1
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Gilchrist JJ, Fang H, Danielli S, Tomkova M, Nassiri I, Ng E, Tong O, Taylor C, Muldoon D, Cohen LRZ, Al-Mossawi H, Lau E, Neville M, Schuster-Boeckler B, Knight JC, Fairfax BP. Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes. CELL GENOMICS 2024; 4:100541. [PMID: 38663408 PMCID: PMC11099345 DOI: 10.1016/j.xgen.2024.100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/24/2023] [Accepted: 03/27/2024] [Indexed: 05/12/2024]
Abstract
To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation.
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Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of Oxford, Oxford OX3 9DU, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hai Fang
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sara Danielli
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Oxford OX3 7DQ, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Esther Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Chelsea Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Dylan Muldoon
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lea R Z Cohen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Evelyn Lau
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matt Neville
- Oxford Centre for Diabetes, Endocrinology, and Metabolism, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LE, UK
| | | | - Julian C Knight
- Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Oncology, University of Oxford, Oxford OX3 9DS, UK.
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2
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Song HW, Benzaoui M, Dwivedi A, Underwood S, Shao L, Achar S, Posarac V, Remley VA, Prochazkova M, Cai Y, Jin P, Somerville RP, Stroncek DF, Altan-Bonnet G, Shah NN, Chien CD, Taylor N, Highfill SL. Manufacture of CD22 CAR T cells following positive versus negative selection results in distinct cytokine secretion profiles and γδ T cell output. Mol Ther Methods Clin Dev 2024; 32:101171. [PMID: 38298420 PMCID: PMC10827561 DOI: 10.1016/j.omtm.2023.101171] [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: 08/02/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Chimeric antigen receptor T cells (CART) have demonstrated curative potential for hematological malignancies, but the optimal manufacturing has not yet been determined and may differ across products. The first step, T cell selection, removes contaminating cell types that can potentially suppress T cell expansion and transduction. While positive selection of CD4/CD8 T cells after leukapheresis is often used in clinical trials, it may modulate signaling cascades downstream of these co-receptors; indeed, the addition of a CD4/CD8-positive selection step altered CD22 CART potency and toxicity in patients. While negative selection may avoid this drawback, it is virtually absent from good manufacturing practices. Here, we performed both CD4/CD8-positive and -negative clinical scale selections of mononuclear cell apheresis products and generated CD22 CARTs per our ongoing clinical trial (NCT02315612NCT02315612). While the selection process did not yield differences in CART expansion or transduction, positively selected CART exhibited a significantly higher in vitro interferon-γ and IL-2 secretion but a lower in vitro tumor killing rate. Notably, though, CD22 CART generated from both selection protocols efficiently eradicated leukemia in NSG mice, with negatively selected cells exhibiting a significant enrichment in γδ CD22 CART. Thus, our study demonstrates the importance of the initial T cell selection process in clinical CART manufacturing.
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Affiliation(s)
- Hannah W. Song
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Benzaoui
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Alka Dwivedi
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Underwood
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lipei Shao
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sooraj Achar
- Laboratory of Integrative Cancer Immunology, NCI, Bethesda, MD, USA
| | | | - Victoria A. Remley
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michaela Prochazkova
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Yihua Cai
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ping Jin
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Robert P. Somerville
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David F. Stroncek
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Nirali N. Shah
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christopher D. Chien
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Steven L. Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD, USA
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3
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Cheng EL, Kacherovsky N, Pun SH. Aptamer-Based Traceless Multiplexed Cell Isolation Systems. ACS APPLIED MATERIALS & INTERFACES 2022; 14:44136-44146. [PMID: 36149728 DOI: 10.1021/acsami.2c11783] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In both biomedical research and clinical cell therapy manufacturing, there is a need for cell isolation systems that recover purified cells in the absence of any selection agent. Reported traceless cell isolation methods using engineered antigen-binding fragments or aptamers have been limited to processing a single cell type at a time. There remains an unmet need for cell isolation processes that rapidly sort multiple target cell types. Here, we utilized two aptamers along with their designated complementary strands (reversal agents) to tracelessly isolate two cell types from a mixed cell population with one aptamer-labeling step and two sequential cell elution steps with reversal agents. We engineered a CD71-binding aptamer (rvCD71apt) and a reversal agent pair to be used simultaneously with our previously reported traceless purification approach using the CD8 aptamer (rvCD8apt) and its reversal agent. We verified the compatibility of the two aptamer displacement mechanisms by flow cytometry and the feasibility of incorporating rvCD71apt with a magnetic solid state. We then combined rvCD71apt with rvCD8apt to isolate activated CD4+ T cells and resting CD8+ cells by eluting these target cells into separate fractions with orthogonal strand displacements. This is the first demonstration of isolating different cell types using two aptamers and reversal agents at the same time. Potentially, different or more aptamers can be included in this traceless multiplexed isolation system for diverse applications with a shortened operation time and a lower production cost.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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4
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Perez-Sanchez C, Barbera Betancourt A, Lyons PA, Zhang Z, Suo C, Lee JC, McKinney EF, Modis LK, Ellson C, Smith KG. miR-374a-5p regulates inflammatory genes and monocyte function in patients with inflammatory bowel disease. J Exp Med 2022; 219:e20211366. [PMID: 35363256 PMCID: PMC8980842 DOI: 10.1084/jem.20211366] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 02/02/2023] Open
Abstract
MicroRNAs are critical regulators of gene expression controlling cellular processes including inflammation. We explored their role in the pathogenesis of inflammatory bowel disease (IBD) and identified reduced expression of miR-374a-5p in IBD monocytes that correlated with a module of up-regulated genes related to the inflammatory response. Key proinflammatory module genes, including for example TNFα, IL1A, IL6, and OSM, were inversely correlated with miR-374a-5p and were validated in vitro. In colonic biopsies, miR-374a-5p was again reduced in expression and inversely correlated with the same inflammatory module, and its levels predicted subsequent response to anti-TNF therapy. Increased miR-374a-5p expression was shown to control macrophage-driven inflammation by suppressing proinflammatory mediators and to reduce the capacity of monocytes to migrate and activate T cells. Our findings suggest that miR-374a-5p reduction is a central driver of inflammation in IBD, and its therapeutic supplementation could reduce monocyte-driven inflammation in IBD or other immune-mediated diseases.
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Affiliation(s)
- Carlos Perez-Sanchez
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Rheumatology Service, Reina Sofia University Hospital, Maimonides Biomedical Research Institute of Córdoba, University of Cordoba, Cordoba, Spain
| | - Ariana Barbera Betancourt
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul A. Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Zinan Zhang
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Chenqu Suo
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Paediatrics, Cambridge University Hospitals, Cambridge, UK
| | - James C. Lee
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Eoin F. McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | - Kenneth G.C. Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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5
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Xhonneux LP, Knight O, Lernmark Å, Bonifacio E, Hagopian WA, Rewers MJ, She JX, Toppari J, Parikh H, Smith KGC, Ziegler AG, Akolkar B, Krischer JP, McKinney EF. Transcriptional networks in at-risk individuals identify signatures of type 1 diabetes progression. Sci Transl Med 2021; 13:eabd5666. [PMID: 33790023 PMCID: PMC8447843 DOI: 10.1126/scitranslmed.abd5666] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/24/2020] [Accepted: 03/12/2021] [Indexed: 12/11/2022]
Abstract
Type 1 diabetes (T1D) is a disease of insulin deficiency that results from autoimmune destruction of pancreatic islet β cells. The exact cause of T1D remains unknown, although asymptomatic islet autoimmunity lasting from weeks to years before diagnosis raises the possibility of intervention before the onset of clinical disease. The number, type, and titer of islet autoantibodies are associated with long-term disease risk but do not cause disease, and robust early predictors of individual progression to T1D onset remain elusive. The Environmental Determinants of Diabetes in the Young (TEDDY) consortium is a prospective cohort study aiming to determine genetic and environmental interactions causing T1D. Here, we analyzed longitudinal blood transcriptomes of 2013 samples from 400 individuals in the TEDDY study before both T1D and islet autoimmunity. We identified and interpreted age-associated gene expression changes in healthy infancy and age-independent changes tracking with progression to both T1D and islet autoimmunity, beginning before other evidence of islet autoimmunity was present. We combined multivariate longitudinal data in a Bayesian joint model to predict individual risk of T1D onset and validated the association of a natural killer cell signature with progression and the model's predictive performance on an additional 356 samples from 56 individuals in the independent Type 1 Diabetes Prediction and Prevention study. Together, our results indicate that T1D is characterized by early and longitudinal changes in gene expression, informing the immunopathology of disease progression and facilitating prediction of its course.
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Affiliation(s)
- Louis-Pascal Xhonneux
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Oliver Knight
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC Skåne University Hospital Malmo, Jan Waldenströms gata 35, Malmö, Sweden
| | - Ezio Bonifacio
- Center for Regenerative Therapies, Technische Universität Dresden, Fetscherstraße 105, 01307, Dresden, Germany
| | - William A Hagopian
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122, USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, 1775 Aurora Ct, Aurora, CO 80045, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1462 Laney Walker Blvd., Augusta, GA 30912, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Kiinamyllynkatu 4-8, 20521 Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, FI-20014 Turun Lyliopisto, Finland
| | - Hemang Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische, Universität München, Forschergruppe Diabetes e.V., Arcisstraße 21, 80333 München, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, 9000 Rockville Pike Bethesda, MD 20892, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
- Cambridge Centre for Artificial Intelligence in Medicine, University of Cambridge, Cambridge, UK
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6
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A CD8 + NK cell transcriptomic signature associated with clinical outcome in relapsing remitting multiple sclerosis. Nat Commun 2021; 12:635. [PMID: 33504809 PMCID: PMC7840761 DOI: 10.1038/s41467-020-20594-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 11/24/2020] [Indexed: 02/07/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS) with the majority of cases characterised by relapsing/remitting (RRMS) attacks of neurologic dysfunction followed by variable resolution. Improving clinical outcomes in RRMS requires both a better understanding of the immunological mechanisms driving recurrent demyelination and better means of predicting future disease course to facilitate early targeted therapy. Here, we apply hypothesis-generating network transcriptomics to CD8+ cells isolated from patients in RRMS, identifying a signature reflecting expansion of a subset of CD8+ natural killer cells (NK8+) associated with favourable outcome. NK8+ are capable of regulating CD4+ T cell activation and proliferation in vitro, with reduced expression of HLA-G binding inhibitory receptors and consequent reduced sensitivity to HLA-G-mediated suppression. We identify surrogate markers of the NK8+ signature in peripheral blood leucocytes and validate their association with clinical outcome in an independent cohort, suggesting their measurement may facilitate early, targeted therapy in RRMS.
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7
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Jones BE, Herrera CA, Agosto-Burgos C, Starmer J, Bass WA, Poulton CJ, Blazek L, Henderson CD, Hu Y, Hogan SL, Hu P, Xiao H, Wu EY, Chen DP, Jennette JC, Free ME, Falk RJ, Ciavatta DJ. ANCA autoantigen gene expression highlights neutrophil heterogeneity where expression in normal-density neutrophils correlates with ANCA-induced activation. Kidney Int 2020; 98:744-757. [PMID: 32446935 DOI: 10.1016/j.kint.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 03/20/2020] [Accepted: 04/02/2020] [Indexed: 12/27/2022]
Abstract
ANCA vasculitis is an autoimmune disease with increased expression of the autoantigen genes, myeloperoxidase (MPO) and proteinase 3 (PRTN3), but the origin and significance of expression is less distinct. To clarify this, we measured MPO and PRTN3 messenger RNA in monocytes, normal-density neutrophils, and in enriched leukocytes from peripheral blood mononuclear cells. Increased autoantigen gene expression was detected in normal-density neutrophils and enriched leukocytes from patients during active disease compared to healthy individuals, with the largest difference in enriched leukocytes. RNA-seq of enriched leukocytes comparing active-remission pairs identified a gene signature for low-density neutrophils. Cell sorting revealed low-density neutrophils contained mature and immature neutrophils depending on the presence or absence of CD10. Both populations contributed to autoantigen expression but the frequency of immature cells in low-density neutrophils did not correlate with low-density neutrophil MPO or PRTN3 expression. Low-density neutrophils were refractory to MPO-ANCA induced oxidative burst, suggesting an alternative role for low-density neutrophils in ANCA vasculitis pathogenesis. In contrast, normal-density neutrophils were activated by MPO-ANCA and monoclonal anti-PR3 antibody. Normal-density neutrophil activation correlated with MPO and PRTN3 mRNA. Increased autoantigen gene expression originating from the mature low-density and normal-density neutrophils suggests transcriptional dysregulation is a hallmark of ANCA vasculitis. Thus, the correlation between autoantigen gene expression and antibody-mediated normal-density neutrophil activation connects autoantigen gene expression with disease pathogenesis.
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Affiliation(s)
- Britta E Jones
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina A Herrera
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Agosto-Burgos
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joshua Starmer
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William A Bass
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Caroline J Poulton
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lauren Blazek
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Candace D Henderson
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yichun Hu
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Susan L Hogan
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peiqi Hu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hong Xiao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eveline Y Wu
- Division of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dhruti P Chen
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J Charles Jennette
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Meghan E Free
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ronald J Falk
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dominic J Ciavatta
- UNC Kidney Center, Division of Nephrology and Hypertension, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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8
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Nielsen MC, Andersen MN, Møller HJ. Monocyte isolation techniques significantly impact the phenotype of both isolated monocytes and derived macrophages in vitro. Immunology 2019; 159:63-74. [PMID: 31573680 DOI: 10.1111/imm.13125] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/30/2019] [Accepted: 09/30/2019] [Indexed: 01/05/2023] Open
Abstract
Monocyte-derived macrophages (MDMs) generated from peripheral blood monocytes are widely used to model human macrophages for in vitro studies. However, the possible impact of different isolation methods on the resulting MDM phenotype is poorly described. We aimed to investigate the effects of three commonly used monocyte isolation techniques on the resulting MDM phenotype. Plastic adhesion, negative selection, and CD14pos selection were compared. Monocyte-derived macrophages were generated by 5-day culture with macrophage and granulocyte-macrophage colony-stimulating factors. We investigated monocyte and MDM yields, purity, viability, and cell phenotype. CD14pos selection resulted in highest monocyte yield (19·8 × 106 cells, equivalent to 70% of total) and purity (98·7%), compared with negative selection (17·7 × 106 cells, 61% of total, 85·0% purity), and plastic adhesion (6·1 × 106 cells, 12·9% of total, 44·2% purity). Negatively selected monocytes were highly contaminated with platelets. Expression of CD163 and CD14 were significantly lower on CD14pos selection and plastic adhesion monocytes, compared with untouched peripheral blood mononuclear cells. After maturation, CD14pos selection also resulted in the highest MDM purity (98·2%) compared with negative selection (94·5%) and plastic adhesion (66·1%). Furthermore, MDMs from plastic adhesion were M1-skewed (CD80high HLA-DRhigh CD163low ), whereas negative selection MDMs were M2-skewed (CD80low HLA-DRlow CD163high ). Choice of monocyte isolation method not only significantly affects yield and purity, but also impacts resulting phenotype of cultured MDMs. These differences may partly be explained by the presence of contaminating cells when using plastic adherence or negative selection. Careful considerations of monocyte isolation methods are important for designing in vitro assays on MDMs.
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Affiliation(s)
- Marlene C Nielsen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
| | - Morten N Andersen
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Holger J Møller
- Department of Clinical Biochemistry, Aarhus University Hospital, Aarhus, Denmark
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9
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Magnotti F, Lefeuvre L, Benezech S, Malsot T, Waeckel L, Martin A, Kerever S, Chirita D, Desjonqueres M, Duquesne A, Gerfaud-Valentin M, Laurent A, Sève P, Popoff MR, Walzer T, Belot A, Jamilloux Y, Henry T. Pyrin dephosphorylation is sufficient to trigger inflammasome activation in familial Mediterranean fever patients. EMBO Mol Med 2019; 11:e10547. [PMID: 31589380 PMCID: PMC6835204 DOI: 10.15252/emmm.201910547] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023] Open
Abstract
Familial Mediterranean fever (FMF) is the most frequent hereditary systemic autoinflammatory syndrome. FMF is usually caused by biallelic mutations in the MEFV gene, encoding Pyrin. Conclusive genetic evidence lacks for about 30% of patients diagnosed with clinical FMF. Pyrin is an inflammasome sensor maintained inactive by two kinases (PKN1/2). The consequences of MEFV mutations on inflammasome activation are still poorly understood. Here, we demonstrate that PKC superfamily inhibitors trigger inflammasome activation in monocytes from FMF patients while they trigger a delayed apoptosis in monocytes from healthy donors. The expression of the pathogenic p.M694V MEFV allele is necessary and sufficient for PKC inhibitors (or mutations precluding Pyrin phosphorylation) to trigger caspase‐1‐ and gasdermin D‐mediated pyroptosis. In line with colchicine efficacy in patients, colchicine fully blocks this response in FMF patients’ monocytes. These results indicate that Pyrin inflammasome activation is solely controlled by Pyrin (de)phosphorylation in FMF patients while a second control mechanism restricts its activation in healthy donors/non‐FMF patients. This study paves the way toward a functional characterization of MEFV variants and a functional test to diagnose FMF.
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Affiliation(s)
- Flora Magnotti
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
| | - Lucie Lefeuvre
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France.,Hospices Civils de Lyon, Lyon, France
| | - Sarah Benezech
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France.,Hospices Civils de Lyon, Lyon, France
| | - Tiphaine Malsot
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
| | - Louis Waeckel
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France.,Hospices Civils de Lyon, Lyon, France
| | - Amandine Martin
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
| | - Sébastien Kerever
- Department of Anesthesiology and Critical Care, St Louis-Lariboisière University Hospital, AP-HP, ECSTRA Team, Epidemiology and Biostatistics, Sorbonne Paris Cité Research Centre, UMR 1153, Inserm, University Denis Diderot-Paris VII, Paris, France
| | - Daria Chirita
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
| | - Marine Desjonqueres
- Hospices Civils de Lyon, Lyon, France.,Service de Néphrologie, Rhumatologie, Dermatologie pédiatriques, HFME, Bron, France
| | - Agnès Duquesne
- Hospices Civils de Lyon, Lyon, France.,Service de Néphrologie, Rhumatologie, Dermatologie pédiatriques, HFME, Bron, France
| | - Mathieu Gerfaud-Valentin
- Hospices Civils de Lyon, Lyon, France.,Service de Médecine Interne, Hôpital de la Croix-Rousse, Lyon, France
| | - Audrey Laurent
- Hospices Civils de Lyon, Lyon, France.,Service de Néphrologie, Rhumatologie, Dermatologie pédiatriques, HFME, Bron, France
| | - Pascal Sève
- Hospices Civils de Lyon, Lyon, France.,Service de Médecine Interne, Hôpital de la Croix-Rousse, Lyon, France
| | | | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
| | - Alexandre Belot
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France.,Hospices Civils de Lyon, Lyon, France.,Service de Néphrologie, Rhumatologie, Dermatologie pédiatriques, HFME, Bron, France
| | - Yvan Jamilloux
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France.,Hospices Civils de Lyon, Lyon, France.,Service de Médecine Interne, Hôpital de la Croix-Rousse, Lyon, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ. Lyon, Lyon, France
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10
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Analysis of the B cell receptor repertoire in six immune-mediated diseases. Nature 2019; 574:122-126. [PMID: 31554970 PMCID: PMC6795535 DOI: 10.1038/s41586-019-1595-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/21/2019] [Indexed: 01/22/2023]
Abstract
B cells are important in the pathogenesis of many, and perhaps all, immune-mediated diseases (IMDs). Each B cell expresses a single B cell receptor (BCR)1, with the diverse range of BCRs expressed by an individual’s total B cell population being termed the “BCR repertoire”. Our understanding of the BCR repertoire in the context of IMDs is incomplete, and defining this could reveal new insights into pathogenesis and therapy. We therefore compared the BCR repertoire in systemic lupus erythematosus (SLE), ANCA-associated vasculitis (AAV), Crohn’s disease (CD), Behçet’s disease (BD), eosinophilic granulomatosis with polyangiitis (EGPA) and IgA vasculitis (IgAV), analysing BCR clonality, and immunoglobulin heavy chain gene (IGHV) and, in particular, isotype usage. An IgA-dominated increased clonality in SLE and CD, together with skewed IGHV gene usage in these and other diseases, suggested a microbial contribution to pathogenesis. Different immunosuppressive treatment had specific and distinct impacts on the repertoire; B cells persisting after rituximab were predominately isotype-switched and clonally expanded, the inverse of those persisting after mycophenolate mofetil. A comparative analysis of the BCR repertoire in immune-mediated disease reveals a complex B cell architecture, providing a platform for understanding pathological mechanisms and designing treatment strategies.
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11
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Biasci D, Lee JC, Noor NM, Pombal DR, Hou M, Lewis N, Ahmad T, Hart A, Parkes M, McKinney EF, Lyons PA, Smith KGC. A blood-based prognostic biomarker in IBD. Gut 2019; 68:1386-1395. [PMID: 31030191 PMCID: PMC6691955 DOI: 10.1136/gutjnl-2019-318343] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/11/2019] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE We have previously described a prognostic transcriptional signature in CD8 T cells that separates patients with IBD into two phenotypically distinct subgroups, termed IBD1 and IBD2. Here we sought to develop a blood-based test that could identify these subgroups without cell separation, and thus be suitable for clinical use in Crohn's disease (CD) and ulcerative colitis (UC). DESIGN Patients with active IBD were recruited before treatment. Transcriptomic analyses were performed on purified CD8 T cells and/or whole blood. Phenotype data were collected prospectively. IBD1/IBD2 patient subgroups were identified by consensus clustering of CD8 T cell transcriptomes. In a training cohort, machine learning was used to identify groups of genes ('classifiers') whose differential expression in whole blood recreated the IBD1/IBD2 subgroups. Genes from the best classifiers were quantitative (q)PCR optimised, and further machine learning was used to identify the optimal qPCR classifier, which was locked down for further testing. Independent validation was sought in separate cohorts of patients with CD (n=66) and UC (n=57). RESULTS In both validation cohorts, a 17-gene qPCR-based classifier stratified patients into two distinct subgroups. Irrespective of the underlying diagnosis, IBDhi patients (analogous to the poor prognosis IBD1 subgroup) experienced significantly more aggressive disease than IBDlo patients (analogous to IBD2), with earlier need for treatment escalation (hazard ratio=2.65 (CD), 3.12 (UC)) and more escalations over time (for multiple escalations within 18 months: sensitivity=72.7% (CD), 100% (UC); negative predictive value=90.9% (CD), 100% (UC)). CONCLUSION This is the first validated prognostic biomarker that can predict prognosis in newly diagnosed patients with IBD and represents a step towards personalised therapy.
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Affiliation(s)
- Daniele Biasci
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - James C Lee
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | | | - Diana R Pombal
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | | | - Nina Lewis
- Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Tariq Ahmad
- University of Exeter Medical School, Exeter, UK
| | - Ailsa Hart
- St Mark's Hospital, London, UK
- Antigen Presentation Research Group, Imperial College, London, UK
| | - Miles Parkes
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eoin F McKinney
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
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12
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Cassatella MA, Östberg NK, Tamassia N, Soehnlein O. Biological Roles of Neutrophil-Derived Granule Proteins and Cytokines. Trends Immunol 2019; 40:648-664. [PMID: 31155315 DOI: 10.1016/j.it.2019.05.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 12/30/2022]
Abstract
Neutrophils, the most abundant white blood cells in human circulation, entertain intense interactions with other leukocyte subsets, platelets, and stromal cells. Molecularly, such interactions are typically communicated through proteins generated during granulopoiesis, stored in granules, or produced on demand. Here, we provide an overview of the mammalian regulation of granule protein production in the bone marrow and the de novo synthesis of cytokines by neutrophils recruited to tissues. In addition, we discuss some of the known biological roles of these protein messengers, and how neutrophil-borne granule proteins and cytokines can synergize to modulate inflammation and tumor development. Decoding the neutrophil interactome is important for therapeutically neutralizing individual proteins to putatively dampen inflammation, or for delivering modified neutrophil-borne proteins to boost host defense.
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Affiliation(s)
| | - Nataliya K Östberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Oliver Soehnlein
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Stockholm, Sweden; Institute for Cardiovascular Prevention (IPEK), Klinikum der LMU, München, Germany; German Centre for Cardiovascular Research (DZHK), Partner site, Munich, Germany.
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13
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Tarique AA, Sly PD, Cardenas DG, Luo L, Stow JL, Bell SC, Wainwright CE, Fantino E. Differential expression of genes and receptors in monocytes from patients with cystic fibrosis. J Cyst Fibros 2018; 18:342-348. [PMID: 30177416 DOI: 10.1016/j.jcf.2018.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/29/2018] [Accepted: 07/30/2018] [Indexed: 11/30/2022]
Abstract
INTRODUCTION We previously reported defective alternative polarization (M2) of macrophages and early expression of classically polarized (M1) macrophage markers in unpolarized monocyte-derived macrophages (MDMs) in patients with cystic fibrosis (CF). The present study assessed whether the mechanism(s) underlying defective macrophage polarization resided in circulating monocytes. METHODS Monocyte subsets (classical, intermediate and non-classical), markers for monocyte activation (CD163) and recruitment (CD195), receptors/genes associated with macrophage differentiation and polarization were analyzed in CF and compared with healthy individuals. RESULTS No differences were observed in the monocyte subsets or in the expression of CD163 or CD195. Expression of the M-CSF receptor, TLR4, γC, IL-4Rα, IL-13Rα1, TIMP-1 and Cox-2 were higher in CF monocytes, albeit at low levels, whereas, LRP1, MMP9, MMP28 were downregulated compared to mooncytes from healthy individuals. CONCLUSIONS Our data suggest that differences in CF monocytes may contribute to the reported CFTR-dependent defect in macrophage differentiation, polarization and function.
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Affiliation(s)
- Abdullah A Tarique
- Child Health Research Centre (CHRC), The University of Queensland, Australia
| | - Peter D Sly
- Child Health Research Centre (CHRC), The University of Queensland, Australia; Department of Respiratory and Sleep Medicine, Children's Health Queensland, Brisbane, Australia.
| | - Diana G Cardenas
- Child Health Research Centre (CHRC), The University of Queensland, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, Australia
| | - Jennifer L Stow
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, Australia
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | - Claire E Wainwright
- Child Health Research Centre (CHRC), The University of Queensland, Australia; Department of Respiratory and Sleep Medicine, Children's Health Queensland, Brisbane, Australia
| | - Emmanuelle Fantino
- Child Health Research Centre (CHRC), The University of Queensland, Australia
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14
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De Smit E, Lukowski SW, Anderson L, Senabouth A, Dauyey K, Song S, Wyse B, Wheeler L, Chen CY, Cao K, Wong Ten Yuen A, Shuey N, Clarke L, Lopez Sanchez I, Hung SSC, Pébay A, Mackey DA, Brown MA, Hewitt AW, Powell JE. Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis. BMC Med Genomics 2018; 11:61. [PMID: 30037347 PMCID: PMC6057030 DOI: 10.1186/s12920-018-0376-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022] Open
Abstract
Background Giant cell arteritis (GCA) is the most common form of vasculitis affecting elderly people. It is one of the few true ophthalmic emergencies but symptoms and signs are variable thereby making it a challenging disease to diagnose. A temporal artery biopsy is the gold standard to confirm GCA, but there are currently no specific biochemical markers to aid diagnosis. We aimed to identify a less invasive method to confirm the diagnosis of GCA, as well as to ascertain clinically relevant predictive biomarkers by studying the transcriptome of purified peripheral CD4+ and CD8+ T lymphocytes in patients with GCA. Methods We recruited 16 patients with histological evidence of GCA at the Royal Victorian Eye and Ear Hospital, Melbourne, Australia, and aimed to collect blood samples at six time points: acute phase, 2–3 weeks, 6–8 weeks, 3 months, 6 months and 12 months after clinical diagnosis. CD4+ and CD8+ T-cells were positively selected at each time point through magnetic-assisted cell sorting. RNA was extracted from all 195 collected samples for subsequent RNA sequencing. The expression profiles of patients were compared to those of 16 age-matched controls. Results Over the 12-month study period, polynomial modelling analyses identified 179 and 4 statistically significant transcripts with altered expression profiles (FDR < 0.05) between cases and controls in CD4+ and CD8+ populations, respectively. In CD8+ cells, two transcripts remained differentially expressed after 12 months; SGTB, associated with neuronal apoptosis, and FCGR3A, associatied with Takayasu arteritis. We detected genes that correlate with both symptoms and biochemical markers used for predicting long-term prognosis. 15 genes were shared across 3 phenotypes in CD4 and 16 across CD8 cells. In CD8, IL32 was common to 5 phenotypes including Polymyalgia Rheumatica, bilateral blindness and death within 12 months. Conclusions This is the first longitudinal gene expression study undertaken to identify robust transcriptomic biomarkers of GCA. Our results show cell type-specific transcript expression profiles, novel gene-phenotype associations, and uncover important biological pathways for this disease. In the acute phase, the gene-phenotype relationships we have identified could provide insight to potential disease severity and as such guide in initiating appropriate patient management. Electronic supplementary material The online version of this article (10.1186/s12920-018-0376-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabeth De Smit
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia.
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Lisa Anderson
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Anne Senabouth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Kaisar Dauyey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Sharon Song
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Bruce Wyse
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Lawrie Wheeler
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Christine Y Chen
- Ophthalmology Department at Monash Health, Department of Surgery, School of Clinical Sciences at Monash Health, Melbourne, 3168, Victoria, Australia
| | - Khoa Cao
- Ophthalmology Department at Monash Health, Department of Surgery, School of Clinical Sciences at Monash Health, Melbourne, 3168, Victoria, Australia
| | - Amy Wong Ten Yuen
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Neil Shuey
- Department of Neuro-Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, 3002, Victoria, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Isabel Lopez Sanchez
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Sandy S C Hung
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Lions Eye Institute, Perth, 6009, Western Australia, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia.,School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, 7000, Tasmania, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
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15
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Banham GD, Flint SM, Torpey N, Lyons PA, Shanahan DN, Gibson A, Watson CJE, O'Sullivan AM, Chadwick JA, Foster KE, Jones RB, Devey LR, Richards A, Erwig LP, Savage CO, Smith KGC, Henderson RB, Clatworthy MR. Belimumab in kidney transplantation: an experimental medicine, randomised, placebo-controlled phase 2 trial. Lancet 2018; 391:2619-2630. [PMID: 29910042 DOI: 10.1016/s0140-6736(18)30984-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND B cells produce alloantibodies and activate alloreactive T cells, negatively affecting kidney transplant survival. By contrast, regulatory B cells are associated with transplant tolerance. Immunotherapies are needed that inhibit B-cell effector function, including antibody secretion, while sparing regulators and minimising infection risk. B lymphocyte stimulator (BLyS) is a cytokine that promotes B-cell activation and has not previously been targeted in kidney transplant recipients. We aimed to determine the safety and activity of an anti-BLyS antibody, belimumab, in addition to standard-of-care immunosuppression in adult kidney transplant recipients. We used an experimental medicine study design with multiple secondary and exploratory endpoints to gain further insight into the effect of belimumab on the generation of de-novo IgG and on the regulatory B-cell compartment. METHODS We undertook a double-blind, randomised, placebo-controlled phase 2 trial of belimumab, in addition to standard-of-care immunosuppression (basiliximab, mycophenolate mofetil, tacrolimus, and prednisolone) at two centres, Addenbrooke's Hospital, Cambridge, UK, and Guy's and St Thomas' Hospital, London, UK. Participants were eligible if they were aged 18-75 years and receiving a kidney transplant and were planned to receive standard-of-care immunosuppression. Participants were randomly assigned (1:1) to receive either intravenous belimumab 10 mg per kg bodyweight or placebo, given at day 0, 14, and 28, and then every 4 weeks for a total of seven infusions. The co-primary endpoints were safety and change in the concentration of naive B cells from baseline to week 24, both of which were analysed in all patients who received a transplant and at least one dose of drug or placebo (the modified intention-to-treat [mITT] population). This trial has been completed and is registered with ClinicalTrials.gov, NCT01536379, and EudraCT, 2011-006215-56. FINDINGS Between Sept 13, 2013, and Feb 8, 2015, of 303 patients assessed for eligibility, 28 kidney transplant recipients were randomly assigned to receive belimumab (n=14) or placebo (n=14). 25 patients (12 [86%] patients assigned to the belimumab group and 13 [93%] patients assigned to the placebo group) received a transplant and were included in the mITT population. We observed similar proportions of adverse events in the belimumab and placebo groups, including serious infections (one [8%] of 12 in the belimumab group and five [38%] of 13 in the placebo group during the 6-month on-treatment phase; and none in the belimumab group and two [15%] in the placebo group during the 6-month follow-up). In the on-treatment phase, one patient in the placebo group died because of fatal myocardial infarction and acute cardiac failure. The co-primary endpoint of a reduction in naive B cells from baseline to week 24 was not met. Treatment with belimumab did not significantly reduce the number of naive B cells from baseline to week 24 (adjusted mean difference between the belimumab and placebo treatment groups -34·4 cells per μL, 95% CI -109·5 to 40·7). INTERPRETATION Belimumab might be a useful adjunct to standard-of-care immunosuppression in renal transplantation, with no major increased risk of infection and potential beneficial effects on humoral alloimmunity. FUNDING GlaxoSmithKline.
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Affiliation(s)
- Gemma D Banham
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Shaun M Flint
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Nicholas Torpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Don N Shanahan
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Adele Gibson
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Christopher J E Watson
- Department of Surgery, University of Cambridge School of Clinical Medicine, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Ann-Marie O'Sullivan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Joseph A Chadwick
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Katie E Foster
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Rachel B Jones
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | - Luke R Devey
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Anna Richards
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Lars-Peter Erwig
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Caroline O Savage
- ImmunoInflammation Therapy Area Unit, GlaxoSmithKline, Stevenage, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Menna R Clatworthy
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK; National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, Cambridge, UK.
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16
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Jamilloux Y, Lefeuvre L, Magnotti F, Martin A, Benezech S, Allatif O, Penel-Page M, Hentgen V, Sève P, Gerfaud-Valentin M, Duquesne A, Desjonquères M, Laurent A, Rémy-Piccolo V, Cimaz R, Cantarini L, Bourdonnay E, Walzer T, Py BF, Belot A, Henry T. Familial Mediterranean fever mutations are hypermorphic mutations that specifically decrease the activation threshold of the Pyrin inflammasome. Rheumatology (Oxford) 2017; 57:100-111. [PMID: 29040788 DOI: 10.1093/rheumatology/kex373] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Indexed: 12/31/2022] Open
Abstract
Objectives FMF is the most frequent autoinflammatory disease and is associated in most patients with bi-allelic MEFV mutations. MEFV encodes Pyrin, an inflammasome sensor activated following RhoGTPase inhibition. The functional consequences of MEFV mutations on the ability of Pyrin variants to act as inflammasome sensors are largely unknown. The aim of this study was to assess whether MEFV mutations affect the ability of Pyrin to detect RhoGTPase inhibition and other inflammasome stimuli. Methods IL-1β and IL-18 released by monocytes from healthy donors (HDs) and FMF patients were measured upon specific engagement of the Pyrin, NLRP3 and NLRC4 inflammasomes. Cell death kinetics following Pyrin activation was monitored in real time. Results Monocytes from FMF patients secreted significantly more IL-1β and IL-18 and died significantly faster than HD monocytes in response to low concentrations of Clostridium difficile toxin B (TcdB), a Pyrin-activating stimulus. Monocytes from patients bearing two MEFV exon 10 pathogenic variants displayed an increased Pyrin inflammasome response compared with monocytes from patients with a single exon 10 pathogenic variant indicating a gene-dosage effect. Using a short priming step, the response of monocytes from FMF patients to NLRP3- and NLRC4-activating stimuli was normal indicating that MEFV mutations trigger a specific hypersensitivity of monocytes to low doses of a Pyrin-engaging stimulus. Conclusion Contrary to the NLRP3 mutations described in cryopyrin-associated periodic syndrome, FMF-associated MEFV mutations do not lead to a constitutive activation of Pyrin. Rather, FMF-associated mutations are hypermorphic mutations that specifically decrease the activation threshold of the Pyrin inflammasome without affecting other canonical inflammasomes.
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Affiliation(s)
- Yvan Jamilloux
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
- Department of Internal Medicine, University Hospital Croix-Rousse, Hospices Civils de Lyon
| | - Lucie Lefeuvre
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
- Department of General Medicine, Hospices Civils de Lyon, Lyon, France
| | - Flora Magnotti
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
- Pediatric Rheumatology Unit, AOU Meyer, University of Firenze, Firenze
- Research Center of Systemic Autoinflammatory Diseases and Behcet's Disease Clinic, Rheumatology Unit, University of Siena, Siena, Italy
| | - Amandine Martin
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
| | - Sarah Benezech
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
| | - Omran Allatif
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
- Bioinformatics and Biostatistics Service (BIBS), University of Lyon, Lyon
| | - Mathilde Penel-Page
- Department of Paediatric Nephrology, Rheumatology, Dermatology, Hôpital Femme-Mère Enfant, Bron
| | - Véronique Hentgen
- French Reference Centre for Autoinflammatory Diseases (CEREMAI), Versailles Hospital, Le Chesnay
| | - Pascal Sève
- Department of Internal Medicine, University Hospital Croix-Rousse, Hospices Civils de Lyon
| | | | - Agnès Duquesne
- Department of Paediatric Nephrology, Rheumatology, Dermatology, Hôpital Femme-Mère Enfant, Bron
| | - Marine Desjonquères
- Department of Paediatric Nephrology, Rheumatology, Dermatology, Hôpital Femme-Mère Enfant, Bron
| | - Audrey Laurent
- Department of Paediatric Nephrology, Rheumatology, Dermatology, Hôpital Femme-Mère Enfant, Bron
| | - Vanessa Rémy-Piccolo
- Department of Paediatric Rheumatology, Hôpital Nord Ouest, Villefranche sur Saône, France
| | - Rolando Cimaz
- Pediatric Rheumatology Unit, AOU Meyer, University of Firenze, Firenze
| | - Luca Cantarini
- Research Center of Systemic Autoinflammatory Diseases and Behcet's Disease Clinic, Rheumatology Unit, University of Siena, Siena, Italy
| | - Emilie Bourdonnay
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
| | - Thierry Walzer
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
| | - Bénédicte F Py
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
| | - Alexandre Belot
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
- Department of Paediatric Nephrology, Rheumatology, Dermatology, Hôpital Femme-Mère Enfant, Bron
| | - Thomas Henry
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007
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17
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Liu Y, Reynolds LM, Ding J, Hou L, Lohman K, Young T, Cui W, Huang Z, Grenier C, Wan M, Stunnenberg HG, Siscovick D, Hou L, Psaty BM, Rich SS, Rotter JI, Kaufman JD, Burke GL, Murphy S, Jacobs DR, Post W, Hoeschele I, Bell DA, Herrington D, Parks JS, Tracy RP, McCall CE, Stein JH. Blood monocyte transcriptome and epigenome analyses reveal loci associated with human atherosclerosis. Nat Commun 2017; 8:393. [PMID: 28855511 PMCID: PMC5577184 DOI: 10.1038/s41467-017-00517-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/05/2017] [Indexed: 12/20/2022] Open
Abstract
Little is known regarding the epigenetic basis of atherosclerosis. Here we present the CD14+ blood monocyte transcriptome and epigenome signatures associated with human atherosclerosis. The transcriptome signature includes transcription coactivator, ARID5B, which is known to form a chromatin derepressor complex with a histone H3K9Me2-specific demethylase and promote adipogenesis and smooth muscle development. ARID5B CpG (cg25953130) methylation is inversely associated with both ARID5B expression and atherosclerosis, consistent with this CpG residing in an ARID5B enhancer region, based on chromatin capture and histone marks data. Mediation analysis supports assumptions that ARID5B expression mediates effects of cg25953130 methylation and several cardiovascular disease risk factors on atherosclerotic burden. In lipopolysaccharide-stimulated human THP1 monocytes, ARID5B knockdown reduced expression of genes involved in atherosclerosis-related inflammatory and lipid metabolism pathways, and inhibited cell migration and phagocytosis. These data suggest that ARID5B expression, possibly regulated by an epigenetically controlled enhancer, promotes atherosclerosis by dysregulating immunometabolism towards a chronic inflammatory phenotype.The molecular mechanisms mediating the impact of environmental factors in atherosclerosis are unclear. Here, the authors examine CD14+ blood monocyte's transcriptome and epigenome signatures to find differential methylation and expression of ARID5B to be associated with human atherosclerosis.
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Affiliation(s)
- Yongmei Liu
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA.
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Li Hou
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Tracey Young
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Wei Cui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | | | - Ma Wan
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences (NCMLS), 6525, GA, Nijmegen, The Netherlands
| | | | - Lifang Hou
- Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, 60208, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Joel D Kaufman
- Department of Environmental and Occupational Health Sciences, Medicine and Epidemiology, University of Washington, Seattle, WA, 98104, USA
| | - Gregory L Burke
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | | | - David R Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Wendy Post
- Department of Pathology and Cardiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Ina Hoeschele
- Biocomplexity Institute and Department of Statistics, Virginia Tech, VA, 24061, USA
| | - Douglas A Bell
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - David Herrington
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - John S Parks
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont, Colchester, VT, 05446, USA
| | - Charles E McCall
- Department of Internal Medicine-Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - James H Stein
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
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18
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Yang J, Ge H, Poulton CJ, Hogan SL, Hu Y, Jones BE, Henderson CD, McInnis EA, Pendergraft WF, Jennette JC, Falk RJ, Ciavatta DJ. Histone modification signature at myeloperoxidase and proteinase 3 in patients with anti-neutrophil cytoplasmic autoantibody-associated vasculitis. Clin Epigenetics 2016; 8:85. [PMID: 27752292 PMCID: PMC5057507 DOI: 10.1186/s13148-016-0251-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is a systemic autoimmune disease characterized by destructive vascular inflammation. Two prominent ANCA autoantigens are myeloperoxidase (MPO) and proteinase 3 (PR3), and transcription of MPO and PRTN3, the genes encoding the autoantigens, is associated with disease activity. We investigated whether patients with AAV have alterations in histone modifications, particularly those associated with transcriptional activation, at MPO and PRTN3. RESULTS We identified a network of genes regulating histone modifications that were differentially expressed in AAV patients compared to healthy controls. We focused on four genes (EHMT1 and EHMT2, ING4, and MSL1) and found their expression correlated with expression of MPO and PRTN3. Methylation of histone H3K9, catalyzed by EHMT1 and EHMT2 and associated with gene silencing, was most depleted at MPO and PRTN3 in patients with active disease and the highest MPO and PRTN3 expression. Acetylation of histone H4K16, modified by complexes containing ING4 and MSL1 and associated with gene activation, was most enriched at MPO and PRTN3 in patients with active disease and the highest MPO and PRTN3 expression. Methylation at H3K4, a mark of transcriptional activation, was enriched at MPO and PRTN3 in patients and healthy controls. CONCLUSIONS MPO and PRTN3 in neutrophils of AAV patients with active disease have a distinct pattern of histone modifications, which implicates epigenetic mechanisms in regulating expression of autoantigen genes and suggests that the epigenome may be involved in AAV pathogenesis.
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Affiliation(s)
- Jiajin Yang
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Heng Ge
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Nephrology, The Second Affiliated Hospital, School of Medicine, Xian Jiaotong University, 157 Xiwu Road, Xian, Shaanxi 710004 People's Republic of China
| | - Caroline J Poulton
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Susan L Hogan
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yichun Hu
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Britta E Jones
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Candace D Henderson
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Elizabeth A McInnis
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - William F Pendergraft
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - J Charles Jennette
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Ronald J Falk
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Dominic J Ciavatta
- UNC Kidney Center, Department of Medicine, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, NC USA.,Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Campus Box 7264, Chapel Hill, NC 27599 USA
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19
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Schwarz EC, Backes C, Knörck A, Ludwig N, Leidinger P, Hoxha C, Schwär G, Grossmann T, Müller SC, Hart M, Haas J, Galata V, Müller I, Fehlmann T, Eichler H, Franke A, Meder B, Meese E, Hoth M, Keller A. Deep characterization of blood cell miRNomes by NGS. Cell Mol Life Sci 2016; 73:3169-81. [PMID: 26874686 PMCID: PMC11108270 DOI: 10.1007/s00018-016-2154-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/25/2016] [Accepted: 02/01/2016] [Indexed: 12/31/2022]
Abstract
A systematic understanding of different factors influencing cell type specific microRNA profiles is essential for state-of-the art biomarker research. We carried out a comprehensive analysis of the biological variability and changes in cell type pattern over time for different cell types and different isolation approaches in technical replicates. All combinations of the parameters mentioned above have been measured, resulting in 108 miRNA profiles that were evaluated by next-generation-sequencing. The largest miRNA variability was due to inter-individual differences (34 %), followed by the cell types (23.4 %) and the isolation technique (17.2 %). The change over time in cell miRNA composition was moderate (<3 %) being close to the technical variations (<1 %). Largest variability (including technical and biological variance) was observed for CD8 cells while CD3 and CD4 cells showed significantly lower variations. ANOVA highlighted that 51.5 % of all miRNAs were significantly influenced by the purification technique. While CD4 cells were least affected, especially miRNA profiles of CD8 cells were fluctuating depending on the cell purification approach. To provide researchers access to the profiles and to allow further analyses of the tested conditions we implemented a dynamic web resource.
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Affiliation(s)
- Eva C Schwarz
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, Homburg, Germany
| | - Christina Backes
- Saarland University, Building E2.1, 66123, Saarbrücken, Germany.
| | - Arne Knörck
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, Homburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Cora Hoxha
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, Homburg, Germany
| | - Gertrud Schwär
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, Homburg, Germany
| | | | - Sabine C Müller
- Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Martin Hart
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Jan Haas
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | | | - Isabelle Müller
- Clinical Hemostaseology and Transfusion Medicine, Saarland University, Homburg, Germany
| | - Tobias Fehlmann
- Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Hermann Eichler
- Clinical Hemostaseology and Transfusion Medicine, Saarland University, Homburg, Germany
| | | | - Benjamin Meder
- Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Markus Hoth
- Biophysics, Center for Integrative Physiology and Molecular Medicine, School of Medicine, Saarland University, Homburg, Germany
| | - Andreas Keller
- Saarland University, Building E2.1, 66123, Saarbrücken, Germany
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20
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Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KGC. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. Genome Med 2016; 8:76. [PMID: 27435189 PMCID: PMC4952362 DOI: 10.1186/s13073-016-0329-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. METHODS We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. RESULTS Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant hits. CONCLUSIONS This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.
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Affiliation(s)
- Arianne C. Richard
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - James E. Peters
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - James C. Lee
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Golnaz Vahedi
- />Department of Genetics, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Alejandro A. Schäffer
- />Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894 USA
| | - Richard M. Siegel
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paul A. Lyons
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Kenneth G. C. Smith
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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21
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McArdle S, Mikulski Z, Ley K. Live cell imaging to understand monocyte, macrophage, and dendritic cell function in atherosclerosis. J Exp Med 2016; 213:1117-31. [PMID: 27270892 PMCID: PMC4925021 DOI: 10.1084/jem.20151885] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 04/28/2016] [Indexed: 02/06/2023] Open
Abstract
Ley et al. provide a review of the technology and accomplishments of dynamic imaging of myeloid cells in atherosclerosis. Intravital imaging is an invaluable tool for understanding the function of cells in healthy and diseased tissues. It provides a window into dynamic processes that cannot be studied by other techniques. This review will cover the benefits and limitations of various techniques for labeling and imaging myeloid cells, with a special focus on imaging cells in atherosclerotic arteries. Although intravital imaging is a powerful tool for understanding cell function, it alone does not provide a complete picture of the cell. Other techniques, such as flow cytometry and transcriptomics, must be combined with intravital imaging to fully understand a cell's phenotype, lineage, and function.
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Affiliation(s)
- Sara McArdle
- Division of Inflammation Biology and Microscopy Core, La Jolla Institute of Allergy and Immunology, La Jolla, CA 92037
| | - Zbigniew Mikulski
- Division of Inflammation Biology and Microscopy Core, La Jolla Institute of Allergy and Immunology, La Jolla, CA 92037
| | - Klaus Ley
- Division of Inflammation Biology and Microscopy Core, La Jolla Institute of Allergy and Immunology, La Jolla, CA 92037
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22
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Flint SM, Jovanovic V, Teo BW, Mak A, Thumboo J, McKinney EF, Lee JC, MacAry P, Kemeny DM, Jayne DR, Fong KY, Lyons PA, Smith KG. Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases. RMD Open 2016; 2:e000183. [PMID: 27252891 PMCID: PMC4879345 DOI: 10.1136/rmdopen-2015-000183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/01/2016] [Accepted: 03/24/2016] [Indexed: 01/05/2023] Open
Abstract
Objectives Type 1 interferons (IFN-1) are implicated in the pathogenesis of systemic lupus erythematosus (SLE), but most studies have only reported the effect of IFN-1 on mixed cell populations. We aimed to define modules of IFN-1-associated genes in purified leucocyte populations and use these as a basis for a detailed comparative analysis. Methods CD4+ and CD8+ T cells, monocytes and neutrophils were purified from patients with SLE, other immune-mediated diseases and healthy volunteers and gene expression then determined by microarray. Modules of IFN-1-associated genes were defined using weighted gene coexpression network analysis. The composition and expression of these modules was analysed. Results 1150 of 1288 IFN-1-associated genes were specific to myeloid subsets, compared with 11 genes unique to T cells. IFN-1 genes were more highly expressed in myeloid subsets compared with T cells. A subset of neutrophil samples from healthy volunteers (HV) and conditions not classically associated with IFN-1 signatures displayed increased IFN-1 gene expression, whereas upregulation of IFN-1-associated genes in T cells was restricted to SLE. Conclusions Given the broad upregulation of IFN-1 genes in neutrophils including in some HV, investigators reporting IFN-1 signatures on the basis of whole blood samples should be cautious about interpreting this as evidence of bona fide IFN-1-mediated pathology. Instead, specific upregulation of IFN-1-associated genes in T cells may be a useful biomarker and a further mechanism by which elevated IFN-1 contributes to autoimmunity in SLE.
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Affiliation(s)
- Shaun M Flint
- Department of Medicine, The University of Cambridge, Cambridge, UK; Cambridge Institute of Medical Research, The University of Cambridge, Cambridge, UK
| | - Vojislav Jovanovic
- Immunology Programme and Department of Microbiology Centre for Life Sciences , National University of Singapore , Singapore , Singapore
| | - Boon Wee Teo
- Department of Medicine , Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore
| | - Anselm Mak
- Department of Medicine , Yong Loo Lin School of Medicine, National University of Singapore , Singapore , Singapore
| | - Julian Thumboo
- Department of Rheumatology and Immunology , Singapore General Hospital , Singapore , Singapore
| | - Eoin F McKinney
- Department of Medicine, The University of Cambridge, Cambridge, UK; Cambridge Institute of Medical Research, The University of Cambridge, Cambridge, UK
| | - James C Lee
- Department of Medicine, The University of Cambridge, Cambridge, UK; Cambridge Institute of Medical Research, The University of Cambridge, Cambridge, UK
| | - Paul MacAry
- Immunology Programme and Department of Microbiology Centre for Life Sciences , National University of Singapore , Singapore , Singapore
| | - David M Kemeny
- Immunology Programme and Department of Microbiology Centre for Life Sciences , National University of Singapore , Singapore , Singapore
| | - David Rw Jayne
- Department of Medicine , The University of Cambridge , Cambridge , UK
| | - Kok Yong Fong
- Department of Rheumatology and Immunology , Singapore General Hospital , Singapore , Singapore
| | - Paul A Lyons
- Department of Medicine, The University of Cambridge, Cambridge, UK; Cambridge Institute of Medical Research, The University of Cambridge, Cambridge, UK
| | - Kenneth Gc Smith
- Department of Medicine, The University of Cambridge, Cambridge, UK; Cambridge Institute of Medical Research, The University of Cambridge, Cambridge, UK; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Hohos NM, Lee K, Ji L, Yu M, Kandasamy MM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J Immunol Methods 2016; 436:1-15. [PMID: 27164004 PMCID: PMC5131182 DOI: 10.1016/j.jim.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease-related stress. We considered the hypothesis that the various classes of peripheral leukocytes differentially regulate the synthesis of 5-methylcytosine (5mCG) and its removal via Ten-Eleven Translocation (TET) dioxygenase catalyzed hydroxymethylation to 5-hydroxymethylcytosine (5hmCG), reflecting their responsiveness to environment. Although it is known that reductions in TET1 and/or TET2 activity lead to the over-proliferation of various leukocyte precursors in bone marrow and in development of chronic myelomonocytic leukemia and myeloproliferative neoplasms, the role of 5mCG hydroxymethylation in peripheral blood is less well studied. RESULTS We developed simplified protocols to rapidly and reiteratively isolate non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B), the turnover of 5mC by demethylation (TET1, 2, 3), and DNA repair (GADD45A, B, G) and in the global and gene-region-specific levels of DNA 5hmCG (CD4+ T cells≫CD14+ monocytes>CD16+ neutrophils>CD19+ B cells>CD56+ NK cells>Siglec8+ eosinophils>CD8+ T cells). CONCLUSIONS Our data taken together suggest a potential hierarchy of responsiveness among classes of leukocytes with CD4+, CD8+ T cells and CD14+ monocytes being the most distinctly poised for a rapid methylome response to physiological stress and disease.
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Affiliation(s)
- Natalie M Hohos
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
| | - Kevin Lee
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | | | - Bradley G Phillips
- Clinical and Administrative Pharmacy, University of Georgia, Athens, GA, USA.
| | - Clifton A Baile
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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Epigenetic regulation of neutrophil development and function. Semin Immunol 2016; 28:83-93. [PMID: 27084194 DOI: 10.1016/j.smim.2016.04.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/14/2022]
Abstract
In addition to performing well-defined effector functions, neutrophils are now recognized as versatile and sophisticated cells with critical immunoregulatory roles. These include the release of a variety of proinflammatory or immunosuppressive cytokines, as well as the expression of genes with regulatory functions. Neutrophils share broad transcriptional features with monocytes, in keeping with the close developmental relation between the two cell types. However, neutrophil-specific gene expression patterns conferring cell type-specific responses to bacterial, viral or fungal components have been identified. Accumulating evidence suggest that these differences reflect the peculiar epigenomic and regulatory landscapes of neutrophils and monocytes, in turn controlled by the specific lineage-determining transcription factors shaping their identity. In this review, we will describe current knowledge on how neutrophil identity and function are controlled at the molecular level, focusing on transcriptional and chromatin regulation of neutrophil development and activation in response to inflammatory stimuli.
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Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease. PLoS Genet 2016; 12:e1005908. [PMID: 27015630 PMCID: PMC4807835 DOI: 10.1371/journal.pgen.1005908] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies (GWAS) have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs) is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91), anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46) and healthy controls (n = 43), revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases. The human immune system has evolved to protect us from infection and cancer, whilst avoiding damage to healthy tissue. If this complex system goes wrong, immune cells may cause inappropriate inflammation and damage, resulting in clinical disease. Examples include inflammatory bowel disease and autoimmune vasculitis, characterised by inflammation in the gut and blood vessels respectively. Genetic studies have identified many variants in our DNA code that predispose to such immune-mediated diseases. The majority of these variants lie outside protein-coding regions, and so how they influence disease risk remains largely unclear. Examining how genetic variants affect gene expression can help bridge this gap in our knowledge, but these effects are highly dependent on the cellular or environmental context such as tissue type or cellular activation status. We investigated the genetic control of gene expression in five white blood cell subtypes taken from patients with active inflammatory bowel disease and autoimmune vasculitis, and from healthy controls. We report the novel observation of distinct variants that only affect gene expression in patients with active inflammatory disease, and show that these effects can disappear following treatment. These findings provide new insights into the genetic basis of important immune-mediated diseases.
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Strehl C, Schellmann S, Maurizi L, Hofmann-Amtenbrink M, Häupl T, Hofmann H, Buttgereit F, Gaber T. Effects of PVA-coated nanoparticles on human T helper cell activity. Toxicol Lett 2016; 245:52-8. [DOI: 10.1016/j.toxlet.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 10/22/2022]
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Baldeón Rojas L, Weigelt K, de Wit H, Ozcan B, van Oudenaren A, Sempértegui F, Sijbrands E, Grosse L, van Zonneveld AJ, Drexhage HA, Leenen PJM. Study on inflammation-related genes and microRNAs, with special emphasis on the vascular repair factor HGF and miR-574-3p, in monocytes and serum of patients with T2D. Diabetol Metab Syndr 2016; 8:6. [PMID: 26779287 PMCID: PMC4714426 DOI: 10.1186/s13098-015-0113-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/19/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Recently, we reported signs of inflammation (raised IL-8, reduced miR-146a) and signs of vascular repair (raised HGF) in the serum of Ecuadorian patients with type 2 diabetes (T2D). In contrast, we found that the circulating monocytes lacked up-regulation of classical inflammatory genes (IL-1B, IL-6, and TNF) and there was even significant down-regulation of PTGS2. Notably, genes and a microRNA involved in adhesion, cell differentiation and morphology (CD9, DHRS3, PTPN7 and miR-34c-5p) were up-regulated in the T2D monocytes, suggesting a role of the anti-inflammatory cells in adhesion, vascular repair and invasion. AIM To determine the gene expression of the vascular repair factor HGF in the circulating monocytes of patients with T2D and to investigate the relationship between HGF and the expression of the other previously tested monocyte genes and the contribution to the raised serum level of HGF. In addition, we tested the level of 6 microRNAs, which were previously found abnormal in the circulating monocytes, in the serum of the patients. METHODS A gene and microRNA expression study in monocytes and serum of 64 Ecuadorian patients with T2D (37-85 years) and 44 non-diabetic controls (32-87 years). RESULTS The gene expression of HGF was significantly raised in the monocytes of the patients with T2D and associated with the expression of genes involved in adhesion, cell differentiation and morphology. HGF gene expression did not correlate with the serum level of HGF. The monocyte expression of pro-inflammatory cytokine genes was also not associated with the serum levels of these cytokines. The level of miR-574-3p was significantly decreased in the serum of the patients with T2D, and correlated in expression with the decreased well-established inflammation-regulating miR-146a. The level of the microRNAs in serum did not correlate with their expression level in monocytes. CONCLUSION In circulating monocytes of Ecuadorian T2D patients, the microRNA and gene expression of important inflammatory/chemotactic/motility/vascular repair factors differs from the expression in serum. While monocytes show a gene expression profile compatible with an anti-inflammatory state, serum shows a molecular profile compatible with an inflammatory state. Both compartments show molecular signs of vascular repair support, i.e. up-regulated HGF levels.
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Affiliation(s)
- Lucy Baldeón Rojas
- />Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
- />Department of Immunology, Central University of Ecuador, Quito, Ecuador
| | - Karin Weigelt
- />Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Harm de Wit
- />Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Behiye Ozcan
- />Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Eric Sijbrands
- />Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Grosse
- />Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Hemmo A. Drexhage
- />Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
- />Prometeo Program SENESCYT, Central University of Ecuador and Universidad de las Fuerzas Armadas, Quito, Ecuador
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28
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Dang MN, Bradford CM, Pozzilli P, Leslie RD. Methylation Analysis in Distinct Immune Cell Subsets in Type 1 Diabetes. Methods Mol Biol 2016; 1433:143-151. [PMID: 26791360 DOI: 10.1007/7651_2015_286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Epigenetics provides a mechanism in which the environment can interact with the genotype to produce a variety of phenotypes. These epigenetic modifications have been associated with altered gene expression and silencing of repetitive elements, and these modifications can be inherited mitotically. DNA methylation is the best characterized epigenetic mark and earlier studies have examined DNA methylation profiles in peripheral blood mononuclear cells in disease. However, any disease-related signatures identified would just display differences in the relative abundance of individual cell types as each cell subset generates a unique methylation profile. Therefore is it important to identify cell- or tissue-specific changes in DNA methylation, particularly in autoimmune diseases such as type 1 diabetes.
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Affiliation(s)
- Mary N Dang
- Centre for Diabetes and Metabolic Medicine, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK.
| | - Claire M Bradford
- Centre for Diabetes and Metabolic Medicine, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Paolo Pozzilli
- Centre for Diabetes and Metabolic Medicine, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
- Department of Endocrinology and Diabetes, University Campus Bio-Medico of Rome, Via Alvaro del Portillo, 21, 00128, Rome, Italy
| | - R David Leslie
- Centre for Diabetes and Metabolic Medicine, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
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29
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McDade TW, M Ross K, L Fried R, Arevalo JMG, Ma J, Miller GE, Cole SW. Genome-Wide Profiling of RNA from Dried Blood Spots: Convergence with Bioinformatic Results Derived from Whole Venous Blood and Peripheral Blood Mononuclear Cells. BIODEMOGRAPHY AND SOCIAL BIOLOGY 2016; 62:182-97. [PMID: 27337553 PMCID: PMC4972449 DOI: 10.1080/19485565.2016.1185600] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genome-wide transcriptional profiling has emerged as a powerful tool for analyzing biological mechanisms underlying social gradients in health, but utilization in population-based studies has been hampered by logistical constraints and costs associated with venipuncture blood sampling. Dried blood spots (DBS) provide a minimally invasive, low-cost alternative to venipuncture, and in this article we evaluate how closely the substantive results from DBS transcriptional profiling correspond to those derived from parallel analyses of gold-standard venous blood samples (PAXgene whole blood and peripheral blood mononuclear cells [PBMC]). Analyses focused on differences in gene expression between African-Americans and Caucasians in a community sample of 82 healthy adults (age 18-70 years; mean 35). Across 19,679 named gene transcripts, DBS-derived values correlated r = .85 with both PAXgene and PBMC values. Results from bioinformatics analyses of gene expression derived from DBS samples were concordant with PAXgene and PBMC samples in identifying increased Type I interferon signaling and up-regulated activity of monocytes and natural killer (NK) cells in African-Americans compared to Caucasian participants. These findings demonstrate the feasibility of DBS in field-based studies of gene expression and encourage future studies of human transcriptome dynamics in larger, more representative samples than are possible with clinic- or lab-based research designs.
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Affiliation(s)
- Thomas W McDade
- a Department of Anthropology , Northwestern University , Evanston , Illinois , USA
- b Cells to Society (C2S): The Center on Social Disparities and Health, Institute for Policy Research , Northwestern University , Evanston , Illinois , USA
- c Program in Child and Brain Development , Canadian Institute for Advanced Research , Toronto , Canada
| | - Kharah M Ross
- d Psychology Department , University of California, Los Angeles , Los Angeles , California , USA
| | - Ruby L Fried
- a Department of Anthropology , Northwestern University , Evanston , Illinois , USA
| | - Jesusa M G Arevalo
- e Department of Medicine, Division of Hematology-Oncology , UCLA School of Medicine , Los Angeles , California , USA
| | - Jeffrey Ma
- f Department of Psychiatry & Biobehavioral Sciences , Cousins Center for Psychoneuroimmunology , University of California, Los Angeles, Los Angeles , California , USA
| | - Gregory E Miller
- b Cells to Society (C2S): The Center on Social Disparities and Health, Institute for Policy Research , Northwestern University , Evanston , Illinois , USA
- g Department of Psychology , Northwestern University , Evanston , Illinois , USA
| | - Steve W Cole
- e Department of Medicine, Division of Hematology-Oncology , UCLA School of Medicine , Los Angeles , California , USA
- f Department of Psychiatry & Biobehavioral Sciences , Cousins Center for Psychoneuroimmunology , University of California, Los Angeles, Los Angeles , California , USA
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30
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Brkic Z, van Bon L, Cossu M, van Helden-Meeuwsen CG, Vonk MC, Knaapen H, van den Berg W, Dalm VA, Van Daele PL, Severino A, Maria NI, Guillen S, Dik WA, Beretta L, Versnel MA, Radstake T. The interferon type I signature is present in systemic sclerosis before overt fibrosis and might contribute to its pathogenesis through high BAFF gene expression and high collagen synthesis. Ann Rheum Dis 2015; 75:1567-73. [DOI: 10.1136/annrheumdis-2015-207392] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 08/28/2015] [Indexed: 12/18/2022]
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31
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Rifatbegovic F, Abbasi MR, Taschner-Mandl S, Kauer M, Weinhäusel A, Handgretinger R, Ambros PF. Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies-A Validation Study. PLoS One 2015; 10:e0137995. [PMID: 26360775 PMCID: PMC4567134 DOI: 10.1371/journal.pone.0137995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps-including transport duration, temperature and, importantly, tumor cell enrichment techniques-are confounding factors for gene expression analysis in DTCs. METHODS LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays. RESULTS Neither storage at -80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes. CONCLUSION Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.
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Affiliation(s)
- Fikret Rifatbegovic
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- * E-mail: (FR); (PFA)
| | - M. Reza Abbasi
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Sabine Taschner-Mandl
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics, Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Peter F. Ambros
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail: (FR); (PFA)
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32
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Roberts MEP, Higgs BW, Brohawn P, Pilataxi F, Guo X, Kuziora M, Bowler RP, White WI. CD4+ T-Cell Profiles and Peripheral Blood Ex-Vivo Responses to T-Cell Directed Stimulation Delineate COPD Phenotypes. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2015; 2:268-280. [PMID: 28848849 DOI: 10.15326/jcopdf.2.4.2015.0131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The heterogeneous clinical phenotypes of chronic obstructive pulmonary disease (COPD) challenge successful drug development. To identify COPD subgroups beyond clinical phenotypes, we interrogated blood immune cell profiles and ex-vivo responses of current and former smokers, with or without COPD, in the longitudinal COPD Genetic Epidemiology study (COPDGene) cohort. CD4+ and CD8+ T cells and monocytes were profiled by flow cytometry. Microarray analysis was performed on the RNA from the aforementioned isolated cells. T-cell directed whole blood ex-vivo stimulation was used to assess functional responses. Blood CD4+ T-cell transcript analysis distinguished patients with COPD from control smokers and also enriched for a subset of patients with COPD that had a history of exacerbations of the disease. Analogous analyses of CD8+ T cells and monocytes failed to discriminate patients with COPD from the control population. Patients with COPD had a diminished cytokine response, compared to control smokers, characterized by low levels of granulocyte-monocyte colony stimulation factor (GM-CSF), interferon gamma (IFN-ɣ), interleukin one-alpha (IL-1α), tumor necrosis factor-alpha (TNF-α) and tumor necrosis factor-beta (TNF-β) secreted in response to T-cell directed ex-vivo stimulation. This cytokine response associated with baseline disease severity (forced expiratory volume in 1 second [FEV1]% predicted), rapidly declining lung function, and emphysema. Our observations indicate that COPD phenotypes can be further differentiated based on blood CD4+ T-cell profiles and resultant immune responses, suggesting a role for these cells in COPD pathophysiology.
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Affiliation(s)
| | - Brandon W Higgs
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
| | - Philip Brohawn
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
| | - Fernanda Pilataxi
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
| | - Xiang Guo
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
| | - Michael Kuziora
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
| | - Russell P Bowler
- National Jewish Health, Department of Medicine, Denver, Colorado
| | - Wendy I White
- MedImmune, Department of Translational Sciences, Gaithersburg, Maryland
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Volden TA, Reyelts CD, Hoke TA, Arikkath J, Bonasera SJ. Validation of Flow Cytometry and Magnetic Bead-Based Methods to Enrich CNS Single Cell Suspensions for Quiescent Microglia. J Neuroimmune Pharmacol 2015; 10:655-65. [PMID: 26260923 DOI: 10.1007/s11481-015-9628-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/30/2015] [Indexed: 11/29/2022]
Abstract
Microglia are resident mononuclear phagocytes within the CNS parenchyma that intimately interact with neurons and astrocytes to remodel synapses and extracellular matrix. We briefly review studies elucidating the molecular pathways that underlie microglial surveillance, activation, chemotaxis, and phagocytosis; we additionally place these studies in a clinical context. We describe and validate an inexpensive and simple approach to obtain enriched single cell suspensions of quiescent parenchymal and perivascular microglia from the mouse cerebellum and hypothalamus. Following preparation of regional CNS single cell suspensions, we remove myelin debris, and then perform two serial enrichment steps for cells expressing surface CD11b. Myelin depletion and CD11b enrichment are both accomplished using antigen-specific magnetic beads in an automated cell separation system. Flow cytometry of the resultant suspensions shows a significant enrichment for CD11b(+)/CD45(+) cells (perivascular microglia) and CD11b(+)/CD45(-) cells (parenchymal microglia) compared to starting suspensions. Of note, cells from these enriched suspensions minimally express Aif1 (aka Iba1), suggesting that the enrichment process does not evoke significant microglial activation. However, these cells readily respond to a functional challenge (LPS) with significant changes in the expression of molecules specifically associated with microglia. We conclude that methods employing a combination of magnetic-bead based sorting and flow cytometry produce suspensions highly enriched for microglia that are appropriate for a variety of molecular and cellular assays.
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Affiliation(s)
- T A Volden
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - C D Reyelts
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - T A Hoke
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - J Arikkath
- Developmental Neuroscience, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - S J Bonasera
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA. .,University of Nebraska Medical Center, 3028 Durham Research Center II, Omaha, NE, 68198-5039, USA.
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Felts SJ, Van Keulen VP, Scheid AD, Allen KS, Bradshaw RK, Jen J, Peikert T, Middha S, Zhang Y, Block MS, Markovic SN, Pease LR. Gene expression patterns in CD4+ peripheral blood cells in healthy subjects and stage IV melanoma patients. Cancer Immunol Immunother 2015; 64:1437-47. [PMID: 26245876 DOI: 10.1007/s00262-015-1745-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/18/2015] [Indexed: 01/09/2023]
Abstract
Melanoma patients exhibit changes in immune responsiveness in the local tumor environment, draining lymph nodes, and peripheral blood. Immune-targeting therapies are revolutionizing melanoma patient care increasingly, and studies show that patients derive clinical benefit from these newer agents. Nonetheless, predicting which patients will benefit from these costly therapies remains a challenge. In an effort to capture individual differences in immune responsiveness, we are analyzing patterns of gene expression in human peripheral blood cells using RNAseq. Focusing on CD4+ peripheral blood cells, we describe multiple categories of immune regulating genes, which are expressed in highly ordered patterns shared by cohorts of healthy subjects and stage IV melanoma patients. Despite displaying conservation in overall transcriptome structure, CD4+ peripheral blood cells from melanoma patients differ quantitatively from healthy subjects in the expression of more than 2000 genes. Moreover, 1300 differentially expressed genes are found in transcript response patterns following activation of CD4+ cells ex vivo, suggesting that widespread functional discrepancies differentiate the immune systems of healthy subjects and melanoma patients. While our analysis reveals that the transcriptome architecture characteristic of healthy subjects is maintained in cancer patients, the genes expressed differentially among individuals and across cohorts provide opportunities for understanding variable immune states as well as response potentials, thus establishing a foundation for predicting individual responses to stimuli such as immunotherapeutic agents.
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Affiliation(s)
- Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Adam D Scheid
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kathleen S Allen
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Renee K Bradshaw
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jin Jen
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Tobias Peikert
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Sumit Middha
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuji Zhang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew S Block
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Svetomir N Markovic
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
- Department of Oncology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Division of Hematology, Department of Internal Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Larry R Pease
- Department of Immunology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA.
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McKinney EF, Lee JC, Jayne DRW, Lyons PA, Smith KGC. T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection. Nature 2015; 523:612-6. [PMID: 26123020 PMCID: PMC4623162 DOI: 10.1038/nature14468] [Citation(s) in RCA: 471] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/10/2015] [Indexed: 12/30/2022]
Abstract
The clinical course of autoimmune and infectious disease varies greatly, even between individuals with the same condition. An understanding of the molecular basis for this heterogeneity could lead to significant improvements in both monitoring and treatment. During chronic infection the process of T-cell exhaustion inhibits the immune response, facilitating viral persistence. Here we show that a transcriptional signature reflecting CD8 T-cell exhaustion is associated with poor clearance of chronic viral infection, but conversely predicts better prognosis in multiple autoimmune diseases. The development of CD8 T-cell exhaustion during chronic infection is driven both by persistence of antigen and by a lack of accessory 'help' signals. In autoimmunity, we find that where evidence of CD4 T-cell co-stimulation is pronounced, that of CD8 T-cell exhaustion is reduced. We can reproduce the exhaustion signature by modifying the balance of persistent stimulation of T-cell antigen receptors and specific CD2-induced co-stimulation provided to human CD8 T cells in vitro, suggesting that each process plays a role in dictating outcome in autoimmune disease. The 'non-exhausted' T-cell state driven by CD2-induced co-stimulation is reduced by signals through the exhaustion-associated inhibitory receptor PD-1, suggesting that induction of exhaustion may be a therapeutic strategy in autoimmune and inflammatory disease. Using expression of optimal surrogate markers of co-stimulation/exhaustion signatures in independent data sets, we confirm an association with good clinical outcome or response to therapy in infection (hepatitis C virus) and vaccination (yellow fever, malaria, influenza), but poor outcome in autoimmune and inflammatory disease (type 1 diabetes, anti-neutrophil cytoplasmic antibody-associated vasculitis, systemic lupus erythematosus, idiopathic pulmonary fibrosis and dengue haemorrhagic fever). Thus, T-cell exhaustion plays a central role in determining outcome in autoimmune disease and targeted manipulation of this process could lead to new therapeutic opportunities.
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Affiliation(s)
- Eoin F McKinney
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - James C Lee
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - David R W Jayne
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Paul A Lyons
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Kenneth G C Smith
- 1] Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK [2] Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
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Ayano M, Tsukamoto H, Kohno K, Ueda N, Tanaka A, Mitoma H, Akahoshi M, Arinobu Y, Niiro H, Horiuchi T, Akashi K. Increased CD226 Expression on CD8+ T Cells Is Associated with Upregulated Cytokine Production and Endothelial Cell Injury in Patients with Systemic Sclerosis. THE JOURNAL OF IMMUNOLOGY 2015; 195:892-900. [PMID: 26109642 DOI: 10.4049/jimmunol.1403046] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 05/26/2015] [Indexed: 02/06/2023]
Abstract
Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular damage and fibrosis of the skin and internal organs. Because activated and oligoclonally expanded CD8(+) T cells can be detected in peripheral blood and lungs of SSc patients, effector memory CD8(+) T cells may play a critical role for organ involvement in SSc; however, the pathogenic functions of effector memory CD8(+) T cells remain incompletely understood. In this study, we performed DNA microarray analysis of the sort-purified effector memory CD8(+) T cells from SSc patients and healthy controls, and showed that the expression of genes related to immune response and cell adhesion, including CD226 (also known as DNAX accessory molecule-1 [DNAM-1]), was significantly altered. Moreover, detailed analysis of CD226 revealed that CD226(high)CD8(+) T cells were increased in SSc patients (mean, 50.7%) compared with healthy controls (32.9%) and were appreciably associated with the severity of skin sclerosis and interstitial lung disease. Furthermore, CD226(+)CD8(+) T cells produced higher amount of various cytokines than CD226(-) ones, and CD226(high)CD8(+) T cells from SSc patients showed upregulated IL-13 production and positive correlation with the cytotoxic capacity of CD8(+) T cells against HUVECs. Finally, the neutralization of CD226 in CD8(+) T cells impaired costimulation, cytokine productions, and cytolysis against HUVECs. These findings indicate that upregulated CD226 expression on CD8(+) T cells reflects disease severity and is involved in SSc pathogenesis via the production of various cytokines, including profibrotic IL-13 and endothelial cell injury, and that CD226 may be a useful target in the treatment of SSc.
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Affiliation(s)
- Masahiro Ayano
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Hiroshi Tsukamoto
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan;
| | - Kentaro Kohno
- Department of Hematology, National Kyushu Medical Center, Fukuoka 810-8563, Japan
| | - Naoyasu Ueda
- Department of Internal Medicine, Miyazaki Prefectural Miyazaki Hospital, Miyazaki 880-8510, Japan
| | - Atsushi Tanaka
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Hiroki Mitoma
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Mitsuteru Akahoshi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yojiro Arinobu
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Hiroaki Niiro
- Clinical Education Center, Kyushu University Hospital, Fukuoka 812-8582, Japan; and
| | - Takahiko Horiuchi
- Department of Internal Medicine, Kyushu University Beppu Hospital, Beppu 874-0836, Japan
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
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Baldeón R L, Weigelt K, de Wit H, Ozcan B, van Oudenaren A, Sempértegui F, Sijbrands E, Grosse L, van Zonneveld AJ, Drexhage HA, Leenen PJM. Type 2 Diabetes Monocyte MicroRNA and mRNA Expression: Dyslipidemia Associates with Increased Differentiation-Related Genes but Not Inflammatory Activation. PLoS One 2015; 10:e0129421. [PMID: 26083362 PMCID: PMC4471054 DOI: 10.1371/journal.pone.0129421] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 05/10/2015] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVE To study the expression pattern of microRNAs and mRNAs related to inflammation in T2D monocytes. DESIGN A microRNA finding study on monocytes of T2D patients and controls using array profiling was followed by a quantitative Real Time PCR (qPCR) study on monocytes of an Ecuadorian validation cohort testing the top over/under-expressed microRNAs. In addition, monocytes of the validation cohort were tested for 24 inflammation-related mRNAs and 2 microRNAs previously found deregulated in (auto)-inflammatory monocytes. RESULTS In the finding study, 142 significantly differentially expressed microRNAs were identified, 15 having the strongest power to discriminate T2D patients from controls (sensitivity 66%, specificity 90%). However, differences in expression of these microRNAs between patients and controls were small. On the basis of >1.4 or <0.6-fold change expression 5 microRNAs were selected for further validation. One microRNA (miR-34c-5p) was validated as significantly over-expressed in T2D monocytes. In addition, we found over expression of 3 mRNAs (CD9, DHRS3 and PTPN7) in the validation cohort. These mRNAs are important for cell morphology, adhesion, shape change, and cell differentiation. Classical inflammatory genes (e.g. TNFAIP3) were only over-expressed in monocytes of patients with normal serum lipids. Remarkably, in dyslipidemia, there was a reduction in the expression of inflammatory genes (e.g. ATF3, DUSP2 and PTGS2). CONCLUSIONS The expression profile of microRNAs/mRNAs in monocytes of T2D patients indicates an altered adhesion, differentiation, and shape change potential. Monocyte inflammatory activation was only found in patients with normal serum lipids. Abnormal lipid values coincided with a reduced monocyte inflammatory state.
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Affiliation(s)
- Lucy Baldeón R
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands; Department of Immunology, Central University of Ecuador, Quito, Ecuador
| | - Karin Weigelt
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Harm de Wit
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Behiye Ozcan
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | | | | | - Eric Sijbrands
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Laura Grosse
- Department of Psychiatry, University of Münster, Münster, Germany
| | | | - Hemmo A Drexhage
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands; Prometeo Program SENESCYT, Central University of Ecuador and Universidad de las Fuerzas Armadas, Quito, Ecuador
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Wu JQ, Saksena MM, Soriano V, Vispo E, Saksena NK. Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs. Virol J 2015; 12:4. [PMID: 25623235 PMCID: PMC4312599 DOI: 10.1186/s12985-014-0236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/30/2014] [Indexed: 01/01/2023] Open
Abstract
Background Despite the easy accessibility and diagnostic utility of PBMCs and their potential to show distinct expression patterns associated with the accelerated disease progression in HIV/HCV co-infection, there has not been a systematic study focusing on the global dysregulations of the biological pathways in PBMCs from HIV, HCV mono- and co-infected individuals. This study aimed at identifying the transcriptome distinctions of PBMCs between these patient groups. Methods Genome-wide transcriptomes of PBMCs from 10 HIV/HCV co-infected patients, 7 HIV+ patients, 5 HCV+ patients, and 5 HIV/HCV sero-negative healthy controls were analyzed using Illumina microarray. Pairwise comparisons were performed to identify differentially expressed genes (DEGs), followed by gene set enrichment analysis (GSEA) to detect the global dysregulations of the biological pathways between HIV, HCV mono- and co-infection. Results Forty-one, 262, and 44 DEGs with fold change > 1.5 and FDR (false discovery rate) <0.05 for the comparisons of HCV versus co-infection, HIV versus co-infection, and HIV versus HCV were identified, respectively. Significantly altered pathways (FDR < 0.05), featured by those involved in immune system, signaling transduction, and cell cycle, were detected. Notably, the differential regulation of cytotoxicity pathway discriminated between HIV, HCV mono- and co-infection (up-regulated in the former versus the latter group: co-infection versus HIV or HCV, HIV versus HCV; FDR <0.001 ~ 0.019). Conversely, the cytokine-cytokine receptor interaction pathway was down-regulated in co-infection versus either HCV (FDR = 0.003) or HIV (FDR = 0.028). For the comparison of HIV versus HCV, the cell cycle (FDR = 0.016) and WNT signaling (FDR = 0.006) pathways were up- and down-regulated in HIV, respectively. Conclusions Our study is the first to identify the differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection, which may reflect the distinct patterns of virus-host cell interactions underlying disease progression. Further inspection of cytotoxicity pathway has pinned down to the expression of the KIR genes to be associated with specific patterns of particular virus-host interactions. Between HIV and HCV, the altered cell cycle and WNT signaling pathways may suggest the different impact of HIV and HCV on cell proliferation and differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12985-014-0236-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Qin Wu
- School of Biomedical Sciences and Pharmacy, Faculty of Health, The University of Newcastle, University Drive, Callaghan, Newcastle, NSW, 2308, Australia.
| | - Monica Miranda Saksena
- Herpes Virus Pathogenesis Lab, Center for Virus Research, Westmead Millennium Institute, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
| | - Vincent Soriano
- Department of Infectious Diseases, Hospital Carlos III, Sinesio Delgado 10, 28029, Madrid, Spain.
| | - Eugenia Vispo
- Department of Infectious Diseases, Hospital Carlos III, Sinesio Delgado 10, 28029, Madrid, Spain.
| | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
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Ladjemi MZ, Lecocq M, Weynand B, Bowen H, Gould HJ, Van Snick J, Detry B, Pilette C. Increased IgA production by B-cells in COPD via lung epithelial interleukin-6 and TACI pathways. Eur Respir J 2014; 45:980-93. [PMID: 25537557 DOI: 10.1183/09031936.00063914] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Despite their relevance to mucosal defense, production of IgA and the function of lung B-cells remain unknown in chronic obstructive pulmonary disease (COPD). We assessed IgA synthesis in the lungs of COPD (n=28) and control (n=21) patients, and regulation of B-cells co-cultured with in vitro-reconstituted airway epithelium. In COPD lung tissue, synthesis of IgA1 was increased, which led to its accumulation in subepithelial areas. In vitro, the COPD bronchial epithelium imprinted normal human B-cells for increased production of IgA (mainly IgA1) and maturation into CD38(+) plasma cells. These effects were associated with upregulation of TACI (transmembrane activator and CAML interactor) and were observed under resting conditions, while being partly inhibited upon stimulation with cigarette smoke extract. Interleukin (IL)-6 and BAFF (B-cell activating factor)/APRIL (a proliferation-inducing ligand) were upregulated in the COPD epithelium and lung tissue, respectively; the IgA-promoting effect of the COPD bronchial epithelium was inhibited by targeting IL-6 and, to a lower extent, by blocking TACI. These data show that in COPD, the bronchial epithelium imprints B-cells with signals promoting maturation into IgA-producing plasma cells through the action of two epithelial/B-cell axes, namely the IL-6/IL-6 receptor and BAFF-APRIL/TACI pathways, while cigarette smoke partly counteracts this IgA-promoting effect.
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Affiliation(s)
- Maha Zohra Ladjemi
- Université Catholique de Louvain (UCL), Institut de Recherche Expérimentale et Clinique (IREC), Pôle de Pneumologie, ORL et Dermatologie, Brussels, Belgium Cliniques universitaires St-Luc, Service de Pneumologie, Brussels, Belgium Institute for Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium
| | - Marylène Lecocq
- Université Catholique de Louvain (UCL), Institut de Recherche Expérimentale et Clinique (IREC), Pôle de Pneumologie, ORL et Dermatologie, Brussels, Belgium Cliniques universitaires St-Luc, Service de Pneumologie, Brussels, Belgium Institute for Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium
| | - Birgit Weynand
- CHU de Mont-Godinne, Service d'anatomopathologie, Yvoir, Belgium
| | - Holly Bowen
- MRC/Asthma UK Centre in Allergic Mechanisms of Asthma, Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Hannah J Gould
- MRC/Asthma UK Centre in Allergic Mechanisms of Asthma, Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Jacques Van Snick
- UCL, C. de Duve Institute of Cellular Pathology, Brussels, Belgium Ludwig Institute for Cancer Research, Brussels, Belgium
| | - Bruno Detry
- Université Catholique de Louvain (UCL), Institut de Recherche Expérimentale et Clinique (IREC), Pôle de Pneumologie, ORL et Dermatologie, Brussels, Belgium Cliniques universitaires St-Luc, Service de Pneumologie, Brussels, Belgium Institute for Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium
| | - Charles Pilette
- Université Catholique de Louvain (UCL), Institut de Recherche Expérimentale et Clinique (IREC), Pôle de Pneumologie, ORL et Dermatologie, Brussels, Belgium Cliniques universitaires St-Luc, Service de Pneumologie, Brussels, Belgium Institute for Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium
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Letzkus M, Luesink E, Starck-Schwertz S, Bigaud M, Mirza F, Hartmann N, Gerstmayer B, Janssen U, Scherer A, Schumacher MM, Verles A, Vitaliti A, Nirmala N, Johnson KJ, Staedtler F. Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials. Clin Transl Med 2014; 3:36. [PMID: 25984272 PMCID: PMC4424390 DOI: 10.1186/s40169-014-0036-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 10/07/2014] [Indexed: 12/12/2022] Open
Abstract
Background Clinically useful biomarkers for patient stratification and monitoring of disease progression and drug response are in big demand in drug development and for addressing potential safety concerns. Many diseases influence the frequency and phenotype of cells found in the peripheral blood and the transcriptome of blood cells. Changes in cell type composition influence whole blood gene expression analysis results and thus the discovery of true transcript level changes remains a challenge. We propose a robust and reproducible procedure, which includes whole transcriptome gene expression profiling of major subsets of immune cell cells directly sorted from whole blood. Methods Target cells were enriched using magnetic microbeads and an autoMACS® Pro Separator (Miltenyi Biotec). Flow cytometric analysis for purity was performed before and after magnetic cell sorting. Total RNA was hybridized on HGU133 Plus 2.0 expression microarrays (Affymetrix, USA). CEL files signal intensity values were condensed using RMA and a custom CDF file (EntrezGene-based). Results Positive selection by use of MACS® Technology coupled to transcriptomics was assessed for eight different peripheral blood cell types, CD14+ monocytes, CD3+, CD4+, or CD8+ T cells, CD15+ granulocytes, CD19+ B cells, CD56+ NK cells, and CD45+ pan leukocytes. RNA quality from enriched cells was above a RIN of eight. GeneChip analysis confirmed cell type specific transcriptome profiles. Storing whole blood collected in an EDTA Vacutainer® tube at 4°C followed by MACS does not activate sorted cells. Gene expression analysis supports cell enrichment measurements by MACS. Conclusions The proposed workflow generates reproducible cell-type specific transcriptome data which can be translated to clinical settings and used to identify clinically relevant gene expression biomarkers from whole blood samples. This procedure enables the integration of transcriptomics of relevant immune cell subsets sorted directly from whole blood in clinical trial protocols.
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Affiliation(s)
- Martin Letzkus
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Evert Luesink
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Marc Bigaud
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Fareed Mirza
- Scientific Capability Development, Pharma-Development, Novartis Pharma AG, Basel, Switzerland
| | - Nicole Hartmann
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | | | - Uwe Janssen
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | | | - Martin M Schumacher
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Aurelie Verles
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Alessandra Vitaliti
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
| | - Nanguneri Nirmala
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA, USA
| | - Keith J Johnson
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA, USA
| | - Frank Staedtler
- Biomarker Development, Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland
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Schmeits PCJ, Schaap MM, Luijten M, van Someren E, Boorsma A, van Loveren H, Peijnenburg AACM, Hendriksen PJM. Detection of the mechanism of immunotoxicity of cyclosporine A in murine in vitro and in vivo models. Arch Toxicol 2014; 89:2325-37. [PMID: 25224403 DOI: 10.1007/s00204-014-1365-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 09/04/2014] [Indexed: 01/25/2023]
Abstract
Transcriptomics in combination with in vitro cell systems is a powerful approach to unravel modes of action of toxicants. An important question is to which extent the modes of action as revealed by transcriptomics depend on cell type, species and study type (in vitro or in vivo). To acquire more insight into this, we assessed the transcriptomic effects of the immunosuppressive drug cyclosporine A (CsA) upon 6 h of exposure of the mouse cytotoxic T cell line CTLL-2, the thymoma EL-4 and primary splenocytes and compared these to the effects in spleens of mice orally treated with CsA for 7 days. EL-4 and CTLL-2 cells showed the highest similarities in response. CsA affected many genes in primary splenocytes that were not affected in EL-4 or CTLL-2. Pathway analysis demonstrated that CsA upregulated the unfolded protein response, endoplasmic reticulum stress and NRF2 activation in EL-4 cells, CTLL-2 cells and primary mouse splenocytes but not in mouse spleen in vivo. As expected, CsA downregulated cell cycle and immune response in splenocytes in vitro, spleens in vivo as well as CTLL-2 in vitro. Genes up- and downregulated in human Jurkat, HepG2 and renal proximal tubular cells were similarly affected in CTLL-2, EL-4 and primary splenocytes in vitro. In conclusion, of the models tested in this study, the known mechanism of immunotoxicity of CsA is best represented in the mouse cytotoxic T cell line CTLL-2. This is likely due to the fact that this cell line is cultured in the presence of a T cell activation stimulant (IL-2) making it more suitable to detect inhibitory effects on T cell activation.
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Affiliation(s)
- P C J Schmeits
- RIKILT Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
| | - M M Schaap
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
- Department of Toxicogenetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - M Luijten
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
- Department of Toxicogenetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - E van Someren
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- Research Group Microbiology and Systems Biology, TNO, P.O. Box 360, 3700 AJ, Zeist, The Netherlands
| | - A Boorsma
- Research Group Microbiology and Systems Biology, TNO, P.O. Box 360, 3700 AJ, Zeist, The Netherlands
| | - H van Loveren
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | - A A C M Peijnenburg
- RIKILT Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
- Department of Toxicogenomics, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - P J M Hendriksen
- RIKILT Institute of Food Safety, Wageningen University and Research Centre, P.O. Box 230, 6700 AE, Wageningen, The Netherlands.
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Human T-follicular helper and T-follicular regulatory cell maintenance is independent of germinal centers. Blood 2014; 124:2666-74. [PMID: 25224411 DOI: 10.1182/blood-2014-07-585976] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The monoclonal anti-CD20 antibody rituximab (RTX) depletes B cells in the treatment of lymphoma and autoimmune disease, and contributes to alloantibody reduction in transplantation across immunologic barriers. The effects of RTX on T cells are less well described. T-follicular helper (Tfh) cells provide growth and differentiation signals to germinal center (GC) B cells to support antibody production, and suppressive T-follicular regulatory (Tfr) cells regulate this response. In mice, both Tfh and Tfr are absolutely dependent on B cells for their formation and on the GC for their maintenance. In this study, we demonstrate that RTX treatment results in a lack of GC B cells in human lymph nodes without affecting the Tfh or Tfr cell populations. These data demonstrate that human Tfh and Tfr do not require an ongoing GC response for their maintenance. The persistence of Tfh and Tfr following RTX treatment may permit rapid reconstitution of the pathological GC response once the B-cell pool begins to recover. Strategies for maintaining remission after RTX therapy will need to take this persistence of Tfh into account.
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Richard AC, Lyons PA, Peters JE, Biasci D, Flint SM, Lee JC, McKinney EF, Siegel RM, Smith KGC. Comparison of gene expression microarray data with count-based RNA measurements informs microarray interpretation. BMC Genomics 2014; 15:649. [PMID: 25091430 PMCID: PMC4143561 DOI: 10.1186/1471-2164-15-649] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/17/2014] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Although numerous investigations have compared gene expression microarray platforms, preprocessing methods and batch correction algorithms using constructed spike-in or dilution datasets, there remains a paucity of studies examining the properties of microarray data using diverse biological samples. Most microarray experiments seek to identify subtle differences between samples with variable background noise, a scenario poorly represented by constructed datasets. Thus, microarray users lack important information regarding the complexities introduced in real-world experimental settings. The recent development of a multiplexed, digital technology for nucleic acid measurement enables counting of individual RNA molecules without amplification and, for the first time, permits such a study. RESULTS Using a set of human leukocyte subset RNA samples, we compared previously acquired microarray expression values with RNA molecule counts determined by the nCounter Analysis System (NanoString Technologies) in selected genes. We found that gene measurements across samples correlated well between the two platforms, particularly for high-variance genes, while genes deemed unexpressed by the nCounter generally had both low expression and low variance on the microarray. Confirming previous findings from spike-in and dilution datasets, this "gold-standard" comparison demonstrated signal compression that varied dramatically by expression level and, to a lesser extent, by dataset. Most importantly, examination of three different cell types revealed that noise levels differed across tissues. CONCLUSIONS Microarray measurements generally correlate with relative RNA molecule counts within optimal ranges but suffer from expression-dependent accuracy bias and precision that varies across datasets. We urge microarray users to consider expression-level effects in signal interpretation and to evaluate noise properties in each dataset independently.
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Affiliation(s)
- Arianne C Richard
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
- />Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD USA
| | - Paul A Lyons
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - James E Peters
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Daniele Biasci
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Shaun M Flint
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - James C Lee
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eoin F McKinney
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Richard M Siegel
- />Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD USA
| | - Kenneth GC Smith
- />Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, UK
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Jones CN, Hoang AN, Dimisko L, Hamza B, Martel J, Irimia D. Microfluidic platform for measuring neutrophil chemotaxis from unprocessed whole blood. J Vis Exp 2014. [PMID: 24962731 DOI: 10.3791/51215] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Neutrophils play an essential role in protection against infections and their numbers in the blood are frequently measured in the clinic. Higher neutrophil counts in the blood are usually an indicator of ongoing infections, while low neutrophil counts are a warning sign for higher risks for infections. To accomplish their functions, neutrophils also have to be able to move effectively from the blood where they spend most of their life, into tissues, where infections occur. Consequently, any defects in the ability of neutrophils to migrate can increase the risks for infections, even when neutrophils are present in appropriate numbers in the blood. However, measuring neutrophil migration ability in the clinic is a challenging task, which is time consuming, requires large volume of blood, and expert knowledge. To address these limitations, we designed a robust microfluidic assays for neutrophil migration, which requires a single droplet of unprocessed blood, circumvents the need for neutrophil separation, and is easy to quantify on a simple microscope. In this assay, neutrophils migrate directly from the blood droplet, through small channels, towards the source of chemoattractant. To prevent the granular flow of red blood cells through the same channels, we implemented mechanical filters with right angle turns that selectively block the advance of red blood cells. We validated the assay by comparing neutrophil migration from blood droplets collected from finger prick and venous blood. We also compared these whole blood (WB) sources with neutrophil migration from samples of purified neutrophils and found consistent speed and directionality between the three sources. This microfluidic platform will enable the study of human neutrophil migration in the clinic and the research setting to help advance our understanding of neutrophil functions in health and disease.
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Affiliation(s)
- Caroline N Jones
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital; Harvard Medical School; Shriners Burns Hospital
| | - Anh N Hoang
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital; Harvard Medical School; Shriners Burns Hospital
| | - Laurie Dimisko
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital
| | - Bashar Hamza
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital
| | - Joseph Martel
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital; Harvard University School of Engineering and Applied Sciences
| | - Daniel Irimia
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital; Harvard Medical School; Shriners Burns Hospital;
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Yi L, Zhao J, Lu J, Chen Y, Chen L, Cheng J, Sun Y, Li Z, Men R, Yang L, Kung H, Yang Z, He ML. Gene expression profiling of CD4⁺ T cells in treatment-naive HIV, HCV mono- or co-infected Chinese. Virol J 2014; 11:27. [PMID: 24520951 PMCID: PMC3943807 DOI: 10.1186/1743-422x-11-27] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/29/2014] [Indexed: 11/28/2022] Open
Abstract
Background Because of the shared transmission routes, co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HIV) is very common. Accumulated clinical evidence showed that one could alter the infectious course of the other virus in HIV and HCV co-infected individuals. However, little is known on the molecular basis of HIV/HCV interactions and their modulations on hosts. Methods In this study, treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/μl were recruited and their gene expression profiles were investigated by microarray assays. The differentially expressed genes were identified and validated by quantitative real-time PCR (qRT-PCR). To further understand the biological meanings of the gene expression profiles in these three groups, GSEA analysis (version 2.0, Broad Institute
http://www.broad.mit.edu/gsea) was performed. Results By gene set enrichment analysis, we revealed that gene sets of cell cycle progression, innate immune response and some transcription factors in CD4+ T cells were mainly affected by HIV; while genes associated with GPCR signaling were the major targets of HCV. Metabolic pathways were modulated by both HCV and HIV viruses. Conclusions This study for the first time offers gene profiling basis for HCV/HIV mono-/co- infections in human beings. HIV infection displayed the great impact on transcription profile of CD4+ T cells in HIV/HCV co-infected individuals. Genes related to cell cycle arrest were significantly mediated by HIV which may lead to dysfunction of CD4+ T cells and acceleration of HCV-related disease progression in the co-infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhengrong Yang
- Stanley Ho Center for Emerging Infectious Diseases, and Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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46
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Genome-wide mRNA and miRNA analysis of peripheral blood mononuclear cells (PBMC) reveals different miRNAs regulating HIV/HCV co-infection. Virology 2014; 450-451:336-49. [PMID: 24503097 DOI: 10.1016/j.virol.2013.12.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/24/2013] [Accepted: 12/19/2013] [Indexed: 12/12/2022]
Abstract
Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is common due to shared transmission routes. The genomic basis of HIV/HCV co-infection and its regulation by microRNA (miRNA) is unknown. Therefore, our objective was to investigate genome-wide mRNA expression and its regulation by miRNA in primary PBMCs derived from 27 patients (5 HCV - mono-infected, 5 HIV-mono-infected, 12 HCV/HIV co-infected, and 5 healthy controls). This revealed 27 miRNAs and 476 mRNAs as differentially expressed (DE) in HCV/HIV co-infection when compared to controls (adj p<0.05). Our study shows the first evidence of miRNAs specific for co-infection, several of which are correlated with key gene targets demonstrating functional relationships to pathways in cancer, immune-function, and metabolism. Notable was the up regulation of HCV-specific miR-122 in co-infection (FC>50, p=4.02E-06), which may have clinical/biological implications.
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Mabbott NA, Gray D. Identification of co-expressed gene signatures in mouse B1, marginal zone and B2 B-cell populations. Immunology 2014; 141:79-95. [PMID: 24032749 PMCID: PMC3893852 DOI: 10.1111/imm.12171] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 01/09/2023] Open
Abstract
In mice, three major B-cell subsets have been identified with distinct functionalities: B1 B cells, marginal zone B cells and follicular B2 B cells. Here, we used the growing body of publicly available transcriptomics data to create an expression atlas of 84 gene expression microarray data sets of distinct mouse B-cell subsets. These data were subjected to network-based cluster analysis using BioLayout Express(3D). Using this analysis tool, genes with related functions clustered together in discrete regions of the network graph and enabled the identification of transcriptional networks that underpinned the functional activity of distinct cell populations. Some gene clusters were expressed highly by most of the cell populations included in this analysis (such as those with activity related to house-keeping functions). Others contained genes with expression patterns specific to distinct B-cell subsets. While these clusters contained many genes typically associated with the activity of the cells they were specifically expressed in, many novel B-cell-subset-specific candidate genes were identified. A large number of uncharacterized genes were also represented in these B-cell lineage-specific clusters. Further analysis of the activities of these uncharacterized candidate genes will lead to the identification of novel B-cell lineage-specific transcription factors and regulators of B-cell function. We also analysed 36 microarray data sets from distinct human B-cell populations. These data showed that mouse and human germinal centre B cells shared similar transcriptional features, whereas mouse B1 B cells were distinct from proposed human B1 B cells.
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Affiliation(s)
- Neil A Mabbott
- The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of EdinburghMidlothian, UK
| | - David Gray
- Ashworth Laboratories, Institute of Immunology and Infection Research, University of EdinburghEdinburgh, UK
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48
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Wu JQ, Sassé TR, Saksena MM, Saksena NK. Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy. Virol J 2013; 10:361. [PMID: 24370116 PMCID: PMC3877975 DOI: 10.1186/1743-422x-10-361] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/18/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contributions of monocytes to HIV persistence, the HIV-monocyte interaction remains elusive. For patients on antiretroviral therapy, previous studies observed a virological suppression rate of >70% and suggested complete viral suppression as the primary goal. Although some studies have reported genetic dysregulations associated with HIV disease progression, research on ex vivo-derived monocytic transcriptomes from HIV+ patients with differential responses to therapy is limited. This study investigated the monocytic transcriptome distinctions between patients with sustained virus suppression and those with virological failure during highly active antiretroviral therapy (HAART). METHODS Genome-wide transcriptomes of primary monocytes from five HIV+ patients on HAART who sustainably controlled HIV to below detection level (BDL), five HIV+ patients on HAART who consecutively experienced viremia, and four healthy HIV sero-negative controls were analyzed using Illumina microarray. Pairwise comparisons were performed to identify differentially expressed genes followed by quantitative PCR validation. Gene set enrichment analysis was used to check the consistency of our dataset with previous studies, as well as to detect the global dysregulations of the biological pathways in monocytes between viremic patients and BDLs. RESULTS Pairwise comparisons including viremic patients versus controls, BDL versus controls, and viremic patients versus BDLs identified 473, 76, and 59 differentially expressed genes (fold change > 2 and FDR < 0.05), respectively. The reliability of our dataset was confirmed by gene set enrichment analysis showing that 6 out of 10 published gene lists were significantly enriched (FDR < 0.01) in at least one of the three pairwise comparisons. In the comparison of viremic patients versus BDLs, gene set enrichment analysis revealed that the pathways characterizing the primary functions of monocytes including antigen processing and presentation, FcγR mediated phagocytosis, and chemokine signaling were significantly up-regulated in viremic patients. CONCLUSIONS This study revealed the first transcriptome distinctions in monocytes between viremic patients and BDLs on HAART. Our results reflected the outcome balanced between the subversion of the monocyte transcriptome by HIV and the compensatory effect adapted by host cells. The up-regulation of antigen presentation pathway in viremic patients particularly highlighted the role of the interface between innate and adaptive immunity in HIV disease progression.
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Affiliation(s)
| | | | | | - Nitin K Saksena
- Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute & Westmead Hospital, University of Sydney, Westmead, Sydney, NSW, 2145, Australia.
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Genome-wide methylation analyses of primary human leukocyte subsets identifies functionally important cell-type-specific hypomethylated regions. Blood 2013; 122:e52-60. [PMID: 24159175 DOI: 10.1182/blood-2013-05-503201] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
DNA methylation is an important mechanism by which gene transcription and hence cellular function are regulated. Here, we provide detailed functional genome-wide methylome maps of 5 primary peripheral blood leukocyte subsets including T cells, B cells, monocytes/macrophages, and neutrophils obtained from healthy individuals. A comparison of these methylomes revealed highly specific cell-lineage and cell-subset methylation profiles. DNA hypomethylation is known to be permissive for gene expression and we identified cell-subset-specific hypomethylated regions (HMRs) that strongly correlate with gene transcription levels suggesting these HMRs may regulate corresponding cell functions. Single-nucleotide polymorphisms associated with immune-mediated disease in genome-wide association studies preferentially localized to these cell-specific regulatory HMRs, offering insight into pathogenesis by highlighting cell subsets in which specific epigenetic changes may drive disease. Our data provide a valuable reference tool for researchers aiming to investigate the role of DNA methylation in regulating primary leukocyte function in health and immune-mediated disease.
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50
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Hoang AN, Jones CN, Dimisko L, Hamza B, Martel J, Kojic N, Irimia D. Measuring neutrophil speed and directionality during chemotaxis, directly from a droplet of whole blood. TECHNOLOGY 2013; 1:49. [PMID: 24809064 PMCID: PMC4010229 DOI: 10.1142/s2339547813500040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Neutrophil chemotaxis is critical for defense against infections and its alterations could lead to chronic inflammation and tissue injury. The central role that transient alterations of neutrophil chemotaxis could have on patient outcomes calls for its quantification in the clinic. However, current methods for measuring neutrophil chemotaxis require large volumes of blood and are time consuming. To address the need for rapid and robust assays, we designed a microfluidic device that measures neutrophil chemotaxis directly from a single droplet of blood. We validated the assay by comparing neutrophil chemotaxis from finger prick, venous blood and purified neutrophil samples. We found consistent average velocity of (19 ± 6 μm/min) and directionality (91.1%) between the three sources. We quantified the variability in neutrophil chemotaxis between healthy donors and found no significant changes over time. We also validated the device in the clinic and documented temporary chemotaxis deficiencies after burn injuries.
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Affiliation(s)
- Anh N. Hoang
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Boston, USA
- Correspondence should be addressed to D.I. ()
| | - Caroline N. Jones
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Shriners Burns Hospital, Boston, USA
- Correspondence should be addressed to D.I. ()
| | - Laurie Dimisko
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Boston, USA
| | - Bashar Hamza
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Boston, USA
| | - Joseph Martel
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Harvard University School of Engineering and Applied Sciences, Boston, USA
| | - Nikola Kojic
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Boston, USA
| | - Daniel Irimia
- The BioMEMS Resource Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Shriners Burns Hospital, Boston, USA
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