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Zhao M, Cheng Y, Gao J, Zhou F. Single-cell mass cytometry in immunological skin diseases. Front Immunol 2024; 15:1401102. [PMID: 39081313 PMCID: PMC11286489 DOI: 10.3389/fimmu.2024.1401102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Immune-related skin diseases represent a collective of dermatological disorders intricately linked to dysfunctional immune system processes. These conditions are primarily characterized by an immoderate activation of the immune system or deviant immune responses, involving diverse immune components including immune cells, antibodies, and inflammatory mediators. However, the precise molecular dysregulation underlying numerous individual cases of these diseases and unique subsets respond under disease conditions remains elusive. Comprehending the mechanisms and determinants governing the homeostasis and functionality of diseases could offer potential therapeutic opportunities for intervention. Mass cytometry enables precise and high-throughput quantitative measurement of proteins within individual cells by utilizing antibodies labeled with rare heavy metal isotopes. Imaging mass cytometry employs mass spectrometry to obtain spatial information on cell-to-cell interactions within tissue sections, simultaneously utilizing more than 40 markers. The application of single-cell mass cytometry presents a unique opportunity to conduct highly multiplexed analysis at the single-cell level, thereby revolutionizing our understanding of cell population heterogeneity and hierarchy, cellular states, multiplexed signaling pathways, proteolysis products, and mRNA transcripts specifically in the context of many autoimmune diseases. This information holds the potential to offer novel approaches for the diagnosis, prognostic assessment, and monitoring responses to treatment, thereby enriching our strategies in managing the respective conditions. This review summarizes the present-day utilization of single-cell mass cytometry in studying immune-related skin diseases, highlighting its advantages and limitations. This technique will become increasingly prevalent in conducting extensive investigations into these disorders, ultimately yielding significant contributions to their accurate diagnosis and efficacious therapeutic interventions.
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Affiliation(s)
- Mingming Zhao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yuqi Cheng
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Jinping Gao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Fusheng Zhou
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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Lindblom J, Beretta L, Borghi MO, Alarcón-Riquelme ME, Parodis I. Serum profiling identifies CCL8, CXCL13, and IL-1RA as markers of active disease in patients with systemic lupus erythematosus. Front Immunol 2023; 14:1257085. [PMID: 38098483 PMCID: PMC10720584 DOI: 10.3389/fimmu.2023.1257085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is a clinically heterogeneous disease that presents a challenge for clinicians. To identify potential biomarkers for diagnosis and disease activity in SLE, we investigated a selected yet broad panel of cytokines and autoantibodies in patients with SLE, healthy controls (HC), and patients with other autoimmune diseases (AIDs). Methods Serum samples from 422 SLE patients, 546 HC, and 1223 other AIDs were analysed within the frame of the European PRECISESADS project (NTC02890121). Cytokine levels were determined using Luminex panels, and autoantibodies using different immunoassays. Results Of the 83 cytokines analysed, 29 differed significantly between patients with SLE and HC. Specifically, CCL8, CXCL13, and IL-1RA levels were elevated in patients with active, but not inactive, SLE versus HC, as well as in patients with SLE versus other AIDs. The levels of these cytokines also correlated with SLE Disease Activity Index 2000 (SLEDAI-2K) scores, among five other cytokines. Overall, the occurrence of autoantibodies was similar across SLEDAI-2K organ domains, and the correlations between autoantibodies and activity in different organ domains were weak. Discussion Our findings suggest that, upon validation, CCL8, CXCL13, and IL-1RA could serve as promising serum biomarkers of activity in SLE.
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Affiliation(s)
- Julius Lindblom
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Maria Orietta Borghi
- IRCCS Istituto Auxologico Italiano, Immunorheumatology Research Laboratory, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Marta E. Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada/Andalusian Regional Government, Medical Genomics, Granada, Spain
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ioannis Parodis
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Gastroenterology, Dermatology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
- Department of Rheumatology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Baxter RM, Wang CS, Garcia-Perez JE, Kong DS, Coleman BM, Larchenko V, Schuyler RP, Jackson C, Ghosh T, Rudra P, Paul D, Claassen M, Rochford R, Cambier JC, Ghosh D, Cooper JC, Smith MJ, Hsieh EWY. Expansion of extrafollicular B and T cell subsets in childhood-onset systemic lupus erythematosus. Front Immunol 2023; 14:1208282. [PMID: 37965329 PMCID: PMC10641733 DOI: 10.3389/fimmu.2023.1208282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
Introduction Most childhood-onset SLE patients (cSLE) develop lupus nephritis (cLN), but only a small proportion achieve complete response to current therapies. The prognosis of children with LN and end-stage renal disease is particularly dire. Mortality rates within the first five years of renal replacement therapy may reach 22%. Thus, there is urgent need to decipher and target immune mechanisms that drive cLN. Despite the clear role of autoantibody production in SLE, targeted B cell therapies such as rituximab (anti-CD20) and belimumab (anti-BAFF) have shown only modest efficacy in cLN. While many studies have linked dysregulation of germinal center formation to SLE pathogenesis, other work supports a role for extrafollicular B cell activation in generation of pathogenic antibody secreting cells. However, whether extrafollicular B cell subsets and their T cell collaborators play a role in specific organ involvement in cLN and/or track with disease activity remains unknown. Methods We analyzed high-dimensional mass cytometry and gene expression data from 24 treatment naïve cSLE patients at the time of diagnosis and longitudinally, applying novel computational tools to identify abnormalities associated with clinical manifestations (cLN) and disease activity (SLEDAI). Results cSLE patients have an extrafollicular B cell expansion signature, with increased frequency of i) DN2, ii) Bnd2, iii) plasmablasts, and iv) peripheral T helper cells. Most importantly, we discovered that this extrafollicular signature correlates with disease activity in cLN, supporting extrafollicular T/B interactions as a mechanism underlying pediatric renal pathogenesis. Discussion This study integrates established and emerging themes of extrafollicular B cell involvement in SLE by providing evidence for extrafollicular B and peripheral T helper cell expansion, along with elevated type 1 IFN activation, in a homogeneous cohort of treatment-naïve cSLE patients, a point at which they should display the most extreme state of their immune dysregulation.
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Affiliation(s)
- Ryan M. Baxter
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Christine S. Wang
- Department of Pediatrics, Section of Rheumatology, School of Medicine, University of Colorado, Children’s Hospital Colorado, Aurora, CO, United States
| | - Josselyn E. Garcia-Perez
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Daniel S. Kong
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Brianne M. Coleman
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Valentyna Larchenko
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Ronald P. Schuyler
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Conner Jackson
- Center for Innovative Design and Analysis, School of Public Health, University of Colorado, Aurora, CO, United States
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, School of Public Health, University of Colorado, Aurora, CO, United States
| | - Pratyaydipta Rudra
- Department of Statistics, Oklahoma State University, Stillwater, OK, United States
| | - Debdas Paul
- Clinical Bioinformatics & Machine Learning in Translational Single-Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Manfred Claassen
- Clinical Bioinformatics & Machine Learning in Translational Single-Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Rosemary Rochford
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - John C. Cambier
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, School of Public Health, University of Colorado, Aurora, CO, United States
| | - Jennifer C. Cooper
- Department of Pediatrics, Section of Rheumatology, School of Medicine, University of Colorado, Children’s Hospital Colorado, Aurora, CO, United States
| | - Mia J. Smith
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
- Department of Pediatrics, Barbara Davis Center for Diabetes, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Elena W. Y. Hsieh
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, Aurora, CO, United States
- Department of Pediatrics, Section of Allergy and Immunology, School of Medicine, University of Colorado, Children’s Hospital Colorado, Aurora, CO, United States
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Koladiya A, Davis KL. Advances in Clinical Mass Cytometry. Clin Lab Med 2023; 43:507-519. [PMID: 37481326 DOI: 10.1016/j.cll.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The advent of high-dimensional single-cell technologies has enabled detection of cellular heterogeneity and functional diversity of immune cells during health and disease conditions. Because of its multiplexing capabilities and limited compensation requirements, mass cytometry or cytometry by time of flight (CyTOF) has played a superior role in immune monitoring compared with flow cytometry. Further, it has higher throughput and lower cost compared with other single-cell techniques. Several published articles have utilized CyTOF to identify cellular phenotypes and features associated with disease outcomes. This article introduces CyTOF-based assays to profile immune cell-types, cell-states, and their applications in clinical research.
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Affiliation(s)
- Abhishek Koladiya
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Cancer Cell Therapy, Stanford University, Stanford, CA, USA.
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Lui VG, Ghosh T, Rymaszewski A, Chen S, Baxter RM, Kong DS, Ghosh D, Routes JM, Verbsky JW, Hsieh EWY. Dysregulated Lymphocyte Antigen Receptor Signaling in Common Variable Immunodeficiency with Granulomatous Lymphocytic Interstitial Lung Disease. J Clin Immunol 2023; 43:1311-1325. [PMID: 37093407 PMCID: PMC10524976 DOI: 10.1007/s10875-023-01485-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/04/2023] [Indexed: 04/25/2023]
Abstract
PURPOSE A subset of common variable immunodeficiency (CVID) patients either presents with or develops autoimmune and lymphoproliferative complications, such as granulomatous lymphocytic interstitial lung disease (GLILD), a major cause of morbidity and mortality in CVID. While a myriad of phenotypic lymphocyte derangements has been associated with and described in GLILD, defects in T and B cell antigen receptor (TCR/BCR) signaling in CVID and CVID with GLILD (CVID/GLILD) remain undefined, hindering discovery of biomarkers for disease monitoring, prognostic prediction, and personalized medicine approaches. METHODS To identify perturbations of immune cell subsets and TCR/BCR signal transduction, we applied mass cytometry analysis to peripheral blood mononuclear cells (PBMCs) from healthy control participants (HC), CVID, and CVID/GLILD patients. RESULTS Patients with CVID, regardless of GLILD status, had increased frequency of HLADR+CD4+ T cells, CD57+CD8+ T cells, and CD21lo B cells when compared to healthy controls. Within these cellular populations in CVID/GLILD patients only, engagement of T or B cell antigen receptors resulted in discordant downstream signaling responses compared to CVID. In CVID/GLILD patients, CD21lo B cells showed perturbed BCR-mediated phospholipase C gamma and extracellular signal-regulated kinase activation, while HLADR+CD4+ T cells and CD57+CD8+ T cells displayed disrupted TCR-mediated activation of kinases most proximal to the receptor. CONCLUSION Both CVID and CVID/GLILD patients demonstrate an activated T and B cell phenotype compared to HC. However, only CVID/GLILD patients exhibit altered TCR/BCR signaling in the activated lymphocyte subsets. These findings contribute to our understanding of the mechanisms of immune dysregulation in CVID with GLILD.
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Affiliation(s)
- Victor G Lui
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, 12800 East 19Th Ave, Mail Stop 8333, RC1 North P18-8117, Aurora, CO, 80045, USA
| | - Tusharkanti Ghosh
- Department of Biostatistics and Informatics, School of Public Health, University of Colorado, Aurora, CO, USA
| | - Amy Rymaszewski
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Shaoying Chen
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Division of Asthma, Allergy, and Clinical Immunology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ryan M Baxter
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, 12800 East 19Th Ave, Mail Stop 8333, RC1 North P18-8117, Aurora, CO, 80045, USA
| | - Daniel S Kong
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, 12800 East 19Th Ave, Mail Stop 8333, RC1 North P18-8117, Aurora, CO, 80045, USA
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, School of Public Health, University of Colorado, Aurora, CO, USA
| | - John M Routes
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - James W Verbsky
- Division of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
- Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, School of Medicine, University of Colorado, 12800 East 19Th Ave, Mail Stop 8333, RC1 North P18-8117, Aurora, CO, 80045, USA.
- Department of Pediatrics, Section of Allergy and Immunology, School of Medicine, University of Colorado, Aurora, CO, USA.
- Children's Hospital Colorado, Aurora, CO, USA.
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Fasano S, Milone A, Nicoletti GF, Isenberg DA, Ciccia F. Precision medicine in systemic lupus erythematosus. Nat Rev Rheumatol 2023; 19:331-342. [PMID: 37041269 DOI: 10.1038/s41584-023-00948-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 04/13/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease that has diverse clinical manifestations, ranging from restricted cutaneous involvement to life-threatening systemic organ involvement. The heterogeneity of pathomechanisms that lead to SLE contributes to between-patient variation in clinical phenotype and treatment response. Ongoing efforts to dissect cellular and molecular heterogeneity in SLE could facilitate the future development of stratified treatment recommendations and precision medicine, which is a considerable challenge for SLE. In particular, some genes involved in the clinical heterogeneity of SLE and some phenotype-related loci (STAT4, IRF5, PDGF genes, HAS2, ITGAM and SLC5A11) have an association with clinical features of the disease. An important part is also played by epigenetic varation (in DNA methylation, histone modifications and microRNAs) that influences gene expression and affects cell function without modifying the genome sequence. Immune profiling can help to identify an individual's specific response to a therapy and can potentially predict outcomes, using techniques such as flow cytometry, mass cytometry, transcriptomics, microarray analysis and single-cell RNA sequencing. Furthermore, the identification of novel serum and urinary biomarkers would enable the stratification of patients according to predictions of long-term outcomes and assessments of potential response to therapy.
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Affiliation(s)
- Serena Fasano
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy.
| | - Alessandra Milone
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovanni Francesco Nicoletti
- Multidisciplinary Department of Medical-Surgical and Dental Specialties, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy
| | - David A Isenberg
- Department of Rheumatology, Division of Medicine, University College London, London, UK
| | - Francesco Ciccia
- Rheumatology Unit, Department of Precision Medicine, Università Degli Studi Della Campania "Luigi Vanvitelli", Naples, Italy.
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Peters AF, Kusche Y, Gerdkamp H, Nattkemper E, Vischedyk K, Münck NA, Weishaupt C, Roth J, Barczyk-Kahlert K, Sunderkötter C, Ehrchen JM. UVA1 radiation attenuates pro-inflammatory functions in human monocytes. J Dermatol 2023; 50:46-56. [PMID: 36184911 DOI: 10.1111/1346-8138.16600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
Abstract
UVA1 therapy is effective in the treatment of inflammatory and autoimmune skin diseases. The mode of action of UVA1 therapy is not completely understood and especially data on cells of the innate immune system like monocytes, which are critically involved in many inflammatory processes, are sparse. We wanted to answer the question whether UVA1 irradiation alters functional properties of human monocytes. We treated human peripheral blood monocytes in vitro with 2 J/cm2 UVA1 light, incubated the cells for 48 h and examined both functional properties and alterations in the gene and protein expression profile. While UVA1 did not alter cell viability or susceptibility to apoptosis inducing agents, it decreased the capacity of monocytes for phagocytosis and to eliminate infectious agents like Leishmania major. Moreover, we measured a significantly reduced production of interleukin (IL)-1β mRNA in lipopolysaccharide activated monocytes after UVA1 treatment. Importantly, UVA1-treated monocytes not only produce less IL-1β, but also upregulate expression of the anti-inflammatory IL-1β decoy receptor. Our data provide evidence that UVA1 radiation not only interferes with fundamental monocyte properties like phagocytosis, pathogen killing and activation, but could also specifically attenuate pro-inflammatory IL-1 effects. This might constitute a hitherto unknown anti-inflammatory mechanism of UVA1 in human monocytes.
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Affiliation(s)
- Anna Franziska Peters
- Department of Dermatology, University of Münster, Münster, Germany.,Institute of Immunology, University of Münster, Münster, Germany
| | - Yvonne Kusche
- Department of Dermatology, University of Münster, Münster, Germany.,Institute of Immunology, University of Münster, Münster, Germany
| | - Henrike Gerdkamp
- Institute of Immunology, University of Münster, Münster, Germany
| | - Eva Nattkemper
- Department of Dermatology, University of Münster, Münster, Germany
| | - Kerstin Vischedyk
- Department of Dermatology, University of Münster, Münster, Germany.,Institute of Immunology, University of Münster, Münster, Germany
| | - Niels-Arne Münck
- Department of Dermatology, University of Münster, Münster, Germany.,Institute of Immunology, University of Münster, Münster, Germany
| | | | - Johannes Roth
- Institute of Immunology, University of Münster, Münster, Germany
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Turnier JL, Yee CM, Madison JA, Rizvi SM, Berthier CC, Wen F, Kahlenberg JM. Imaging Mass Cytometry Reveals Predominant Innate Immune Signature and Endothelial-Immune Cell Interaction in Juvenile Myositis Compared to Lupus Skin. Arthritis Rheumatol 2022; 74:2024-2031. [PMID: 35762881 PMCID: PMC9771877 DOI: 10.1002/art.42283] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/17/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Cutaneous inflammation can signal disease in juvenile dermatomyositis (DM) and childhood-onset systemic lupus erythematosus (cSLE), but we do not fully understand cellular mechanisms of cutaneous inflammation. In this study, we used imaging mass cytometry to characterize cutaneous inflammatory cell populations and cell-cell interactions in juvenile DM as compared to cSLE. METHODS We performed imaging mass cytometry analysis on skin biopsy samples from juvenile DM patients (n = 6) and cSLE patients (n = 4). Tissue slides were processed and incubated with metal-tagged antibodies for CD14, CD15, CD16, CD56, CD68, CD11c, HLA-DR, blood dendritic cell antigen 2, CD20, CD27, CD138, CD4, CD8, E-cadherin, CD31, pan-keratin, and type I collagen. Stained tissue was ablated, and raw data were acquired using the Hyperion imaging system. We utilized the Phenograph unsupervised clustering algorithm to determine cell marker expression and permutation test by histoCAT to perform neighborhood analysis. RESULTS We identified 14 cell populations in juvenile DM and cSLE skin, including CD14+ and CD68+ macrophages, myeloid and plasmacytoid dendritic cells (pDCs), CD4+ and CD8+ T cells, and B cells. Overall, cSLE skin had a higher inflammatory cell infiltrate, with increased CD14+ macrophages, pDCs, and CD8+ T cells and immune cell-immune cell interactions. Juvenile DM skin displayed a stronger innate immune signature, with a higher overall percentage of CD14+ macrophages and prominent endothelial cell-immune cell interaction. CONCLUSION Our findings identify immune cell population differences, including CD14+ macrophages, pDCs, and CD8+ T cells, in juvenile DM skin compared to cSLE skin, and highlight a predominant innate immune signature and endothelial cell-immune cell interaction in juvenile DM, providing insight into candidate cell populations and interactions to better understand disease-specific pathophysiology.
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Affiliation(s)
- Jessica L. Turnier
- Divison of Pediatric Rheumatology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine M. Yee
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacqueline A. Madison
- Divison of Pediatric Rheumatology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA,Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Syed M. Rizvi
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Celine C. Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Fei Wen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Michelle Kahlenberg
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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Sasaki T, Bracero S, Keegan J, Chen L, Cao Y, Stevens E, Qu Y, Wang G, Nguyen J, Sparks JA, Holers VM, Alves SE, Lederer JA, Costenbader KH, Rao DA. Longitudinal Immune Cell Profiling in Patients With Early Systemic Lupus Erythematosus. Arthritis Rheumatol 2022; 74:1808-1821. [PMID: 35644031 PMCID: PMC10238884 DOI: 10.1002/art.42248] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/29/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To investigate the immune cell profiles of patients with systemic lupus erythematosus (SLE), and to identify longitudinal changes in those profiles over time. METHODS We employed mass cytometry with 3 different panels of 38-39 markers (an immunophenotyping panel, a T cell/monocyte panel, and a B cell panel) in cryopreserved peripheral blood mononuclear cells (PBMCs) from 9 patients with early SLE, 15 patients with established SLE, and 14 controls without autoimmune disease. We used machine learning-driven clustering, flow self-organizing maps, and dimensional reduction with t-distributed stochastic neighbor embedding to identify unique cell populations in early SLE and established SLE. We used mass cytometry data of PBMCs from 19 patients with early rheumatoid arthritis (RA) and 23 controls to compare levels of specific cell populations in early RA and SLE. For the 9 patients with early SLE, longitudinal mass cytometry analysis was applied to PBMCs at enrollment, 6 months after enrollment, and 1 year after enrollment. Serum samples were also assayed for 65 cytokines using Luminex multiplex assay, and associations between cell types and cytokines/chemokines were assessed. RESULTS Levels of peripheral helper T cells, follicular helper T (Tfh) cells, and several Ki-67+ proliferating subsets (ICOS+Ki-67+ CD8 T cells, Ki-67+ regulatory T cells, CD19intermediate Ki-67high plasmablasts, and PU.1high Ki-67high monocytes) were increased in patients with early SLE, with more prominent alterations than were seen in patients with early RA. Longitudinal mass cytometry and multiplex serum cytokine assays of samples from patients with early SLE revealed that levels of Tfh cells and CXCL10 had decreased 1 year after enrollment. Levels of CXCL13 were positively correlated with levels of several of the expanded cell populations in early SLE. CONCLUSION Two major helper T cell subsets and unique Ki-67+ proliferating immune cell subsets were expanded in patients in the early phase of SLE, and the immunologic features characteristic of early SLE evolved over time.
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Affiliation(s)
- Takanori Sasaki
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sabrina Bracero
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua Keegan
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Lin Chen
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ye Cao
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Emma Stevens
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Yujie Qu
- Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Guoxing Wang
- Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - Jennifer Nguyen
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jeffrey A. Sparks
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - V. Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephen E. Alves
- Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA
| | - James A. Lederer
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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10
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Li J, Liang J, Wu L, Xu Y, Xiao C, Yang X, Sun R, Zhao J, Xu J, Liu Q, Zhou B. CYT387, a JAK-Specific Inhibitor Impedes Osteoclast Activity and Oophorectomy-Induced Osteoporosis via Modulating RANKL and ROS Signaling Pathways. Front Pharmacol 2022; 13:829862. [PMID: 35345816 PMCID: PMC8957263 DOI: 10.3389/fphar.2022.829862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/26/2022] [Indexed: 12/25/2022] Open
Abstract
Osteoclasts are of hematopoietic lineage and have the ability to degrade mineralized bone tissues. Abnormalities in osteoclastic activity under certain pathological conditions are common in bone diseases such as osteoporosis, osteosclerosis, and arthritis. Although many kinds of drugs are currently used to treat osteoporosis, they have obvious adverse reactions and limitations. CYT387 is a new small-molecule Janus kinase (JAK) inhibitor involved in hematopoiesis, immune modulation, fertility, lactation, and embryonic development. However, it has remained unclear whether CYT387 functionally impacts osteoclast formation. Our study demonstrated through osteoclast formation assay in vitro, that the use of CYT387 is a potential drug candidate for treating osteoclast-associated bone disease. The effects of CYT387 on osteoclast formation, bone resorption, NFATc1 activation, and especially intracellular ROS levels were investigated in vitro. Further, we examined the preclinical prospects of CYT387 using an oophorectomy (OVX) mouse model of osteoporosis with its anti-osteoclast activity in vivo. On the whole, this study shows that CYT387 holds promise for treating osteoclast-related bone illnesses including osteoporosis.
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Affiliation(s)
- Jing Li
- Collaborative Innovation Center of Regenerative Medicine and Medical Biological Resources Development and Application, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Jiamin Liang
- Research Centre for Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Liwei Wu
- Collaborative Innovation Center of Regenerative Medicine and Medical Biological Resources Development and Application, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Yang Xu
- Research Centre for Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | | | - Xue Yang
- The Second Nanning People's Hospital, Nanning, China
| | - Ran Sun
- Collaborative Innovation Center of Regenerative Medicine and Medical Biological Resources Development and Application, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Jinmin Zhao
- Research Centre for Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
| | - Jiake Xu
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Qian Liu
- Research Centre for Regenerative Medicine, Orthopaedic Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bo Zhou
- Collaborative Innovation Center of Regenerative Medicine and Medical Biological Resources Development and Application, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning, China
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11
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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
| | - 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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12
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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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13
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Stensland ZC, Coleman BM, Rihanek M, Baxter RM, Gottlieb PA, Hsieh EW, Sarapura VD, Simmons KM, Cambier JC, Smith MJ. Peripheral immunophenotyping of AITD subjects reveals alterations in immune cells in pediatric vs adult-onset AITD. iScience 2022; 25:103626. [PMID: 35005561 PMCID: PMC8718984 DOI: 10.1016/j.isci.2021.103626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/28/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022] Open
Abstract
Autoimmune thyroid disease (AITD) is caused by aberrant activation of the immune system allowing autoreactive B and T cells to target the thyroid gland leading to disease. Although AITD is more frequently diagnosed in adults, children are also affected but rarely studied. Here, we performed phenotypic and functional characterization of peripheral blood immune cells from pediatric and adult-onset AITD patients and age-matched controls using mass cytometry. Major findings indicate that unlike adult-onset AITD patients, pediatric AITD patients exhibit a decrease in anergic B cells (BND) and DN2 B cells and an increase in immature B cells compared to age-matched controls. These results indicate alterations in peripheral blood immune cells seen in pediatric-onset AITD could lead to rapid progression of disease. Hence, this study demonstrates diversity of AITD by showing differences in immune cell phenotypes and function based on age of onset, and may inform future therapies. Penetrance of high-risk HLA-DR3 haplotype is higher in pediatric AITD patients Pediatric AITD patients display altered frequency of autoreactive B cell subsets Immune cell subset frequency and function is similar in adult AITD and controls
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Affiliation(s)
- Zachary C. Stensland
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brianne M. Coleman
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Marynette Rihanek
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ryan M. Baxter
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter A. Gottlieb
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Elena W.Y. Hsieh
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, Section of Allergy and Immunology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Virginia D. Sarapura
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
| | - Kimber M. Simmons
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - John C. Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mia J. Smith
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Corresponding author
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14
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Liu C, Chu D, Kalantar‐Zadeh K, George J, Young HA, Liu G. Cytokines: From Clinical Significance to Quantification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004433. [PMID: 34114369 PMCID: PMC8336501 DOI: 10.1002/advs.202004433] [Citation(s) in RCA: 261] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/26/2021] [Indexed: 05/24/2023]
Abstract
Cytokines are critical mediators that oversee and regulate immune and inflammatory responses via complex networks and serve as biomarkers for many diseases. Quantification of cytokines has significant value in both clinical medicine and biology as the levels provide insights into physiological and pathological processes and can be used to aid diagnosis and treatment. Cytokines and their clinical significance are introduced from the perspective of their pro- and anti-inflammatory effects. Factors affecting cytokines quantification in biological fluids, native levels in different body fluids, sample processing and storage conditions, sensitivity to freeze-thaw, and soluble cytokine receptors are discussed. In addition, recent advances in in vitro and in vivo assays, biosensors based on different signal outputs and intracellular to extracellular protein expression are summarized. Various quantification platforms for high-sensitivity and reliable measurement of cytokines in different scenarios are discussed, and commercially available cytokine assays are compared. A discussion of challenges in the development and advancement of technologies for cytokine quantification that aim to achieve real-time multiplex cytokine analysis for point-of-care situations applicable for both biomedical research and clinical practice are discussed.
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Affiliation(s)
- Chao Liu
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
| | - Dewei Chu
- School of Materials Science and EngineeringUniversity of New South WalesSydneyNSW2052Australia
| | | | - Jacob George
- Storr Liver CentreWestmead Institute of Medical ResearchUniversity of Sydney and Department of Gastroenterology and HepatologyWestmead HospitalWestmeadNSW2145Australia
| | - Howard A. Young
- Laboratory of Cancer ImmunometabolismCenter for Cancer ResearchNational Cancer Institute at FrederickFrederickMD21702USA
| | - Guozhen Liu
- School of Life and Health SciencesThe Chinese University of Hong KongShenzhen518172P. R. China
- Graduate School of Biomedical EngineeringUniversity of New South WalesSydneyNSW2052Australia
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15
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Yager N, Cole S, Lledo Lara A, Maroof A, Penkava F, Knight JC, Bowness P, Al-Mossawi H. Ex vivo mass cytometry analysis reveals a profound myeloid proinflammatory signature in psoriatic arthritis synovial fluid. Ann Rheum Dis 2021; 80:1559-1567. [PMID: 34226188 DOI: 10.1136/annrheumdis-2021-220280] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/21/2021] [Indexed: 11/04/2022]
Abstract
OBJECTIVES A number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine production ex vivo in unstimulated lymphoid and myeloid cells. METHODS Fresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 hours. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations, single-cell RNA-seq, ELISA and LEGENDplex analysis of PsA SF were also performed. RESULTS We observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of any in vitro stimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be among those most highly upregulated by PsA monocytes/macrophages in SF; and both proteins were elevated in PsA SF. CONCLUSIONS Using multiomic analyses, we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance.
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Affiliation(s)
- Nicole Yager
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | - Alicia Lledo Lara
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Frank Penkava
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Julian C Knight
- The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Bowness
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Hussein Al-Mossawi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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16
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Co-evolution of tumor and immune cells during progression of multiple myeloma. Nat Commun 2021; 12:2559. [PMID: 33963182 PMCID: PMC8105337 DOI: 10.1038/s41467-021-22804-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply single cell RNA and linked-read whole genome sequencing to profile 29 longitudinal samples at different disease stages from 14 patients. Here, we collect 17,267 plasma cells and 57,719 immune cells, discovering patient-specific plasma cell profiles and immune cell expression changes. Patients with the same genetic alterations tend to have both plasma cells and immune cells clustered together. By integrating bulk genomics and single cell mapping, we track plasma cell subpopulations across disease stages and find three patterns: stability (from precancer to diagnosis), and gain or loss (from diagnosis to relapse). In multiple patients, we detect “B cell-featured” plasma cell subpopulations that cluster closely with B cells, implicating their cell of origin. We validate AP-1 complex differential expression (JUN and FOS) in plasma cell subpopulations using CyTOF-based protein assays, and integrated analysis of single-cell RNA and CyTOF data reveals AP-1 downstream targets (IL6 and IL1B) potentially leading to inflammation regulation. Our work represents a longitudinal investigation for tumor and microenvironment during MM progression and paves the way for expanding treatment options. Clonal evolution in multiple myeloma (MM) needs to be understood in both the tumor and its microenvironment. Here the authors perform single-cell multi-omics profiling of samples from MM patients at different stages, finding transitions in the immune cell composition throughout progression.
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17
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Mass Cytometry, Imaging Mass Cytometry, and Multiplexed Ion Beam Imaging Use in a Clinical Setting. Clin Lab Med 2021; 41:297-308. [PMID: 34020765 DOI: 10.1016/j.cll.2021.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass cytometry (MC), imaging mass cytometry (IMC), and multiplexed ion beam imaging (MIBI) represent a new generation of tools to understand increasingly complex systems. Although these technologies differ in their intended applications, with MC being most similar to flow cytometry, and IMC/MIBI being similar to immunohistochemistry, they all share a time of flight mass spectrometry (TOF MS) platform. These TOF MS platforms use metal conjugated antibodies as opposed to fluorophores, increasing the measurable parameters up to approximately 50 with a theoretic limit approximately 100 parameters. These tools are being adapted to understand highly complex systems in basic and clinical research.
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18
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David P, Hansen FJ, Bhat A, Weber GF. An overview of proteomic methods for the study of 'cytokine storms'. Expert Rev Proteomics 2021; 18:83-91. [PMID: 33849358 DOI: 10.1080/14789450.2021.1911652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: The cytokine storm is a form of excessive systemic inflammatory reaction triggered by a myriad of factors that may lead to multi-organ failure, and finally to death. The cytokine storm can occur in a number of infectious and noninfectious diseases including COVID-19, sepsis, ebola, avian influenza, and graft versus host disease, or during the severe inflammatory response syndrome.Area covered: This review mainly focuses on the most common and well-known methods of protein studies (PAGE, SDS-PAGE, and high- performance liquid chromatography). It also discusses other modern technologies in proteomics like mass spectrometry, soft ionization techniques, cytometric bead assays, and the next generation of microarrays that have been used to get an in-depth understanding of the pathomechanisms involved during the cytokine storm.Expert opinion: Overactivation of leukocytes drives the production and secretion of inflammatory cytokines fueling the cytokine storm. These events lead to a systemic hyper-inflammation, circulatory collapse and shock, and finally to multiorgan failure. Therefore, monitoring the patient's systemic cytokine levels with proteomic technologies that are redundant, economical, and require minimal sample volume for real-time assessment might help in a better clinical evaluation and management of critically ill patients.
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Affiliation(s)
- Paul David
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Frederik J Hansen
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Adil Bhat
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Georg F Weber
- Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
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19
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Zielinski JM, Luke JJ, Guglietta S, Krieg C. High Throughput Multi-Omics Approaches for Clinical Trial Evaluation and Drug Discovery. Front Immunol 2021; 12:590742. [PMID: 33868223 PMCID: PMC8044891 DOI: 10.3389/fimmu.2021.590742] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022] Open
Abstract
High throughput single cell multi-omics platforms, such as mass cytometry (cytometry by time-of-flight; CyTOF), high dimensional imaging (>6 marker; Hyperion, MIBIscope, CODEX, MACSima) and the recently evolved genomic cytometry (Citeseq or REAPseq) have enabled unprecedented insights into many biological and clinical questions, such as hematopoiesis, transplantation, cancer, and autoimmunity. In synergy with constantly adapting new single-cell analysis approaches and subsequent accumulating big data collections from these platforms, whole atlases of cell types and cellular and sub-cellular interaction networks are created. These atlases build an ideal scientific discovery environment for reference and data mining approaches, which often times reveals new cellular disease networks. In this review we will discuss how combinations and fusions of different -omic workflows on a single cell level can be used to examine cellular phenotypes, immune effector functions, and even dynamic changes, such as metabolomic state of different cells in a sample or even in a defined tissue location. We will touch on how pre-print platforms help in optimization and reproducibility of workflows, as well as community outreach. We will also shortly discuss how leveraging single cell multi-omic approaches can be used to accelerate cellular biomarker discovery during clinical trials to predict response to therapy, follow responsive cell types, and define novel druggable target pathways. Single cell proteome approaches already have changed how we explore cellular mechanism in disease and during therapy. Current challenges in the field are how we share these disruptive technologies to the scientific communities while still including new approaches, such as genomic cytometry and single cell metabolomics.
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Affiliation(s)
- Jessica M. Zielinski
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
| | - Jason J. Luke
- Hillman Cancer Center, Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Silvia Guglietta
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
| | - Carsten Krieg
- Hollings Cancer Center, Medical University of South Carolina (MUSC), Charleston, SC, United States
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20
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Okamato Y, Ghosh T, Okamoto T, Schuyler RP, Seifert J, Charry LL, Visser A, Feser M, Fleischer C, Pedrick C, August J, Moss L, Bemis EA, Norris JM, Kuhn KA, Demoruelle MK, Deane KD, Ghosh D, Holers VM, Hsieh EWY. 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 2021; 117:102581. [PMID: 33310262 PMCID: PMC7855988 DOI: 10.1016/j.jaut.2020.102581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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Affiliation(s)
- Yuko Okamato
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA; Tokyo Women's Medical University School of Medicine, Department of Rheumatology, Tokyo, Japan.
| | - Tusharkanti Ghosh
- Colorado School of Public Health, Department of Biostatistics and Informatics, Aurora, CO, USA
| | - Tsukasa Okamoto
- University of Colorado Denver, Department of Medicine, Aurora, CO, USA
| | - Ronald P Schuyler
- University of Colorado School of Medicine, Department of Immunology and Microbiology, Aurora, CO, USA
| | - Jennifer Seifert
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Laura Lenis Charry
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Ashley Visser
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Marie Feser
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Chelsie Fleischer
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Chong Pedrick
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Justin August
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Laurakay Moss
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Elizabeth A Bemis
- Colorado School of Public Health, Department of Epidemiology, Aurora, CO, USA
| | - Jill M Norris
- Colorado School of Public Health, Department of Epidemiology, Aurora, CO, USA
| | - Kristine A Kuhn
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | | | - Kevin D Deane
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Debashis Ghosh
- Colorado School of Public Health, Department of Biostatistics and Informatics, Aurora, CO, USA
| | - V Michael Holers
- University of Colorado Denver, Division of Rheumatology, Aurora, CO, USA
| | - Elena W Y Hsieh
- University of Colorado School of Medicine, Department of Immunology and Microbiology, Aurora, CO, USA; University of Colorado School of Medicine, Children's Hospital Colorado, Department of Pediatrics, Section of Allergy & Immunology, Aurora, CO, USA
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21
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Rybakowska P, Burbano C, Van Gassen S, Varela N, Aguilar-Quesada R, Saeys Y, Alarcón-Riquelme ME, Marañón C. Stabilization of Human Whole Blood Samples for Multicenter and Retrospective Immunophenotyping Studies. Cytometry A 2020; 99:524-537. [PMID: 33070416 DOI: 10.1002/cyto.a.24241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/14/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Whole blood is often collected for large-scale immune monitoring studies to track changes in cell frequencies and responses using flow (FC) or mass cytometry (MC). In order to preserve sample composition and phenotype, blood samples should be analyzed within 24 h after bleeding, restricting the recruitment, analysis protocols, as well as biobanking. Herein, we have evaluated two whole blood preservation protocols that allow rapid sample processing and long-term stability. Two fixation buffers were used, Phosphoflow Fix and Lyse (BD) and Proteomic Stabilizer (PROT) to fix and freeze whole blood samples for up to 6 months. After analysis by an 8-plex panel by FC and a 26-plex panel by MC, manual gating of circulating leukocyte populations and cytokines was performed. Additionally, we tested the stability of a single sample over a 13-months period using 45 consecutive aliquots and a 34-plex panel by MC. We observed high correlation and low bias toward any cell population when comparing fresh and 6 months frozen blood with FC and MC. This correlation was confirmed by hierarchical clustering. Low coefficients of variation (CV) across studied time points indicate good sample preservation for up to 6 months. Cytokine detection stability was confirmed by low CVs, with some differences between fresh and fixed conditions. Thirteen months regular follow-up of PROT samples showed remarkable sample stability. Whole blood can be preserved for phenotyping and cytokine-response studies provided the careful selection of a compatible antibody panel. However, possible changes in cell morphology, differences in antibody affinity, and changes in cytokine-positive cell frequencies when compared to fresh blood should be considered. Our setting constitutes a valuable tool for multicentric and retrospective studies. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Paulina Rybakowska
- Department of Medical Genomics, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS, Granada, Spain
| | - Catalina Burbano
- Grupo de Inmunología Celular e Inmunogenética, Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Sofie Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Nieves Varela
- Department of Medical Genomics, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS, Granada, Spain
| | | | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
| | - Marta E Alarcón-Riquelme
- Department of Medical Genomics, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS, Granada, Spain.,Unit for Chronic Inflammatory Diseases, Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Concepción Marañón
- Department of Medical Genomics, GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS, Granada, Spain
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22
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Sulen A, Islam S, Wolff ASB, Oftedal BE. The prospects of single-cell analysis in autoimmunity. Scand J Immunol 2020; 92:e12964. [PMID: 32869859 DOI: 10.1111/sji.12964] [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: 05/01/2020] [Revised: 07/18/2020] [Accepted: 08/21/2020] [Indexed: 12/29/2022]
Abstract
In the last decade, there has been a tremendous development of technologies focused on analysing various molecular attributes in single cells, with an ever-increasing number of parameters becoming available at the DNA, RNA and protein levels. Much of this progress has involved cells in suspension, but also in situ analysis of tissues has taken great leaps. Paralleling the development in the laboratory, and because of increasing complexity, the analysis of single-cell data is also constantly being updated with new algorithms and analysis platforms. Our immune system shares this complexity, and immunologists have therefore been in the forefront of this technological development. These technologies clearly open new avenues for immunology research, maybe particularly within autoimmunity where the interaction between the faulty immune system and the thymus or the target organ is important. However, the technologies currently available can seem overwhelming and daunting. The aim of this review is to remedy this by giving a balanced overview of the prospects of using single-cell analysis in basal and clinical autoimmunity research, with an emphasis on endocrine autoimmunity.
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Affiliation(s)
- André Sulen
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Shahinul Islam
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette S B Wolff
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bergithe E Oftedal
- KG Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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23
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van Hooij A, Tió-Coma M, Verhard EM, Khatun M, Alam K, Tjon Kon Fat E, de Jong D, Sufian Chowdhury A, Corstjens P, Richardus JH, Geluk A. Household Contacts of Leprosy Patients in Endemic Areas Display a Specific Innate Immunity Profile. Front Immunol 2020; 11:1811. [PMID: 32849645 PMCID: PMC7431626 DOI: 10.3389/fimmu.2020.01811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/07/2020] [Indexed: 12/28/2022] Open
Abstract
Leprosy is a chronic infectious disease, caused by Mycobacterium leprae, that can lead to severe life-long disabilities. The transmission of M. leprae is continuously ongoing as witnessed by the stable new case detection rate. The majority of exposed individuals does, however, not develop leprosy and is protected from infection by innate immune mechanisms. In this study the relation between innate immune markers and M. leprae infection as well as the occurrence of leprosy was studied in household contacts (HCs) of leprosy patients with high bacillary loads. Serum proteins associated with innate immunity (ApoA1, CCL4, CRP, IL-1Ra, IL-6, IP-10, and S100A12) were determined by lateral flow assays (LFAs) in conjunction with the presence of M. leprae DNA in nasal swabs (NS) and/or slit-skin smears (SSS). The HCs displayed ApoA1 and S100A12 levels similar to paucibacillary patients and could be differentiated from endemic controls based on the levels of these markers. In the 31 households included the number (percentage) of HCs that were concomitantly diagnosed with leprosy, or tested positive for M. leprae DNA in NS and SSS, was not equally divided. Specifically, households where M. leprae infection and leprosy disease was not observed amongst members of the household were characterized by higher S100A12 and lower CCL4 levels in whole blood assays of HCs in response to M. leprae. Lateral flow assays provide a convenient diagnostic tool to quantitatively measure markers of the innate immune response and thereby detect individuals which are likely infected with M. leprae and at risk of developing disease or transmitting bacteria. Low complexity diagnostic tests measuring innate immunity markers can therefore be applied to help identify who should be targeted for prophylactic treatment.
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Affiliation(s)
- Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Els M Verhard
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Dhaka, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Dhaka, Bangladesh
| | - Elisa Tjon Kon Fat
- Department Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Danielle de Jong
- Department Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Abu Sufian Chowdhury
- Rural Health Program, The Leprosy Mission International Bangladesh, Dhaka, Bangladesh
| | - Paul Corstjens
- Department Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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24
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Single-cell mass cytometry on peripheral blood identifies immune cell subsets associated with primary biliary cholangitis. Sci Rep 2020; 10:12584. [PMID: 32724082 PMCID: PMC7387528 DOI: 10.1038/s41598-020-69358-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023] Open
Abstract
The relationship between primary biliary cholangitis (PBC), a chronic cholestatic autoimmune liver disease, and the peripheral immune system remains to be fully understood. Herein, we performed the first mass cytometry (CyTOF)-based, immunophenotyping analysis of the peripheral immune system in PBC at single-cell resolution. CyTOF was performed on peripheral blood mononuclear cells (PBMCs) from PBC patients (n = 33) and age-/sex-matched healthy controls (n = 33) to obtain immune cell abundance and marker expression profiles. Hierarchical clustering methods were applied to identify immune cell types and subsets significantly associated with PBC. Subsets of gamma-delta T cells (CD3+TCRgd+), CD8+ T cells (CD3+CD8+CD161+PD1+), and memory B cells (CD3−CD19+CD20+CD24+CD27+) were found to have lower abundance in PBC than in control. In contrast, higher abundance of subsets of monocytes and naïve B cells were observed in PBC compared to control. Furthermore, several naïve B cell (CD3−CD19+CD20+CD24−CD27−) subsets were significantly higher in PBC patients with cirrhosis (indicative of late-stage disease) than in those without cirrhosis. Alternatively, subsets of memory B cells were lower in abundance in cirrhotic relative to non-cirrhotic PBC patients. Future immunophenotyping investigations could lead to better understanding of PBC pathogenesis and progression, and also to the discovery of novel biomarkers and treatment strategies.
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25
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Stanley N, Stelzer IA, Tsai AS, Fallahzadeh R, Ganio E, Becker M, Phongpreecha T, Nassar H, Ghaemi S, Maric I, Culos A, Chang AL, Xenochristou M, Han X, Espinosa C, Rumer K, Peterson L, Verdonk F, Gaudilliere D, Tsai E, Feyaerts D, Einhaus J, Ando K, Wong RJ, Obermoser G, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. VoPo leverages cellular heterogeneity for predictive modeling of single-cell data. Nat Commun 2020; 11:3738. [PMID: 32719375 PMCID: PMC7385162 DOI: 10.1038/s41467-020-17569-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/03/2020] [Indexed: 12/29/2022] Open
Abstract
High-throughput single-cell analysis technologies produce an abundance of data that is critical for profiling the heterogeneity of cellular systems. We introduce VoPo (https://github.com/stanleyn/VoPo), a machine learning algorithm for predictive modeling and comprehensive visualization of the heterogeneity captured in large single-cell datasets. In three mass cytometry datasets, with the largest measuring hundreds of millions of cells over hundreds of samples, VoPo defines phenotypically and functionally homogeneous cell populations. VoPo further outperforms state-of-the-art machine learning algorithms in classification tasks, and identified immune-correlates of clinically-relevant parameters.
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Affiliation(s)
- Natalie Stanley
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Ina A Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Amy S Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Thanaphong Phongpreecha
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, USA
| | - Huda Nassar
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Sajjad Ghaemi
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
- Digital Technologies Research Centre, National Research Council Canada, Toronto, ON, Canada
| | - Ivana Maric
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Anthony Culos
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Maria Xenochristou
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Xiaoyuan Han
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Kristen Rumer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Laura Peterson
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Dyani Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
- Department of Plastic Surgery, Stanford University, Stanford, USA
| | - Eileen Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University, Stanford, USA
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, USA
| | | | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, USA.
- Department of Pediatrics, Stanford University, Stanford, USA.
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26
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Yang L, George J, Wang J. Deep Profiling of Cellular Heterogeneity by Emerging Single-Cell Proteomic Technologies. Proteomics 2020; 20:e1900226. [PMID: 31729152 PMCID: PMC7225074 DOI: 10.1002/pmic.201900226] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/14/2019] [Indexed: 12/20/2022]
Abstract
The ability to comprehensively profile cellular heterogeneity in functional proteome is crucial in advancing the understanding of cell behavior, organism development, and disease mechanisms. Conventional bulk measurement by averaging the biological responses across a population often loses the information of cellular variations. Single-cell proteomic technologies are becoming increasingly important to understand and discern cellular heterogeneity. The well-established methods for single-cell protein analysis based on flow cytometry and fluorescence microscopy are limited by the low multiplexing ability owing to the spectra overlap of fluorophores for labeling antibodies. Recent advances in mass spectrometry (MS), microchip, and reiterative staining-based techniques for single-cell proteomics have enabled the evaluation of cellular heterogeneity with high throughput, increased multiplexity, and improved sensitivity. In this review, the principles, developments, advantages, and limitations of these advanced technologies in analysis of single-cell proteins, along with their biological applications to study cellular heterogeneity, are described. At last, the remaining challenges, possible strategies, and future opportunities that will facilitate the improvement and broad applications of single-cell proteomic technologies in cell biology and medical research are discussed.
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Affiliation(s)
- Liwei Yang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
| | - Justin George
- Department of Chemistry, State University of New York, University at Albany, Albany, NY 12222
| | - Jun Wang
- Multiplex Biotechnology Laboratory, Department of Biomedical Engineering, State University of New York at Stony Brook, Stony Brook, NY 11794
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27
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John A, Qin B, Kalari KR, Wang L, Yu J. Patient-specific multi-omics models and the application in personalized combination therapy. Future Oncol 2020; 16:1737-1750. [PMID: 32462937 DOI: 10.2217/fon-2020-0119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The rapid advancement of high-throughput technologies and sharp decrease in cost have opened up the possibility to generate large amount of multi-omics data on an individual basis. The development of high-throughput -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and microbiomics, enables the application of multi-omics technologies in the clinical settings. Combination therapy, defined as disease treatment with two or more drugs to achieve efficacy with lower doses or lower drug toxicity, is the basis for the care of diseases like cancer. Patient-specific multi-omics data integration can help the identification and development of combination therapies. In this review, we provide an overview of different -omics platforms, and discuss the methods for multi-omics, high-throughput, data integration, personalized combination therapy.
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Affiliation(s)
- August John
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Gastroenterology Research Unit, Mayo Clinic, Rochester, MN 55905, USA.,Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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28
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Magnusson L, Barcenilla H, Pihl M, Bensing S, Espes D, Carlsson PO, Casas R. Mass Cytometry Studies of Patients With Autoimmune Endocrine Diseases Reveal Distinct Disease-Specific Alterations in Immune Cell Subsets. Front Immunol 2020; 11:288. [PMID: 32153591 PMCID: PMC7047233 DOI: 10.3389/fimmu.2020.00288] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/05/2020] [Indexed: 01/10/2023] Open
Abstract
Although there is evidence that autoimmune diseases share similar immunogenetic mechanisms, studies comparing peripheral CD45+ cells from patients with autoimmune endocrine diseases in parallel are limited. In this study, we applied high-dimensional single-cell mass cytometry to phenotypically characterize PBMC from patients with new-onset (N-T1D) and long-standing type 1 diabetes, Hashimoto's thyroiditis (HT), Graves' disease and autoimmune Addison's disease (AD), as well as healthy controls. The frequency of CD20loCD27hiCD38hiHLA-DRint plasmablasts, CD86+CD14loCD16+ non-classical monocytes and two subsets of CD56dimHLA-DR+IFN-γ+ NK cells were increased in patients with HT. Subsets of CD56dimCD69+HLA-DR- NK cells and CD8+ TEMRA cells, both expressing IFN-γ, were expanded and reduced, respectively, in the N-T1D group. In addition, patients with AD were characterized by an increased percentage of central memory CD8+ T cells that expressed CCR4, GATA3, and IL-2. We demonstrate that patients with N-T1D, HT, and AD had altered frequencies of distinct subsets within antigen-presenting and cytotoxic cell lineages. Previously unreported alterations of specific cell subsets were identified in samples from patients with HT and AD. Our study might contribute to a better understanding of shared and diverging immunological features between autoimmune endocrine diseases.
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Affiliation(s)
- Louise Magnusson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Division of Children and Women Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Hugo Barcenilla
- Division of Children and Women Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Mikael Pihl
- Core Facility Flow Cytometry Unit, Faculty of Medicine, Linköping University, Linköping, Sweden
| | - Sophie Bensing
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Espes
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Per-Ola Carlsson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Rosaura Casas
- Division of Children and Women Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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29
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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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30
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Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol 2020; 16:87-99. [PMID: 31892734 PMCID: PMC7232872 DOI: 10.1038/s41584-019-0338-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
The cellular complexity and functional diversity of the human immune system necessitate the use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as rheumatic diseases, as well as other autoimmune and inflammatory disorders. Proteomic technologies that use elemental (heavy metal) reporter ions, such as mass cytometry (also known as CyTOF) and analogous high-dimensional imaging approaches (including multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC)), have been developed from their low-dimensional counterparts, flow cytometry and immunohistochemistry, to meet this need. A growing number of studies have been published that use these technologies to identify functional biomarkers and therapeutic targets in rheumatic diseases, but the full potential of their application to rheumatic disease research has yet to be fulfilled. This Review introduces the underlying technologies for high-dimensional immune monitoring and discusses aspects necessary for their successful implementation, including study design principles, analytical tools and future developments for the field of rheumatology.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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31
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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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32
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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33
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Fisher DAC, Miner CA, Engle EK, Hu H, Collins TB, Zhou A, Allen MJ, Malkova ON, Oh ST. Cytokine production in myelofibrosis exhibits differential responsiveness to JAK-STAT, MAP kinase, and NFκB signaling. Leukemia 2019; 33:1978-1995. [PMID: 30718771 PMCID: PMC6813809 DOI: 10.1038/s41375-019-0379-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The distinct clinical features of myelofibrosis (MF) have been attributed in part to dysregulated inflammatory cytokine production. Circulating cytokine levels are elevated in MF patients; a subset of which have been shown to be poor prognostic indicators. In this study, cytokine overproduction was examined in MF patient plasma and in MF blood cells ex vivo using mass cytometry. Plasma cytokines measured following treatment with ruxolitinib remained markedly abnormal, indicating that aberrant cytokine production persists despite therapeutic JAK2 inhibition. In MF patient samples, 14/15 cytokines measured by mass cytometry were found to be constitutively overproduced, with the principal cellular source for most cytokines being monocytes, implicating a non-cell-autonomous role for monocyte-derived cytokines impacting disease-propagating stem/progenitor cells in MF. The majority of cytokines elevated in MF exhibited ex vivo hypersensitivity to thrombopoietin (TPO), toll-like receptor (TLR) ligands, and/or tumor necrosis factor (TNF). A subset of this group (including TNF, IL-6, IL-8, IL-10) was minimally sensitive to ruxolitinib. All TPO/TLR/TNF-sensitive cytokines, however, were sensitive to pharmacologic inhibition of NFκB and/or MAP kinase signaling. These results indicate that NFκB and MAP kinase signaling maintain cytokine overproduction in MF, and that inhibition of these pathways may provide optimal control of inflammatory pathophysiology in MF.
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Affiliation(s)
- Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cathrine A Miner
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth K Engle
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hengrui Hu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Program in Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Taylor B Collins
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy Zhou
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Allen
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Olga N Malkova
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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34
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Tay SH, Yaung KN, Leong JY, Yeo JG, Arkachaisri T, Albani S. Immunomics in Pediatric Rheumatic Diseases. Front Med (Lausanne) 2019; 6:111. [PMID: 31231652 PMCID: PMC6558393 DOI: 10.3389/fmed.2019.00111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/03/2019] [Indexed: 02/04/2023] Open
Abstract
The inherent complexity in the immune landscape of pediatric rheumatic disease necessitates a holistic system approach. Uncertainty in the mechanistic workings and etiological driving forces presents difficulty in personalized treatments. The development and progression of immunomics are well suited to deal with this complexity. Immunomics encompasses a spectrum of biological processes that entail genomics, transcriptomics, epigenomics, proteomics, and cytomics. In this review, we will discuss how various high dimensional technologies in immunomics have helped to grow a wealth of data that provide salient clues and biological insights into the pathogenesis of autoimmunity. Interfaced with critical unresolved clinical questions and unmet medical needs, these platforms have helped to identify candidate immune targets, refine patient stratification, and understand treatment response or resistance. Yet the unprecedented growth in data has presented both opportunities and challenges. Researchers are now facing huge heterogeneous data sets from different origins that need to be integrated and exploited for further data mining. We believe that the utilization and integration of these platforms will help unravel the complexities and expedite both discovery and validation of clinical targets.
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Affiliation(s)
| | | | - Jing Yao Leong
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Joo Guan Yeo
- Duke-NUS Medical School, Singapore, Singapore.,Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Duke-NUS Medical School, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Duke-NUS Medical School, Singapore, Singapore.,Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
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35
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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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36
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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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37
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Reyes M, Vickers D, Billman K, Eisenhaure T, Hoover P, Browne EP, Rao DA, Hacohen N, Blainey PC. Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures. SCIENCE ADVANCES 2019; 5:eaau9223. [PMID: 30746468 PMCID: PMC6357748 DOI: 10.1126/sciadv.aau9223] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/07/2018] [Indexed: 05/12/2023]
Abstract
Specialized immune cell subsets are involved in autoimmune disease, cancer immunity, and infectious disease through a diverse range of functions mediated by overlapping pathways and signals. However, subset-specific responses may not be detectable in analyses of whole blood samples, and no efficient approach for profiling cell subsets at high throughput from small samples is available. We present a low-input microfluidic system for sorting immune cells into subsets and profiling their gene expression. We validate the system's technical performance against standard subset isolation and library construction protocols and demonstrate the importance of subset-specific profiling through in vitro stimulation experiments. We show the ability of this integrated platform to identify subset-specific disease signatures by profiling four immune cell subsets in blood from patients with systemic lupus erythematosus (SLE) and matched control subjects. The platform has the potential to make multiplexed subset-specific analysis routine in many research laboratories and clinical settings.
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Affiliation(s)
- Miguel Reyes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dwayne Vickers
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Paul Hoover
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Immunology, Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Corresponding author. (N.H.); (P.C.B.)
| | - Paul C. Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Corresponding author. (N.H.); (P.C.B.)
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38
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Han G, Spitzer MH, Bendall SC, Fantl WJ, Nolan GP. Metal-isotope-tagged monoclonal antibodies for high-dimensional mass cytometry. Nat Protoc 2018; 13:2121-2148. [PMID: 30258176 PMCID: PMC7075473 DOI: 10.1038/s41596-018-0016-7] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Advances in single-cell mass cytometry have increasingly improved highly multidimensional characterization of immune cell heterogeneity. The immunoassay multiplexing capacity relies on monoclonal antibodies labeled with stable heavy-metal isotopes. To date, a variety of rare-earth elements and noble and post-transition metal isotopes have been used in mass cytometry; nevertheless, the methods used for antibody conjugation differ because of the individual metal coordination chemistries and distinct stabilities of various metal cations. Herein, we provide three optimized protocols for conjugating monoclonal IgG antibodies with 48 high-purity heavy-metal isotopes: (i) 38 isotopes of lanthanides, 2 isotopes of indium, and 1 isotope of yttrium; (ii) 6 isotopes of palladium; and (iii) 1 isotope of bismuth. Bifunctional chelating agents containing coordinative ligands of monomeric DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) or polymeric pentetic acid (DTPA) were used to stably sequester isotopic cations in aqueous solutions and were subsequently coupled to IgG antibodies using site-specific biorthogonal reactions. Furthermore, quantification methods based on antibody inherent absorption at 280 nm and on extrinsic absorption at 562 nm after staining with bicinchoninic acid (BCA) are reported to determine metal-isotope-tagged antibodies. In addition, a freeze-drying procedure to prepare palladium isotopic mass tags is described. To demonstrate the utility, experiments using six palladium-tagged CD45 antibodies for barcoding assays of live immune cells in cytometry by time-of-flight (CyTOF) are described. Conjugation of pure isotopes of lanthanides, indium, or yttrium takes ~3.5 h. Conjugation of bismuth takes ~4 h. Preparation of palladium mass tags takes ~8 h. Conjugation of pure isotopes of palladium takes ~2.5 h. Antibody titration takes ~4 h.
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Affiliation(s)
- Guojun Han
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wendy J Fantl
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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39
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Stern L, McGuire H, Avdic S, Rizzetto S, Fazekas de St Groth B, Luciani F, Slobedman B, Blyth E. Mass Cytometry for the Assessment of Immune Reconstitution After Hematopoietic Stem Cell Transplantation. Front Immunol 2018; 9:1672. [PMID: 30093901 PMCID: PMC6070614 DOI: 10.3389/fimmu.2018.01672] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022] Open
Abstract
Mass cytometry, or Cytometry by Time-Of-Flight, is a powerful new platform for high-dimensional single-cell analysis of the immune system. It enables the simultaneous measurement of over 40 markers on individual cells through the use of monoclonal antibodies conjugated to rare-earth heavy-metal isotopes. In contrast to the fluorochromes used in conventional flow cytometry, metal isotopes display minimal signal overlap when resolved by single-cell mass spectrometry. This review focuses on the potential of mass cytometry as a novel technology for studying immune reconstitution in allogeneic hematopoietic stem cell transplant (HSCT) recipients. Reconstitution of a healthy donor-derived immune system after HSCT involves the coordinated regeneration of innate and adaptive immune cell subsets in the recipient. Mass cytometry presents an opportunity to investigate immune reconstitution post-HSCT from a systems-level perspective, by allowing the phenotypic and functional features of multiple cell populations to be assessed simultaneously. This review explores the current knowledge of immune reconstitution in HSCT recipients and highlights recent mass cytometry studies contributing to the field.
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Affiliation(s)
- Lauren Stern
- University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Discipline of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Helen McGuire
- University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Ramaciotti Facility for Human Systems Biology, University of Sydney, Sydney, NSW, Australia.,Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Selmir Avdic
- University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Discipline of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - Barbara Fazekas de St Groth
- University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Ramaciotti Facility for Human Systems Biology, University of Sydney, Sydney, NSW, Australia.,Discipline of Pathology, School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Fabio Luciani
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Barry Slobedman
- University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Discipline of Infectious Diseases and Immunology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- University of Sydney, Sydney, NSW, Australia.,Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, Australia.,Blood and Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead, Sydney, NSW, Australia
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40
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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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41
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Lo MS. Insights Gained From the Study of Pediatric Systemic Lupus Erythematosus. Front Immunol 2018; 9:1278. [PMID: 29922296 PMCID: PMC5996073 DOI: 10.3389/fimmu.2018.01278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
The pathophysiology of systemic lupus erythematosus (SLE) has been intensely studied but remains incompletely defined. Currently, multiple mechanisms are known to contribute to the development of SLE. These include inadequate clearance of apoptotic debris, aberrant presentation of self nucleic antigens, loss of tolerance, and inappropriate activation of T and B cells. Genetic, hormonal, and environmental influences are also known to play a role. The study of lupus in children, in whom there is presumed to be greater genetic influence, has led to new understandings that are applicable to SLE pathophysiology as a whole. In particular, characterization of inherited disorders associated with excessive type I interferon production has elucidated specific mechanisms by which interferon is induced in SLE. In this review, we discuss several monogenic forms of lupus presenting in childhood and also review recent insights gained from cytokine and autoantibody profiling of pediatric SLE.
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Affiliation(s)
- Mindy S Lo
- Division of Immunology, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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42
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Italiani P, Manca ML, Angelotti F, Melillo D, Pratesi F, Puxeddu I, Boraschi D, Migliorini P. IL-1 family cytokines and soluble receptors in systemic lupus erythematosus. Arthritis Res Ther 2018; 20:27. [PMID: 29422069 PMCID: PMC5806463 DOI: 10.1186/s13075-018-1525-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
Background Dysregulated production of cytokines has a critical role in systemic lupus. The aim of this work is to identify, by a comprehensive analysis of IL-1 family cytokines and receptors in serum, correlation between cytokines/receptors’ levels and the clinical and serological features of the disease. Methods A full clinical evaluation was performed in 74 patients with systemic lupus erythematosus (SLE). C3, C4, anti-dsDNA and anti-C1q antibodies were measured. Cytokines of the IL-1 family (IL-1α, IL-1β, IL-33, IL-18), soluble receptors (sIL-1R1, sIL-1R2, sIL-1R3, ST2/sIL-1R4) and antagonists (IL-1Ra, IL-18 binding protein (IL-18BP)) were measured in serum by multiarray ELISA. Free IL-18 was calculated as the amount of IL-18 not inhibited by IL-18BP. Data were analysed by non-parametric tests and by multivariate analysis, using partial least squares (PLS) models. Results Total IL-18, IL-18BP, sIL-1R4 and IL-1Ra levels were higher in SLE vs. controls. Total and free IL-18 and sIL-1R4 were higher in patients with active vs. inactive disease and correlated with ECLAM, anti-C1q and anti-dsDNA antibodies. sIL-1R2 was higher in patients with inactive disease, was negatively correlated with ECLAM and anti-C1q antibodies and was positively correlated with C3 levels. PLS identified sIL-1R4, sIL-1R2 and anti-dsDNA as variables distinguishing patients with active from those with inactive disease; sIL-1R4, IL-18BP and anti-dsDNA identified patients with active nephritis; sIL-1R4, C3, IL-18 and free IL-18 identified patients with haematological involvement. Conclusion The data support the use of IL-18, sIL-1R2 and sIL-1R4 as biomarkers of disease activity and organ involvement, and suggest that failure in the inhibition of IL-1 activation may be a critical event in the active stages of SLE.
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Affiliation(s)
- Paola Italiani
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | - Maria Laura Manca
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Angelotti
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Daniela Melillo
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | - Federico Pratesi
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Ilaria Puxeddu
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Diana Boraschi
- Institute of Protein Biochemistry, National Research Council, Naples, Italy
| | - Paola Migliorini
- Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
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43
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Wu H, Zhang J. miR-126 in Peripheral Blood Mononuclear Cells Negatively Correlates with Risk and Severity and is Associated with Inflammatory Cytokines as well as Intercellular Adhesion Molecule-1 in Patients with Coronary Artery Disease. Cardiology 2018; 139:110-118. [PMID: 29316562 DOI: 10.1159/000484236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/16/2017] [Indexed: 12/19/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate the association of miR-126 with risk and severity of coronary artery disease (CAD) as well as its correlation with inflammatory cytokines and endothelial related proteins. METHODS In total, 215 patients suspected of CAD who underwent coronary angiography were enrolled in this case control study and were divided into a CAD group (n = 119) and control group (n = 96). miR-126 relative expression was assessed by real-time polymerase chain reaction. RESULTS The relative expression of miR-126 decreased in CAD patients compared to controls (p < 0.001), and the receiver operating characteristic curve showed a good diagnostic value of miR-126 for CAD risk with an area under the curve of 0.801 (95% CI 0.740-0.861). Additionally, miR-126 was negatively correlated with high-sensitivity C-reactive protein levels (p < 0.001) and reversely associated with TNF-α (p = 0.008) and IL-6 (p < 0.001) levels, while it was positively correlated with the IL-10 level (p < 0.001). In addition, miR-126 was negatively associated with intercellular adhesion molecule-1 (ICAM-1) levels (p = 0.001), and no association of miR-126 with vascular endothelial growth factor was detected (p = 0.142). Meanwhile, the miR-126 relative level was negatively associated with the Gensini score (p < 0.001). CONCLUSIONS Peripheral blood mononuclear cell miR-126 predicts risk and severity and correlates with inflammatory cytokines as well as ICAM-1 in patients with CAD.
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Affiliation(s)
- Huiliang Wu
- Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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44
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Abstract
Cancer immunotherapy fights against cancer by modulating the immune response and is delivering encouraging results in clinical treatments. However, it is challenging to achieve durable response in all cancer patients during treatment due to the diversity and dynamic nature of immune system as well as inter- and intratumor heterogeneity. A comprehensive assessment of system immunity and tumor microenvironment is crucial for effective and safe cancer therapy, which can potentially be resolved by single-cell proteomic analysis. Single-cell proteomic technologies enable system-wide profiling of protein levels in a number of single cells within the immune system and tumor microenvironment, and thereby provide direct assessment of the functional state of the immune cells and tumor-immune interaction that could be used to evaluate efficacy of immunotherapy and to improve clinical outcome. In this chapter, we summarized current single-cell proteomic technologies and their applications in cancer immunotherapy.
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45
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Kupcova Skalnikova H, Cizkova J, Cervenka J, Vodicka P. Advances in Proteomic Techniques for Cytokine Analysis: Focus on Melanoma Research. Int J Mol Sci 2017; 18:E2697. [PMID: 29236046 PMCID: PMC5751298 DOI: 10.3390/ijms18122697] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Melanoma is a skin cancer with permanently increasing incidence and resistance to therapies in advanced stages. Reports of spontaneous regression and tumour infiltration with T-lymphocytes makes melanoma candidate for immunotherapies. Cytokines are key factors regulating immune response and intercellular communication in tumour microenvironment. Cytokines may be used in therapy of melanoma to modulate immune response. Cytokines also possess diagnostic and prognostic potential and cytokine production may reflect effects of immunotherapies. The purpose of this review is to give an overview of recent advances in proteomic techniques for the detection and quantification of cytokines in melanoma research. Approaches covered span from mass spectrometry to immunoassays for single molecule detection (ELISA, western blot), multiplex assays (chemiluminescent, bead-based (Luminex) and planar antibody arrays), ultrasensitive techniques (Singulex, Simoa, immuno-PCR, proximity ligation/extension assay, immunomagnetic reduction assay), to analyses of single cells producing cytokines (ELISpot, flow cytometry, mass cytometry and emerging techniques for single cell secretomics). Although this review is focused mainly on cancer and particularly melanoma, the discussed techniques are in general applicable to broad research field of biology and medicine, including stem cells, development, aging, immunology and intercellular communication.
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Affiliation(s)
- Helena Kupcova Skalnikova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
| | - Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 16500 Prague, Czech Republic.
| | - Jakub Cervenka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12843 Prague 4, Czech Republic.
| | - Petr Vodicka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
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