis identified two distinct subsets in CD14hi monocytes characterized by H3 modification and unique cytokine/metabolomic signatures. CD14hi monocytes with elevated TLR-stimulated H3 citrullination were significantly increased in ACPA (+) at-risk subjects. These cells were skewed to produce TNFα, MIP1β, IFNα, and partially IL-12. Additionally, they demonstrate peptidyl arginine deiminase 4 (PAD4) mediated upregulation of the glycolytic enzyme PFKFB3. These CD14hi monocytes with elevated H3 citrullination morphologically formed monocyte extracellular traps (METs). Taken together, dysregulated PAD4-driven cytokine production as well as MET formation in CD14hi monocytes in ACPA (+) at-risk subjects likely plays an important role in the development of RA via promoting and perpetuating inflammation and generation of citrullinated autoantigens.
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15
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Luo Q, Li X, Fu B, Zhang L, Fang L, Qing C, Guo Y, Huang Z, Li J. Expression profile and diagnostic value of circRNAs in peripheral blood from patients with systemic lupus erythematosus. Mol Med Rep 2020; 23:1. [PMID: 33169172 PMCID: PMC7673322 DOI: 10.3892/mmr.2020.11639] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 07/28/2020] [Indexed: 12/18/2022] Open
Abstract
Circular RNAs (circRNAs) have gained attention due to their performance in disease diagnosis. However, the characteristics of circRNAs in peripheral blood from patients with systemic lupus erythematosus (SLE) remain unknown. Therefore, the aim of the present study was to determine the expression profile and diagnostic potential of circRNAs in peripheral blood from patients with SLE. The global circRNA expression in the peripheral blood of patients with SLE and healthy controls (HCs) was detected using a circRNA microarray. Then, the expression levels of three upregulated circRNAs were selected for further validation by reverse transcription‑quantitative PCR (RT‑qPCR) in a training set. Moreover, the diagnostic value of these circRNAs was assessed by constructing a receiver operating characteristic curve, and then verified in a blind testing set. In total, 1,566 circRNAs were identified to be dysregulated between patients with SLE and HCs (≥2 fold change, P<0.05). Furthermore, the RT‑qPCR results were consistent with the microarray data, in that all three selected circRNAs, hsa_circ_0082688, hsa_circ_0082689 and hsa_circ_0008675, were significantly upregulated in patients with SLE (P<0.05). Results from the training set demonstrated that the combination of hsa_circ_0082688‑hsa_circ_0082689 may provide the most beneficial diagnostic potential. Moreover, the blind test results indicated that the combination model of hsa_circ_0082688‑hsa_circ_0082689 could effectively discriminate between patients with SLE from patients with rheumatoid arthritis and HCs, with a sensitivity of 91.30%, a specificity of 78.57% and an accuracy of 82.28%. Moreover, the combination model of hsa_circ_0082688‑hsa_circ_0082689 + anti‑dsDNA could more effectively discriminated the SLE group from the control groups, with a sensitivity of 95.65%, a specificity of 100.00% and an accuracy of 98.73%. In addition, correlation analysis results suggested that all three circRNAs in patients with SLE did not correlate with the SLE disease activity index. In conclusion, the expression levels of hsa_circ_0082688‑hsa_circ_0082689 may serve as potential biomarkers for SLE diagnosis.
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Affiliation(s)
- Qing Luo
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xue Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Biqi Fu
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 710065, P.R. China
| | - Lu Zhang
- Department of Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Le Fang
- Department of Blood Transfusion, 521 Hospital of Ordnance Industry, Xi'an, Shanxi 710065, P.R. China
| | - Cheng Qing
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yang Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zikun Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Junming Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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16
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Allen ME, Rus V, Szeto GL. Leveraging Heterogeneity in Systemic Lupus Erythematosus for New Therapies. Trends Mol Med 2020; 27:152-171. [PMID: 33046407 DOI: 10.1016/j.molmed.2020.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/01/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
Systemic lupus erythematosus (SLE) is a multisystem, chronic autoimmune disease where treatment varies by patient and disease activity. Strong preclinical results and clinical correlates have motivated development of many drugs, but many of these have failed to achieve efficacy in clinical trials. FDA approval of belimumab in 2011 was the first successful SLE drug in nearly six decades. In this article, we review insights into the molecular and clinical heterogeneity of SLE from transcriptomics studies and detail their potential impact on drug development and clinical practices. We critically examine the pipeline of SLE drugs, including past failures and their associated lessons and current promising approaches. Finally, we identify opportunities for integrating these findings and drug development with new multidisciplinary advances to enhance future SLE treatment.
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Affiliation(s)
- Marilyn E Allen
- Department of Chemical, Biochemical & Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Violeta Rus
- Department of Medicine, Division of Rheumatology & Clinical Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gregory L Szeto
- Department of Chemical, Biochemical & Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, USA; Department of Experimental Immunology, Allen Institute for Immunology, Seattle, WA, USA.
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17
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Zhang T, Warden AR, Li Y, Ding X. Progress and applications of mass cytometry in sketching immune landscapes. Clin Transl Med 2020; 10:e206. [PMID: 33135337 PMCID: PMC7556381 DOI: 10.1002/ctm2.206] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Recently emerged mass cytometry (cytometry by time-of-flight [CyTOF]) technology permits the identification and quantification of inherently diverse cellular systems, and the simultaneous measurement of functional attributes at the single-cell resolution. By virtue of its multiplex ability with limited need for compensation, CyTOF has led a critical role in immunological research fields. Here, we present an overview of CyTOF, including the introduction of CyTOF principle and advantages that make it a standalone tool in deciphering immune mysteries. We then discuss the functional assays, introduce the bioinformatics to interpret the data yield via CyTOF, and depict the emerging clinical and research applications of CyTOF technology in sketching immune landscape in a wide variety of diseases.
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Affiliation(s)
- Ting Zhang
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Antony R. Warden
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Yiyang Li
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Xianting Ding
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
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18
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Lago SG, Tomasik J, van Rees GF, Ramsey JM, Haenisch F, Cooper JD, Broek JA, Suarez-Pinilla P, Ruland T, Auyeug B, Mikova O, Kabacs N, Arolt V, Baron-Cohen S, Crespo-Facorro B, Bahn S. Exploring the neuropsychiatric spectrum using high-content functional analysis of single-cell signaling networks. Mol Psychiatry 2020; 25:2355-2372. [PMID: 30038233 DOI: 10.1038/s41380-018-0123-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 05/04/2018] [Accepted: 05/25/2018] [Indexed: 12/26/2022]
Abstract
Neuropsychiatric disorders overlap in symptoms and share genetic risk factors, challenging their current classification into distinct diagnostic categories. Novel cross-disorder approaches are needed to improve our understanding of the heterogeneous nature of neuropsychiatric diseases and overcome existing bottlenecks in their diagnosis and treatment. Here we employ high-content multi-parameter phospho-specific flow cytometry, fluorescent cell barcoding and automated sample preparation to characterize ex vivo signaling network responses (n = 1764) measured at the single-cell level in B and T lymphocytes across patients diagnosed with four major neuropsychiatric disorders: autism spectrum condition (ASC), bipolar disorder (BD), major depressive disorder (MDD), and schizophrenia (SCZ; n = 25 each), alongside matched healthy controls (n = 100). We identified 25 nodes (individual cell subtype-epitope-ligand combinations) significantly altered relative to the control group, with variable overlap between different neuropsychiatric diseases and heterogeneously expressed at the level of each individual patient. Reconstruction of the diagnostic categories from the altered nodes revealed an overlapping neuropsychiatric spectrum extending from MDD on one end, through BD and SCZ, to ASC on the other end. Network analysis showed that although the pathway structure of the epitopes was broadly preserved across the clinical groups, there were multiple discrete alterations in network connectivity, such as disconnections within the antigen/integrin receptor pathway and increased negative regulation within the Akt1 pathway in CD4+ T cells from ASC and SCZ patients, in addition to increased correlation of Stat1 (pY701) and Stat5 (pY694) responses in B cells from BD and MDD patients. Our results support the "dimensional" approach to neuropsychiatric disease classification and suggest potential novel drug targets along the neuropsychiatric spectrum.
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Affiliation(s)
- Santiago G Lago
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jakub Tomasik
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Geertje F van Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jordan M Ramsey
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Frieder Haenisch
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jason D Cooper
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Jantine A Broek
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Paula Suarez-Pinilla
- Department of Psychiatry, Marqués de Valdecilla University Hospital, IDIVAL, School of Medicine, University of Cantabria, Santander, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
| | - Tillmann Ruland
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Bonnie Auyeug
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.,Psychology Department, Edinburgh University, Scotland, UK
| | - Olya Mikova
- Foundation Biological Psychiatry, Sofia, Bulgaria
| | - Nikolett Kabacs
- Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Volker Arolt
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK.,CLASS Clinic, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, UK
| | - Benedicto Crespo-Facorro
- Department of Psychiatry, Marqués de Valdecilla University Hospital, IDIVAL, School of Medicine, University of Cantabria, Santander, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Santander, Spain
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
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19
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Waugh KA, Araya P, Pandey A, Jordan KR, Smith KP, Granrath RE, Khanal S, Butcher ET, Estrada BE, Rachubinski AL, McWilliams JA, Minter R, Dimasi T, Colvin KL, Baturin D, Pham AT, Galbraith MD, Bartsch KW, Yeager ME, Porter CC, Sullivan KD, Hsieh EW, Espinosa JM. Mass Cytometry Reveals Global Immune Remodeling with Multi-lineage Hypersensitivity to Type I Interferon in Down Syndrome. Cell Rep 2020; 29:1893-1908.e4. [PMID: 31722205 DOI: 10.1016/j.celrep.2019.10.038] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/28/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023] Open
Abstract
People with Down syndrome (DS; trisomy 21) display a different disease spectrum relative to the general population, including lower rates of solid malignancies and higher incidence of neurological and autoimmune conditions. However, the mechanisms driving this unique clinical profile await elucidation. We completed a deep mapping of the immune system in adults with DS using mass cytometry to evaluate 100 immune cell types, which revealed global immune dysregulation consistent with chronic inflammation, including key changes in the myeloid and lymphoid cell compartments. Furthermore, measurement of interferon-inducible phosphorylation events revealed widespread hypersensitivity to interferon-α in DS, with cell-type-specific variations in downstream intracellular signaling. Mechanistically, this could be explained by overexpression of the interferon receptors encoded on chromosome 21, as demonstrated by increased IFNAR1 surface expression in all immune lineages tested. These results point to interferon-driven immune dysregulation as a likely contributor to the developmental and clinical hallmarks of DS.
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Affiliation(s)
- Katherine A Waugh
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Paula Araya
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ahwan Pandey
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80302, USA
| | - Kimberly R Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Keith P Smith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ross E Granrath
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Santosh Khanal
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Eric T Butcher
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Belinda Enriquez Estrada
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Angela L Rachubinski
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jennifer A McWilliams
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ross Minter
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tiana Dimasi
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kelley L Colvin
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Dmitry Baturin
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Andrew T Pham
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kyle W Bartsch
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael E Yeager
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christopher C Porter
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elena W Hsieh
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80302, USA.
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20
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Han X, Vesely MD, Yang W, Sanmamed MF, Badri T, Alawa J, López-Giráldez F, Gaule P, Lee SW, Zhang JP, Nie X, Nassar A, Boto A, Flies DB, Zheng L, Kim TK, Moeckel GW, McNiff JM, Chen L. PD-1H (VISTA)-mediated suppression of autoimmunity in systemic and cutaneous lupus erythematosus. Sci Transl Med 2020; 11:11/522/eaax1159. [PMID: 31826980 DOI: 10.1126/scitranslmed.aax1159] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Systemic lupus erythematosus (SLE) and discoid lupus erythematosus (DLE) of the skin are autoimmune diseases characterized by inappropriate immune responses against self-proteins; the key elements that determine disease pathogenesis and progression are largely unknown. Here, we show that mice lacking immune inhibitory receptor VISTA or programmed death-1 homolog (PD-1H KO) on a BALB/c background spontaneously develop cutaneous and systemic autoimmune diseases resembling human lupus. Cutaneous lupus lesions of PD-1H KO mice have clustering of plasmacytoid dendritic cells (pDCs) similar to human DLE. Using mass cytometry, we identified proinflammatory neutrophils as critical early immune infiltrating cells within cutaneous lupus lesions of PD-1H KO mice. We also found that PD-1H is highly expressed on immune cells in human SLE, DLE lesions, and cutaneous lesions of MRL/lpr mice. A PD-1H agonistic monoclonal antibody in MRL/lpr mice reduces cutaneous disease, autoantibodies, inflammatory cytokines, chemokines, and immune cell expansion. Furthermore, PD-1H on both T cells and myeloid cells including neutrophils and pDCs could transmit inhibitory signals, resulting in reduced activation and function, establishing PD-1H as an inhibitory receptor on T cells and myeloid cells. On the basis of these findings, we propose that PD-1H is a critical element in the pathogenesis and progression of lupus, and PD-1H activation could be effective for treatment of systemic and cutaneous lupus.
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Affiliation(s)
- Xue Han
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Matthew D Vesely
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.,Department of Dermatology, Yale University, New Haven, CT 06520, USA
| | - Wendy Yang
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Miguel F Sanmamed
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Ti Badri
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Jude Alawa
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Francesc López-Giráldez
- Department of Genetics, Yale University, New Haven, CT 06520, USA.,Yale Center for Genome Analysis, Yale University, New Haven, CT 06477, USA
| | - Patricia Gaule
- Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Sang Won Lee
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Jian-Ping Zhang
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Xinxin Nie
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Ala Nassar
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Agedi Boto
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.,Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Dallas B Flies
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Linghua Zheng
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Tae Kon Kim
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA.,Department of Medicine, Yale University, New Haven, CT 06520, USA
| | | | - Jennifer M McNiff
- Department of Dermatology, Yale University, New Haven, CT 06520, USA.,Department of Pathology, Yale University, New Haven, CT 06520, USA
| | - Lieping Chen
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA. .,Department of Dermatology, Yale University, New Haven, CT 06520, USA.,Department of Medicine, Yale University, New Haven, CT 06520, USA
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21
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Lun XK, Bodenmiller B. Profiling Cell Signaling Networks at Single-cell Resolution. Mol Cell Proteomics 2020; 19:744-756. [PMID: 32132232 PMCID: PMC7196580 DOI: 10.1074/mcp.r119.001790] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
Signaling networks process intra- and extracellular information to modulate the functions of a cell. Deregulation of signaling networks results in abnormal cellular physiological states and often drives diseases. Network responses to a stimulus or a drug treatment can be highly heterogeneous across cells in a tissue because of many sources of cellular genetic and non-genetic variance. Signaling network heterogeneity is the key to many biological processes, such as cell differentiation and drug resistance. Only recently, the emergence of multiplexed single-cell measurement technologies has made it possible to evaluate this heterogeneity. In this review, we categorize currently established single-cell signaling network profiling approaches by their methodology, coverage, and application, and we discuss the advantages and limitations of each type of technology. We also describe the available computational tools for network characterization using single-cell data and discuss potential confounding factors that need to be considered in single-cell signaling network analyses.
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Affiliation(s)
- Xiao-Kang Lun
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland; Molecular Life Sciences PhD Program, Life Science Zürich Graduate School, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland.
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22
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Rybakowska P, Alarcón-Riquelme ME, Marañón C. Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry. Comput Struct Biotechnol J 2020; 18:874-886. [PMID: 32322369 PMCID: PMC7163213 DOI: 10.1016/j.csbj.2020.03.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
High-dimensional, single-cell cell technologies revolutionized the way to study biological systems, and polychromatic flow cytometry (FC) and mass cytometry (MC) are two of the drivers of this revolution. As up to 30-50 dimensions respectively can be measured per single-cell, they allow deep phenotyping combined with cellular functions studies, like cytokine production or protein phosphorylation. In parallel, the bioinformatics field develops algorithms that are able to process incoming data and extract the most useful and meaningful biological information. However, the success of automated analysis tools depends on the generation of high-quality data. In this review we present the most recent FC and MC computational approaches that are used to prepare, process and interpret high-content cytometry data. We also underscore proper experimental design as a key step for obtaining good quality data.
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Affiliation(s)
- Paulina Rybakowska
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
| | - Marta E. Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
- Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Concepción Marañón
- GENYO, Centre for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Spain
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23
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Abstract
Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and organisms. The coordination of individual immune cells is essential for the generation of effective immune responses to pathogens while immune tolerance is maintained to protect the host. In rheumatic diseases, when immune responses are dysregulated, pathologically important cells might represent only a small fraction of the immune system. Interrogation of the contributions of individual immune cells to pathogenesis and disease progression should therefore reveal important insights into the complicated aetiology of rheumatic diseases. Technological advances are enabling the high-dimensional dissection of single cells at multiple omics levels, which could facilitate the identification of dysregulated molecular mechanisms in patients with rheumatic diseases and the discovery of new therapeutic targets and biomarkers. The single-cell technologies that have been developed over the past decade and the experimental platforms that enable multi-omics integrative analyses have already made inroads into immunology-related fields of study and have potential for use in rheumatology. Layers of omics data derived from single cells are likely to fundamentally change our understanding of the molecular pathways that underpin the pathogenesis of rheumatic diseases.
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24
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The epigenetic face of lupus: Focus on antigen-presenting cells. Int Immunopharmacol 2020; 81:106262. [PMID: 32045873 DOI: 10.1016/j.intimp.2020.106262] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022]
Abstract
In recent years, epigenetic mechanisms became widely known due to their ability to regulate and maintain physiological processes such as cell growth, development, differentiation and genomic stability. When dysregulated, epigenetic mechanisms, may introduce gene expression changes and disturbance in immune homeostasis leading to autoimmune diseases. Systemic lupus erythematosus (SLE), the most extensively studied autoimmune disorder, has already been correlated with epigenetic modifications, especially in T cells. Since these cell rely on antigen presentation, it may be assumed that erroneous activity of antigen-presenting cells (APCs), culminates in T cell abnormalities. In this review we summarize and discuss the epigenetic modifications in SLE affected APCs, with the focus on dendritic cells (DCs), B cells and monocytes. Unravelling this aspect of SLE pathogenesis, might result in identification of new disease biomarkers and putative therapeutic approaches.
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25
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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: 104] [Impact Index Per Article: 26.0] [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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26
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Schuyler RP, Jackson C, Garcia-Perez JE, Baxter RM, Ogolla S, Rochford R, Ghosh D, Rudra P, Hsieh EWY. Minimizing Batch Effects in Mass Cytometry Data. Front Immunol 2019; 10:2367. [PMID: 31681275 PMCID: PMC6803429 DOI: 10.3389/fimmu.2019.02367] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/20/2019] [Indexed: 01/28/2023] Open
Abstract
Cytometry by Time-Of-Flight (CyTOF) uses antibodies conjugated to isotopically pure metals to identify and quantify a large number of cellular features with single-cell resolution. A barcoding approach allows for 20 unique samples to be pooled and processed together in one tube, reducing the intra-barcode technical variability. However, with only 20 samples per barcode, multiple barcode sets (batches) are required to address questions in robustly powered study designs. A batch adjustment procedure is required to reduce variability across batches and to facilitate direct comparison of runs performed across multiple barcodes run over weeks, months, or years. We describe a method using technical replicates that are included in each run to determine and apply an appropriate adjustment per batch without manual intervention. The use of technical replicate samples (i.e., anchors or reference samples) avoids assumptions of sample homogeneity among batches, and allows direct estimation of batch effects and appropriate adjustment parameters applicable to all samples within a batch. Quantification of cell subpopulations and mean signal intensity pre- and post-adjustment using both manual gating and unsupervised clustering demonstrate substantial mitigation of batch effects in the anchor samples used for this adjustment calculation, and in a second validation set of technical replicates.
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Affiliation(s)
- Ronald P Schuyler
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Conner Jackson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Josselyn E Garcia-Perez
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Ryan M Baxter
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Sidney Ogolla
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Pratyaydipta Rudra
- Department of Statistics, Oklahoma State University, Stillwater, OK, United States
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.,Division of Allergy and Immunology, Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital Colorado, Aurora, CO, United States
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27
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Galli E, Hartmann FJ, Schreiner B, Ingelfinger F, Arvaniti E, Diebold M, Mrdjen D, van der Meer F, Krieg C, Nimer FA, Sanderson N, Stadelmann C, Khademi M, Piehl F, Claassen M, Derfuss T, Olsson T, Becher B. GM-CSF and CXCR4 define a T helper cell signature in multiple sclerosis. Nat Med 2019; 25:1290-1300. [PMID: 31332391 PMCID: PMC6689469 DOI: 10.1038/s41591-019-0521-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022]
Abstract
Cytokine dysregulation is a central driver of chronic inflammatory diseases such as multiple sclerosis (MS). Here we sought to determine the characteristic cellular and cytokine polarization profile in patients with relapsing-remitting multiple sclerosis (RRMS) by high-dimensional single-cell mass cytometry (CyTOF). Using a combination of neural network-based representation learning algorithms, we identified an expanded T helper cell subset in MS patients, characterized by the expression of GM-CSF and the C-X-C chemokine receptor type 4. This cellular signature, which includes expression of very late antigen 4 (VLA4) in peripheral blood, was also enriched in the central nervous system of RRMS patients. In independent validation cohorts, we confirmed that this cell population is increased in MS patients compared to other inflammatory and non-inflammatory conditions. Lastly, we also found the population to be reduced under effective disease-modifying therapy, suggesting that the identified T cell profile represents a specific therapeutic target in MS.
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Affiliation(s)
- Edoardo Galli
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Felix J Hartmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.,Department of Dermatology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Bettina Schreiner
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.,Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Florian Ingelfinger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Eirini Arvaniti
- Institute for Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Diebold
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Dunja Mrdjen
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Franziska van der Meer
- Institut für Neuropathologie, Klinik für Neurologie, Universitätsmedizin Göttingen, Gottingen, Germany
| | - Carsten Krieg
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.,Department of Microbiology and Immunology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Faiez Al Nimer
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Nicholas Sanderson
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Christine Stadelmann
- Institut für Neuropathologie, Klinik für Neurologie, Universitätsmedizin Göttingen, Gottingen, Germany
| | - Mohsen Khademi
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Piehl
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Manfred Claassen
- Institute for Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Derfuss
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
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28
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Toghi Eshghi S, Au-Yeung A, Takahashi C, Bolen CR, Nyachienga MN, Lear SP, Green C, Mathews WR, O'Gorman WE. Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses. Front Immunol 2019; 10:1194. [PMID: 31231371 PMCID: PMC6560168 DOI: 10.3389/fimmu.2019.01194] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/10/2019] [Indexed: 11/17/2022] Open
Abstract
Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data. While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse immune cell populations. We applied a comprehensive 38-parameter mass cytometry panel to human blood and compared the frequencies of 28 immune cell subsets using both conventional bivariate and t-SNE-guided manual gating. t-SNE analysis was capable of stratifying every general cellular lineage and most sub-lineages with high correlation between conventional and t-SNE-guided cell frequency calculations. However, specific immune cell subsets delineated by the manual gating of continuous variables were not fully separated in t-SNE space thus causing discrepancies in subset identification and quantification between these analytical approaches. Overall, these studies highlight the consistency between t-SNE and conventional hand-gating in stratifying general immune cell lineages while demonstrating that particular cell subsets defined by conventional manual gating may be intermingled in t-SNE space.
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Affiliation(s)
- Shadi Toghi Eshghi
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Amelia Au-Yeung
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Chikara Takahashi
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | | | - Maclean N Nyachienga
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Sean P Lear
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Cherie Green
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - W Rodney Mathews
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - William E O'Gorman
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
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29
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McKay PF, Cizmeci D, Aldon Y, Maertzdorf J, Weiner J, Kaufmann SH, Lewis DJ, van den Berg RA, Del Giudice G, Shattock RJ. Identification of potential biomarkers of vaccine inflammation in mice. eLife 2019; 8:46149. [PMID: 31084714 PMCID: PMC6555592 DOI: 10.7554/elife.46149] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022] Open
Abstract
Systems vaccinology approaches have been used successfully to define early signatures of the vaccine-induced immune response. However, the possibility that transcriptomics can also identify a correlate or surrogate for vaccine inflammation has not been fully explored. We have compared four licensed vaccines with known safety profiles, as well as three agonists of Toll-like receptors (TLRs) with known inflammatory potential, to elucidate the transcriptomic profile of an acceptable response to vaccination versus that of an inflammatory reaction. In mice, we looked at the transcriptomic changes in muscle at the injection site, the lymph node that drained the muscle, and the peripheral blood mononuclear cells (PBMCs)isolated from the circulating blood from 4 hr after injection and over the next week. A detailed examination and comparative analysis of these transcriptomes revealed a set of novel biomarkers that are reflective of inflammation after vaccination. These biomarkers are readily measurable in the peripheral blood, providing useful surrogates of inflammation, and provide a way to select candidates with acceptable safety profiles. Measles, whooping cough and other diseases can cause serious illness and death in humans, especially in young children and other vulnerable individuals. Giving people vaccines ‘trains’ their immune system to recognize and fight the microbes that cause the conditions. During an infection, the immune system triggers a set of responses that limit the spread of the infectious agent and eliminate it from the body. This can include swelling of tissues (known as inflammation), which in rare cases, can be life threatening. Inoculations work by sparking a mild immune response in the body. Before a new vaccine is licensed for use, it is thoroughly tested in mice and rodents, and then in human volunteers, to ensure it will cause little or no inflammation. Finding a way to predict early on whether a vaccine candidate will trigger dangerous levels of inflammation would improve this process. To explore this, McKay, Cizmeci et al. injected the muscle tissue of different groups of mice with one of four licensed vaccines which, by definition, cause little or no inflammation. Other groups of animals were given one of three drugs known to trigger inflammation. Over the following seven days the team repeatedly collected blood as well as cells from the muscle tissue and the lymph nodes. These samples were then analysed to find out which genes were switched on or off at any given time. The experiments show that the responses of genes in the blood and lymph cells of the mice are connected to those in the muscle cells. Therefore, blood samples may provide a quick and convenient way to assess how an animal is responding to a potential new vaccine. By comparing the genes switched on or off in response to the different vaccines and drugs, McKay, Cizemeci et al. were able to identify a set of genes (known as “biomarkers”) that are associated with inflammation in animals. These biomarkers can be used to spot early on whether a new treatment is triggering inflammation. The next step would then be to identify a similar or identical set of biomarkers in other animals used in vaccine research, and in humans. Ultimately, this approach could make the assessment of the safety of a new vaccine candidate easier.
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Affiliation(s)
- Paul F McKay
- Department of Medicine, Division of Infectious Diseases, Section of Virology, Imperial College London, London, United Kingdom
| | - Deniz Cizmeci
- Department of Medicine, Division of Infectious Diseases, Section of Virology, Imperial College London, London, United Kingdom
| | - Yoann Aldon
- Department of Medicine, Division of Infectious Diseases, Section of Virology, Imperial College London, London, United Kingdom
| | - Jeroen Maertzdorf
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - January Weiner
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Stefan He Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - David Jm Lewis
- The NIHR Imperial Clinical Research Facility, Imperial Centre for Translational and Experimental Medicine, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, United Kingdom
| | | | | | - Robin J Shattock
- Department of Medicine, Division of Infectious Diseases, Section of Virology, Imperial College London, London, United Kingdom
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30
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Immune Profiling and Precision Medicine in Systemic Lupus Erythematosus. Cells 2019; 8:cells8020140. [PMID: 30744169 PMCID: PMC6406577 DOI: 10.3390/cells8020140] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/24/2019] [Accepted: 02/09/2019] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder with a wide range of clinical symptoms. Enormous progress has been made in the immunological and genetic understanding of SLE. However, the biology of disease heterogeneity in SLE has remained largely unexplored. Human immune profiling studies, helped by recent technological advances especially in single-cell and “omics” analyses, are now shedding light on the cellular and molecular basis of clinical symptoms and disease flares in individual patients. Peripheral blood immunophenotyping analysis with flow cytometry or mass cytometry are identifying responsible cell subsets and markers characteristic of disease heterogeneity. Transcriptome analysis is discovering molecular networks responsible for disease activity, disease subtype and future relapse. In this review, we summarize recent advances in the immune profiling analysis of SLE patients and discuss how they will be used for future precision medicine.
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31
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Bringeland GH, Bader L, Blaser N, Budzinski L, Schulz AR, Mei HE, Myhr KM, Vedeler CA, Gavasso S. Optimization of Receptor Occupancy Assays in Mass Cytometry: Standardization Across Channels with QSC Beads. Cytometry A 2019; 95:314-322. [PMID: 30688025 PMCID: PMC6590231 DOI: 10.1002/cyto.a.23723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/03/2019] [Accepted: 01/08/2019] [Indexed: 01/03/2023]
Abstract
Receptor occupancy, the ratio between amount of drug bound and amount of total receptor on single cells, is a biomarker for treatment response to therapeutic monoclonal antibodies. Receptor occupancy is traditionally measured by flow cytometry. However, spectral overlap in flow cytometry limits the number of markers that can be measured simultaneously. This restricts receptor occupancy assays to the analysis of major cell types, although rare cell populations are of potential therapeutic relevance. We therefore developed a receptor occupancy assay suitable for mass cytometry. Measuring more markers than currently available in flow cytometry allows simultaneous receptor occupancy assessment and high-parameter immune phenotyping in whole blood, which should yield new insights into disease activity and therapeutic effects. However, varying sensitivity across the mass cytometer detection range may lead to misinterpretation of the receptor occupancy when drug and receptor are detected in different channels. In this report, we describe a method for optimization of mass cytometry receptor occupancy measurements by using antibody-binding quantum simply cellular (QSC) beads for standardization across channels with different sensitivities. We evaluated the method in a mass cytometry-based receptor occupancy assay for natalizumab, a therapeutic antibody used in multiple sclerosis treatment that binds to α4-integrin, which is expressed on leukocyte cell surfaces. Peripheral blood leukocytes from a treated patient were stained with a panel containing metal-conjugated antibodies for detection of natalizumab and α4-integrin. QSC beads with known antibody binding capacity were stained with the same metal-conjugated antibodies and were used to standardize the signal intensity in the leukocyte sample before calculating receptor occupancy. We found that QSC bead standardization across channels corrected for sensitivity differences for detection of drug and receptor and generated more accurate results than observed without standardization. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Gerd Haga Bringeland
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Lucius Bader
- Bergen group of Epidemiology and Biomarkers in Rheumatic Disease, Department of Rheumatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nello Blaser
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Lisa Budzinski
- German Rheumatism Research Centre Berlin (DRFZ), Berlin, Germany
| | - Axel R Schulz
- German Rheumatism Research Centre Berlin (DRFZ), Berlin, Germany
| | - Henrik E Mei
- German Rheumatism Research Centre Berlin (DRFZ), Berlin, Germany
| | - Kjell-Morten Myhr
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Christian A Vedeler
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Sonia Gavasso
- Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
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32
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Galli E, Friebel E, Ingelfinger F, Unger S, Núñez NG, Becher B. The end of omics? High dimensional single cell analysis in precision medicine. Eur J Immunol 2019; 49:212-220. [DOI: 10.1002/eji.201847758] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 11/17/2018] [Accepted: 01/15/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Edoardo Galli
- Institute of Experimental ImmunologyUniversity of Zurich Zurich Switzerland
| | - Ekaterina Friebel
- Institute of Experimental ImmunologyUniversity of Zurich Zurich Switzerland
| | | | - Susanne Unger
- Institute of Experimental ImmunologyUniversity of Zurich Zurich Switzerland
| | | | - Burkhard Becher
- Institute of Experimental ImmunologyUniversity of Zurich Zurich Switzerland
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33
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Abstract
Sample barcoding is a powerful method for harmonizing mass cytometry data. By assigning a unique combination of barcode labels to each cell sample, a set of individual samples can be pooled and further processed and acquired as a large, single sample. For assays that require uncompromised profiling of cell-surface markers on live cells, barcoding by metal-labeled antibodies targeting cell-surface epitopes is the barcoding approach of choice. Here we provide an optimized and validated protocol for cell-surface barcoding of ten PBMC samples with palladium-labeled β2-microglobulin (B2M) antibodies used in a 5-choose-2 barcoding scheme, for subsequent immune phenotyping by mass cytometry. We further provide details on the generation of palladium-labeled antibodies utilizing amine-reactive isothiocyanobenzyl-EDTA (ITCB-EDTA) that permits the implementation of antibody-based barcoding not interfering with lanthanide channels typically used for analyte detection in mass cytometry assays.
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Affiliation(s)
- Axel Ronald Schulz
- Mass Cytometry Lab, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Henrik E Mei
- Mass Cytometry Lab, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Berlin, Germany.
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34
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Brodin P. The biology of the cell - insights from mass cytometry. FEBS J 2018; 286:1514-1522. [PMID: 30390411 DOI: 10.1111/febs.14693] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/02/2018] [Indexed: 12/15/2022]
Abstract
In single-cell biology there is an ongoing push toward more and more comprehensive measurements made in individual cells. By combining measurements of proteins, mRNA, genetic, and epigenetic traits, in contexts of cell stimulation or drug treatment, novel single-cell analyses will help understand the determinants of cellular identity, differentiation decisions, and regulatory mechanisms governing cellular function in health and disease. Mass cytometry is a flexible methodology not only developed toward this aim, allowing analyses of cells in suspension such as blood but also extended for the analyses of tissue sections. Here, I will discuss the different measurements possible by mass cytometry and not only discuss its potential but also its limitations now and in the years to come.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Unit of Clinical Pediatrics, Department of Women's and Children's health, Karolinska Institutet, Solna, Sweden.,Department of Newborn Medicine, Karolinska University Hospital, Solna, Sweden
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35
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Devine RD, Sekhri P, Behbehani GK. Effect of storage time and temperature on cell cycle analysis by mass cytometry. Cytometry A 2018; 93:1141-1149. [PMID: 30378741 DOI: 10.1002/cyto.a.23630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/29/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022]
Abstract
Cell cycle analysis is a recognized and important application of flow cytometry and, more recently, mass cytometry (MCM). Both technologies have been utilized for analysis of the cell cycle state of ex vivo samples from patients with hematologic malignancies. Clinical samples are frequently stored for hours at room temperature or cryogenically frozen before processing and analysis; however, how these processing methods alter cell cycle state is not well described. To understand how storage time and temperature affect the analysis of cell cycle distribution by MCM, two leukemia cell lines, HL-60 and MOLM13, and primary human cells from three human bone marrow aspirates were stored and frozen under a variety of conditions that are likely to be encountered in a clinical setting. Our findings indicate that short delays in sample processing (less than 1 h), have little to no effect on cell cycle distribution, while longer delays or cryopreservation cause significant disruptions to the cell cycle fraction characterized by consistent reductions in IdU incorporation and variable alterations in other cell cycle phases. Analysis of the recovery of cryopreserved leukemia cell lines and marrow cells demonstrated that cell cycle alterations persist for at least 48 h after thawing. Our findings demonstrate that accurate cell cycle analysis requires that samples be processed rapidly after collection, and that cryopreservation significantly alters cell cycle fractions. Measurement of IdU incorporation was the most sensitive to both delays in processing and cryopreservation, while estimation of the total cycling cell fraction using Ki-67 or phosphorylated retinoblastoma protein were least altered by the conditions tested. These findings provide guidance for the ideal approach to collection of samples for cell cycle analysis and can aid interpretation of cell cycle data from samples that cannot be collected under ideal circumstances. © 2018 International Society for Advancement of Cytometry.
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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, 43210
| | - Palak Sekhri
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
| | - Gregory K Behbehani
- Department of Medicine, Division of Hematology, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, 43210
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36
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Baxter RM, Kong DS, Garcia-Perez JE, O'Gorman WE, Hsieh EWY. Single-cell Analysis of Immunophenotype and Cytokine Production in Peripheral Whole Blood via Mass Cytometry. J Vis Exp 2018. [PMID: 30010641 DOI: 10.3791/57780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cytokines play a pivotal role in the pathogenesis of autoimmune diseases. Hence, the measurement of cytokine levels has been the focus of multiple studies in an attempt to understand the precise mechanisms that lead to the breakdown of self-tolerance and subsequent autoimmunity. Approaches thus far have been based on the study of one specific aspect of the immune system (a single or few cell types or cytokines), and do not offer a global assessment of complex autoimmune disease. While patient sera-based studies have afforded important insights into autoimmunity, they do not provide the specific cellular source of the dysregulated cytokines detected. A comprehensive single-cell approach to evaluate cytokine production in multiple immune cell subsets, within the context of "intrinsic" patient-specific plasma circulating factors, is described here. This approach enables monitoring of the patient-specific immune phenotype (surface markers) and function (cytokines), either in its native "intrinsic pathogenic" disease state, or in the presence of therapeutic agents (in vivo or ex vivo).
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Affiliation(s)
- Ryan M Baxter
- Department of Immunology and Microbiology, University of Colorado School of Medicine
| | - Daniel S Kong
- Department of Immunology and Microbiology, University of Colorado School of Medicine
| | | | | | - Elena W Y Hsieh
- Department of Immunology and Microbiology, University of Colorado School of Medicine; Department of Pediatrics, Division of Allergy and Immunology, University of Colorado School of Medicine;
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37
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Li Y, Wu T. Proteomic approaches for novel systemic lupus erythematosus (SLE) drug discovery. Expert Opin Drug Discov 2018; 13:765-777. [DOI: 10.1080/17460441.2018.1480718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yaxi Li
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
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38
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Johnson JL, Vahedi G. Do Memory CD4 T Cells Keep Their Cell-Type Programming: Plasticity versus Fate Commitment? Epigenome: A Dynamic Vehicle for Transmitting and Recording Cytokine Signaling. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028779. [PMID: 28432132 DOI: 10.1101/cshperspect.a028779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CD4+ T cells are critical for the elimination of an immense array of microbial pathogens. Although there are aspects of helper T-cell differentiation that can be modeled as a classic cell-fate commitment, CD4+ T cells also maintain considerable flexibility in their transcriptional program. Here, we present an overview of chromatin biology during cellular reprogramming and, within this context, envision how the scope of cellular reprogramming may be expanded to further our understanding of the controversy surrounding CD4+ T lymphocyte plasticity or determinism.
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Affiliation(s)
- John L Johnson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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39
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Hedrich CM, Smith EMD, Beresford MW. Juvenile-onset systemic lupus erythematosus (jSLE) - Pathophysiological concepts and treatment options. Best Pract Res Clin Rheumatol 2018; 31:488-504. [PMID: 29773269 DOI: 10.1016/j.berh.2018.02.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The systemic autoimmune/inflammatory condition systemic lupus erythematosus (SLE) manifests before the age of 16 years in 10-20% of all cases. Clinical courses are more severe, and organ complications are more common in patients with juvenile SLE. Varying gender distribution in different age groups and increasing severity with younger age and the presence of monogenic disease in early childhood indicate distinct differences in the pathophysiology of juvenile versus adult-onset SLE. Regardless of these differences, classification criteria and treatment options are identical. In this article, we discuss age-specific pathomechanisms of juvenile-onset SLE, which are currently available and as future treatment options, and propose reclassification of different forms of SLE along the inflammatory spectrum from autoinflammation to autoimmunity.
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Affiliation(s)
- Christian M Hedrich
- Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK.
| | - Eve M D Smith
- Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK
| | - Michael W Beresford
- Department of Women's & Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK; Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, UK
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40
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Starchenko A, Lauffenburger DA. In vivo systems biology approaches to chronic immune/inflammatory pathophysiology. Curr Opin Biotechnol 2018; 52:9-16. [PMID: 29494996 DOI: 10.1016/j.copbio.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/11/2018] [Indexed: 12/19/2022]
Abstract
Systems biology offers an emphasis on integrative computational analysis of complex multi-component processes to enhance capability for predictive insights concerning operation of those processes. The immune system represents a prominent arena in which such processes are manifested for vital roles in physiology and pathology, encompassing dozens of cell types and hundreds of reciprocal interactions. Chronic, debilitating pathologies involving immune system dysregulation have become recognized as increasing in incidence over recent decades. While clinical consequences of immune dysregulation in such pathologies are well characterized, treatment options remain limited and focus on ameliorating symptoms. Because it is difficult to recapitulate more than a severely limited facet of the immune system in vitro, application of systems biology approaches to autoimmune and inflammatory pathophysiology in vivo has opened a new door toward discerning disease sub-groups and developing associated stratification strategies for patient treatment. In particular, early instances of these approaches have demonstrated advances in uncovering previously under-appreciated dysregulation of signaling networks between immune system and tissue cells, raising promise for improving upon current therapeutic approaches.
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Affiliation(s)
- Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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41
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Arts RJW, Joosten LAB, Netea MG. The Potential Role of Trained Immunity in Autoimmune and Autoinflammatory Disorders. Front Immunol 2018. [PMID: 29515591 PMCID: PMC5826224 DOI: 10.3389/fimmu.2018.00298] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During induction of trained immunity, monocytes and macrophages undergo a functional and transcriptional reprogramming toward increased activation. Important rewiring of cellular metabolism of the myeloid cells takes place during induction of trained immunity, including a shift toward glycolysis induced through the mTOR pathway, as well as glutaminolysis and cholesterol synthesis. Subsequently, this leads to modulation of the function of epigenetic enzymes, resulting in important changes in chromatin architecture that enables increased gene transcription. However, in addition to the beneficial effects of trained immunity as a host defense mechanism, we hypothesize that trained immunity also plays a deleterious role in the induction and/or maintenance of autoimmune and autoinflammatory diseases if inappropriately activated.
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Affiliation(s)
- Rob J W Arts
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Medical Genetics, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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42
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Gonzalez VD, Samusik N, Chen TJ, Savig ES, Aghaeepour N, Quigley DA, Huang YW, Giangarrà V, Borowsky AD, Hubbard NE, Chen SY, Han G, Ashworth A, Kipps TJ, Berek JS, Nolan GP, Fantl WJ. Commonly Occurring Cell Subsets in High-Grade Serous Ovarian Tumors Identified by Single-Cell Mass Cytometry. Cell Rep 2018; 22:1875-1888. [PMID: 29444438 PMCID: PMC8556706 DOI: 10.1016/j.celrep.2018.01.053] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 12/18/2017] [Accepted: 01/17/2018] [Indexed: 01/16/2023] Open
Abstract
We have performed an in-depth single-cell phenotypic characterization of high-grade serous ovarian cancer (HGSOC) by multiparametric mass cytometry (CyTOF). Using a CyTOF antibody panel to interrogate features of HGSOC biology, combined with unsupervised computational analysis, we identified noteworthy cell types co-occurring across the tumors. In addition to a dominant cell subset, each tumor harbored rarer cell phenotypes. One such group co-expressed E-cadherin and vimentin (EV), suggesting their potential role in epithelial mesenchymal transition, which was substantiated by pairwise correlation analyses. Furthermore, tumors from patients with poorer outcome had an increased frequency of another rare cell type that co-expressed vimentin, HE4, and cMyc. These poorer-outcome tumors also populated more cell phenotypes, as quantified by Simpson's diversity index. Thus, despite the recognized genomic complexity of the disease, the specific cell phenotypes uncovered here offer a focus for therapeutic intervention and disease monitoring.
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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 94305, USA
| | - Nikolay Samusik
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tiffany J Chen
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erica S Savig
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nima Aghaeepour
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 Third Street, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Ying-Wen Huang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Valeria Giangarrà
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander D Borowsky
- Center for Comparative Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Pathology and Laboratory Medicine, Comprehensive Cancer Center, University of California, Davis School of Medicine, Sacramento, CA 95817, USA
| | - Neil E Hubbard
- Center for Comparative Medicine, University of California, Davis, Davis, CA 95616, USA; Department of Pathology and Laboratory Medicine, Comprehensive Cancer Center, University of California, Davis School of Medicine, Sacramento, CA 95817, USA
| | - Shih-Yu Chen
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Guojun Han
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 Third Street, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, 1450 Third Street, San Francisco, CA 94158, USA
| | - Thomas J Kipps
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jonathan S Berek
- Stanford Comprehensive Cancer Institute and Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J Fantl
- Stanford Comprehensive Cancer Institute and Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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43
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44
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Muehling LM, Lawrence MG, Woodfolk JA. Pathogenic CD4 + T cells in patients with asthma. J Allergy Clin Immunol 2017; 140:1523-1540. [PMID: 28442213 PMCID: PMC5651193 DOI: 10.1016/j.jaci.2017.02.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 02/07/2017] [Accepted: 02/20/2017] [Indexed: 02/08/2023]
Abstract
Asthma encompasses a variety of clinical phenotypes that involve distinct T cell-driven inflammatory processes. Improved understanding of human T-cell biology and the influence of innate cytokines on T-cell responses at the epithelial barrier has led to new asthma paradigms. This review captures recent knowledge on pathogenic CD4+ T cells in asthmatic patients by drawing on observations in mouse models and human disease. In patients with allergic asthma, TH2 cells promote IgE-mediated sensitization, airway hyperreactivity, and eosinophilia. Here we discuss recent discoveries in the myriad molecular pathways that govern the induction of TH2 differentiation and the critical role of GATA-3 in this process. We elaborate on how cross-talk between epithelial cells, dendritic cells, and innate lymphoid cells translates to T-cell outcomes, with an emphasis on the actions of thymic stromal lymphopoietin, IL-25, and IL-33 at the epithelial barrier. New concepts on how T-cell skewing and epitope specificity are shaped by multiple environmental cues integrated by dendritic cell "hubs" are discussed. We also describe advances in understanding the origins of atypical TH2 cells in asthmatic patients, the role of TH1 cells and other non-TH2 types in asthmatic patients, and the features of T-cell pathogenicity at the single-cell level. Progress in technologies that enable highly multiplexed profiling of markers within a single cell promise to overcome barriers to T-cell discovery in human asthmatic patients that could transform our understanding of disease. These developments, along with novel T cell-based therapies, position us to expand the assortment of molecular targets that could facilitate personalized treatments.
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Affiliation(s)
- Lyndsey M Muehling
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Monica G Lawrence
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Judith A Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va.
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45
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Cepika AM, Banchereau R, Segura E, Ohouo M, Cantarel B, Goller K, Cantrell V, Ruchaud E, Gatewood E, Nguyen P, Gu J, Anguiano E, Zurawski S, Baisch JM, Punaro M, Baldwin N, Obermoser G, Palucka K, Banchereau J, Amigorena S, Pascual V. A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis. J Exp Med 2017; 214:3449-3466. [PMID: 28935693 PMCID: PMC5679164 DOI: 10.1084/jem.20170412] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 07/25/2017] [Accepted: 09/08/2017] [Indexed: 12/26/2022] Open
Abstract
The etiology of autoinflammation in systemic juvenile idiopathic arthritis is unclear. Cepika et al. use integrated analysis of multidimensional blood stimulation data, applied to patients while off treatment and in complete remission, to reveal underlying cellular and molecular mechanisms that might predispose to disease. The etiology of sporadic human chronic inflammatory diseases remains mostly unknown. To fill this gap, we developed a strategy that simultaneously integrates blood leukocyte responses to innate stimuli at the transcriptional, cellular, and secreted protein levels. When applied to systemic juvenile idiopathic arthritis (sJIA), an autoinflammatory disease of unknown etiology, this approach identified gene sets associated with specific cytokine environments and activated leukocyte subsets. During disease remission and off treatment, sJIA patients displayed dysregulated responses to TLR4, TLR8, and TLR7 stimulation. Isolated sJIA monocytes underexpressed the IL-1 inhibitor aryl hydrocarbon receptor (AHR) at baseline and accumulated higher levels of intracellular IL-1β after stimulation. Supporting the demonstration that AHR down-regulation skews monocytes toward macrophage differentiation, sJIA monocytes differentiated in vitro toward macrophages, away from the dendritic cell phenotype. This might contribute to the increased incidence of macrophage activation syndrome in these patients. Integrated analysis of high-dimensional data can thus unravel immune alterations predisposing to complex inflammatory diseases.
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Affiliation(s)
| | | | - Elodie Segura
- Institut National de la Santé et de la Recherche Medicale U932, Institut Curie, PSL Research University, Paris, France
| | - Marina Ohouo
- Baylor Institute for Immunology Research, Dallas, TX
| | | | | | | | - Emily Ruchaud
- Baylor Institute for Immunology Research, Dallas, TX
| | | | - Phuong Nguyen
- Baylor Institute for Immunology Research, Dallas, TX
| | - Jinghua Gu
- Baylor Institute for Immunology Research, Dallas, TX
| | | | | | | | | | | | | | - Karolina Palucka
- Baylor Institute for Immunology Research, Dallas, TX.,The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Sebastian Amigorena
- Institut National de la Santé et de la Recherche Medicale U932, Institut Curie, PSL Research University, Paris, France
| | - Virginia Pascual
- Baylor Institute for Immunology Research, Dallas, TX .,University of Texas Southwestern Medical Center, Dallas, TX.,Texas Scottish Rite Hospital for Children, Dallas, TX
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Identification of long non-coding RNAs GAS5, linc0597 and lnc-DC in plasma as novel biomarkers for systemic lupus erythematosus. Oncotarget 2017; 8:23650-23663. [PMID: 28423570 PMCID: PMC5410334 DOI: 10.18632/oncotarget.15569] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 01/31/2017] [Indexed: 01/09/2023] Open
Abstract
Despite increasing evidence that long non-coding RNAs (lncRNAs) widely take part in human diseases, the role of lncRNAs in systemic lupus erythematosus (SLE) is largely unknown. In this study, we performed a two-stage study to explore the plasma levels of five lncRNAs (GAS5, linc0949, linc0597, HOTAIRM1 and lnc-DC) and their potential as SLE biomarkers. Compared with healthy controls, plasma levels of GAS5 and lnc-DC were significantly decreased (P < 0.001 and P = 0.002, respectively) while linc0597 were overexpressed in SLE patients (P < 0.001). When SLE patients were divided into SLE without nephritis and lupus nephritis (LN), the levels of lnc-DC were significantly higher in LN compared with SLE without nephritis (P = 0.018), but no significant difference in levels of GAS5 and linc0597 were found between LN and SLE without nephritis; plasma linc0949 level showed no significant difference in all comparisons. Further evaluation on potential biomarkers showed that GAS5, linc0597 and lnc-DC may specifically identify patients with SLE, the combination of GAS5 and linc0597 provided better diagnostic accuracy; lnc-DC may discriminate LN from SLE without nephritis. In summary, GAS5, linc0597 and lnc-DC in plasma could be potential biomarkers for SLE.
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47
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Novel tools for primary immunodeficiency diagnosis: making a case for deep profiling. Curr Opin Allergy Clin Immunol 2017; 16:549-556. [PMID: 27749361 DOI: 10.1097/aci.0000000000000319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW This review gives an overview of the systems-immunology single-cell proteomic and transcriptomic approaches that can be applied to study primary immunodeficiency. It also introduces recent advances in multiparameter tissue imaging, which allows extensive immune phenotyping in disease-affected tissue. RECENT FINDINGS Mass cytometry is a variation of flow cytometry that uses rare earth metal isotopes instead of fluorophores as tags bound to antibodies, allowing simultaneous measurement of over 40 parameters per single-cell. Mass cytomety enables comprehensive single-cell immunophenotyping and functional assessments, capturing the complexity of the immune system, and the molecularly heterogeneous consequences of primary immunodeficiency defects. Protein epitopes and transcripts can be simultaneously detected allowing immunophenotype and gene expression evaluation in mixed cell populations. Multiplexed epitope imaging has the potential to provide extensive phenotypic characterization at the subcellular level, in the context of 3D tissue microenvironment. SUMMARY Mass cytometry and multiplexed epitope imaging can complement genetic methods in diagnosis and study of the pathogenesis of primary immunodeficiencies. The ability to understand the effect of a specific defect across multiple immune cell types and pathways, and in affected tissues, may provide new insight into tissue-specific disease pathogenesis and evaluate effects of therapeutic interventions.
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48
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Aghaeepour N, Kin C, Ganio EA, Jensen KP, Gaudilliere DK, Tingle M, Tsai A, Lancero HL, Choisy B, McNeil LS, Okada R, Shelton AA, Nolan GP, Angst MS, Gaudilliere BL. Deep Immune Profiling of an Arginine-Enriched Nutritional Intervention in Patients Undergoing Surgery. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 199:ji1700421. [PMID: 28794234 PMCID: PMC5807249 DOI: 10.4049/jimmunol.1700421] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/11/2017] [Indexed: 01/08/2023]
Abstract
Application of high-content immune profiling technologies has enormous potential to advance medicine. Whether these technologies reveal pertinent biology when implemented in interventional clinical trials is an important question. The beneficial effects of preoperative arginine-enriched dietary supplements (AES) are highly context specific, as they reduce infection rates in elective surgery, but possibly increase morbidity in critically ill patients. This study combined single-cell mass cytometry with the multiplex analysis of relevant plasma cytokines to comprehensively profile the immune-modifying effects of this much-debated intervention in patients undergoing surgery. An elastic net algorithm applied to the high-dimensional mass cytometry dataset identified a cross-validated model consisting of 20 interrelated immune features that separated patients assigned to AES from controls. The model revealed wide-ranging effects of AES on innate and adaptive immune compartments. Notably, AES increased STAT1 and STAT3 signaling responses in lymphoid cell subsets after surgery, consistent with enhanced adaptive mechanisms that may protect against postsurgical infection. Unexpectedly, AES also increased ERK and P38 MAPK signaling responses in monocytic myeloid-derived suppressor cells, which was paired with their pronounced expansion. These results provide novel mechanistic arguments as to why AES may exert context-specific beneficial or adverse effects in patients with critical illness. This study lays out an analytical framework to distill high-dimensional datasets gathered in an interventional clinical trial into a fairly simple model that converges with known biology and provides insight into novel and clinically relevant cellular mechanisms.
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Affiliation(s)
- Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Cindy Kin
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94121
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Kent P Jensen
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94121; and
| | - Dyani K Gaudilliere
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94121
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Amy Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Hope L Lancero
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Benjamin Choisy
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Leslie S McNeil
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Robin Okada
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Andrew A Shelton
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94121
| | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94121
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121
| | - Brice L Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94121;
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49
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Tsokos GC, Lo MS, Costa Reis P, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol 2017; 12:716-730. [PMID: 27872476 DOI: 10.1038/nrrheum.2016.186] [Citation(s) in RCA: 743] [Impact Index Per Article: 106.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aetiology of systemic lupus erythematosus (SLE) is multifactorial, and includes contributions from the environment, stochastic factors, and genetic susceptibility. Great gains have been made in understanding SLE through the use of genetic variant identification, mouse models, gene expression studies, and epigenetic analyses. Collectively, these studies support the concept that defective clearance of immune complexes and biological waste (such as apoptotic cells), neutrophil extracellular traps, nucleic acid sensing, lymphocyte signalling, and interferon production pathways are all central to loss of tolerance and tissue damage. Increased understanding of the pathogenesis of SLE is driving a renewed interest in targeted therapy, and researchers are now on the verge of developing targeted immunotherapy directed at treating either specific organ system involvement or specific subsets of patients with SLE. Accordingly, this Review places these insights within the context of our current understanding of the pathogenesis of SLE and highlights pathways that are ripe for therapeutic targeting.
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Affiliation(s)
- George C Tsokos
- Division of Rheumatology, Beth Israel Deaconess Medical Center, Harvard Medical School, 110 Francis Street, Boston, Massachusetts 02215, USA
| | - Mindy S Lo
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
| | - Patricia Costa Reis
- Department of Pediatrics, Lisbon Medical School, Lisbon University, Santa Maria Hospital, Avenida Professor Egas Moniz, 1649-035 Lisbon, Portugal
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
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50
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O'Gorman WE, Kong DS, Balboni IM, Rudra P, Bolen CR, Ghosh D, Davis MM, Nolan GP, Hsieh EWY. Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients. J Autoimmun 2017; 81:S0896-8411(16)30412-7. [PMID: 28389038 PMCID: PMC5628110 DOI: 10.1016/j.jaut.2017.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 12/11/2022]
Abstract
Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease with heightened disease severity in children. The incomplete understanding of the precise cellular and molecular events that drive disease activity pose a significant hurdle to the development of targeted therapeutic agents. Here, we performed single-cell phenotypic and functional characterization of pediatric SLE patients and healthy controls blood via mass cytometry. We identified a distinct CD14hi monocyte cytokine signature, with increased levels of monocyte chemoattractant protein-1 (MCP1), macrophage inflammatory protein-1β (Mip1β), and interleukin-1 receptor antagonist (IL-1RA). This signature was shared by every clinically heterogeneous patient, and reproduced in healthy donors' blood upon ex-vivo exposure to plasma from clinically active patients only. This SLE-plasma induced signature was abrogated by JAK1/JAK2 selective inhibition. This study demonstrates the utility of mass cytometry to evaluate immune dysregulation in pediatric autoimmunity, by identification of a multi-parametric immune signature that can be further dissected to delineate the events that drive disease pathogenesis.
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Affiliation(s)
- W E O'Gorman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - D S Kong
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - I M Balboni
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - P Rudra
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - C R Bolen
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - D Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - M M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - G P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - E W Y Hsieh
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Division of Allergy and Immunology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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