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Lin CMA, Isaacs JD, Cooles FAH. Role of IFN-α in Rheumatoid Arthritis. Curr Rheumatol Rep 2024; 26:37-52. [PMID: 38051494 PMCID: PMC10787895 DOI: 10.1007/s11926-023-01125-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 12/07/2023]
Abstract
PURPOSE OF REVIEW Type 1 interferons (IFN-I) are of increasing interest across a wide range of autoimmune rheumatic diseases. Historically, research into their role in rheumatoid arthritis (RA) has been relatively neglected, but recent work continues to highlight a potential contribution to RA pathophysiology. RECENT FINDINGS We emphasise the importance of disease stage when examining IFN-I in RA and provide an overview on how IFN-I may have a direct role on a variety of relevant cellular functions. We explore how clinical trajectory may be influenced by increased IFN-I signalling, and also, the limitations of scores composed of interferon response genes. Relevant environmental triggers and inheritable RA genetic risk relating to IFN-I signalling are explored with emphasis on intriguing data potentially linking IFN-I exposure, epigenetic changes, and disease relevant processes. Whilst these data cumulatively illustrate a likely role for IFN-I in RA, they also highlight the knowledge gaps, particularly in populations at risk for RA, and suggest directions for future research to both better understand IFN-I biology and inform targeted therapeutic strategies.
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Affiliation(s)
- Chung M A Lin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John D Isaacs
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Faye A H Cooles
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
- Musculoskeletal Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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2
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Ji L, Li T, Chen H, Yang Y, Lu E, Liu J, Qiao W, Chen H. The crucial regulatory role of type I interferon in inflammatory diseases. Cell Biosci 2023; 13:230. [PMID: 38124132 PMCID: PMC10734085 DOI: 10.1186/s13578-023-01188-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023] Open
Abstract
Type I interferon (IFN-I) plays crucial roles in the regulation of inflammation and it is associated with various inflammatory diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and periodontitis, impacting people's health and quality of life. It is well-established that IFN-Is affect immune responses and inflammatory factors by regulating some signaling. However, currently, there is no comprehensive overview of the crucial regulatory role of IFN-I in distinctive pathways as well as associated inflammatory diseases. This review aims to provide a narrative of the involvement of IFN-I in different signaling pathways, mainly mediating the related key factors with specific targets in the pathways and signaling cascades to influence the progression of inflammatory diseases. As such, we suggested that IFN-Is induce inflammatory regulation through the stimulation of certain factors in signaling pathways, which displays possible efficient treatment methods and provides a reference for the precise control of inflammatory diseases.
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Affiliation(s)
- Ling Ji
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Tianle Li
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Huimin Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Yanqi Yang
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
- Division of Pediatric Dentistry and Orthodontics, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China
| | - Eryi Lu
- Department of Stomatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 160 Pujian Road, Shanghai, China
| | - Jieying Liu
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Qiao
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
| | - Hui Chen
- Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Hong Kong, SAR, People's Republic of China.
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Prince Philip Dental Hospital, Level 3, 34 Hospital Road, Sai Ying Pun, Hong Kong, SAR, People's Republic of China.
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3
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Moro RN, Biswas U, Kharat SS, Duzanic FD, Das P, Stavrou M, Raso MC, Freire R, Chaudhuri AR, Sharan SK, Penengo L. Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15. Nat Commun 2023; 14:6140. [PMID: 37783689 PMCID: PMC10545780 DOI: 10.1038/s41467-023-41801-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
DNA replication and repair defects or genotoxic treatments trigger interferon (IFN)-mediated inflammatory responses. However, whether and how IFN signaling in turn impacts the DNA replication process has remained elusive. Here we show that basal levels of the IFN-stimulated gene 15, ISG15, and its conjugation (ISGylation) are essential to protect nascent DNA from degradation. Moreover, IFNβ treatment restores replication fork stability in BRCA1/2-deficient cells, which strictly depends on topoisomerase-1, and rescues lethality of BRCA2-deficient mouse embryonic stem cells. Although IFNβ activates hundreds of genes, these effects are specifically mediated by ISG15 and ISGylation, as their inactivation suppresses the impact of IFNβ on DNA replication. ISG15 depletion significantly reduces cell proliferation rates in human BRCA1-mutated triple-negative, whereas its upregulation results in increased resistance to the chemotherapeutic drug cisplatin in mouse BRCA2-deficient breast cancer cells, respectively. Accordingly, cells carrying BRCA1/2 defects consistently show increased ISG15 levels, which we propose as an in-built mechanism of drug resistance linked to BRCAness.
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Affiliation(s)
- Ramona N Moro
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland
| | - Uddipta Biswas
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland
| | - Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, 21702, MD, USA
| | - Filip D Duzanic
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland
| | - Prosun Das
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, the Netherlands
| | - Maria Stavrou
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland
| | - Maria C Raso
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland
| | - Raimundo Freire
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200, La Laguna, Spain
- Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015GD, Rotterdam, the Netherlands
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, 21702, MD, USA
| | - Lorenza Penengo
- University of Zurich, Institute of Molecular Cancer Research, 8057, Zurich, Switzerland.
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4
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Qiao J, Zhang SX, Chang MJ, Zhao R, Song S, Hao JW, Wang C, Hu JX, Gao C, Wang CH, Li XF. Deep stratification by transcriptome molecular characters for precision treatment of patients with systemic lupus erythematosus. Rheumatology (Oxford) 2023; 62:2574-2584. [PMID: 36308437 DOI: 10.1093/rheumatology/keac625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 07/20/2023] Open
Abstract
OBJECTIVES To leverage the high clinical heterogeneity of systemic lupus erythematosus (SLE), we developed and validated a new stratification scheme by integrating genome-scale transcriptomic profiles to identify patient subtypes sharing similar transcriptomic markers and drug targets. METHODS A normalized compendium of transcription profiles was created from peripheral blood mononuclear cells (PBMCs) of 1046 SLE patients and 86 healthy controls (HCs), covering an intersection of 13 689 genes from six microarray datasets. Upregulated differentially expressed genes were subjected to functional and network analysis in which samples were grouped using unsupervised clustering to identify patient subtypes. Then, clustering stability was evaluated by the stratification of six integrated RNA-sequencing datasets using the same method. Finally, the Xgboost classifier was applied to the independent datasets to identify factors associated with treatment outcomes. RESULTS Based on 278 upregulated DEGs of the transcript profiles, SLE patients were classified into three subtypes (subtype A-C) each with distinct molecular and cellular signatures. Neutrophil activation-related pathways were markedly activated in subtype A (named NE-driving), whereas lymphocyte and IFN-related pathways were more enriched in subtype B (IFN-driving). As the most severe subtype, subtype C [NE-IFN-dual-driving (Dual-driving)] shared functional mechanisms with both NE-driving and IFN-driving, which was closely associated with clinical features and could be used to predict the responses of treatment. CONCLUSION We developed the largest cohesive SLE transcriptomic compendium for deep stratification using the most comprehensive microarray and RNA sequencing datasets to date. This result could guide future design of molecular diagnosis and the development of stratified therapy for SLE patients.
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Affiliation(s)
- Jun Qiao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Min-Jing Chang
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision, Shanxi Medical University, Taiyuan, China
| | - Rong Zhao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Shan Song
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Jia-Wei Hao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Can Wang
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision, Shanxi Medical University, Taiyuan, China
| | - Jing-Xi Hu
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Cai-Hong Wang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Xiao-Feng Li
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
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5
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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers. F1000Res 2023; 10:275. [PMID: 37448622 PMCID: PMC10336363 DOI: 10.12688/f1000research.36395.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 07/15/2023] Open
Abstract
Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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Affiliation(s)
| | | | | | | | | | | | | | - Davide Bedognetti
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, 16126, Italy
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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6
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Carter LM, Alase A, Wigston Z, Psarras A, Burska A, Sutton E, Yusof MYM, Reynolds JA, McHugh N, Emery P, Wittmann M, Bruce IN, Vital EM. Gene Expression and Autoantibody Analysis Revealing Distinct Ancestry-Specific Profiles Associated With Response to Rituximab in Refractory Systemic Lupus Erythematosus. Arthritis Rheumatol 2023; 75:697-710. [PMID: 36409591 PMCID: PMC10953047 DOI: 10.1002/art.42404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Gene expression profiles are associated with the clinical heterogeneity of systemic lupus erythematosus (SLE) but are not well studied as biomarkers for therapy. We studied gene expression and response to rituximab in a multiethnic UK cohort who were refractory to standard therapy. METHODS We evaluated baseline expression levels of transcripts known to associate with clinical features of SLE using a 96-probe TaqMan array and whole blood samples from 213 patients with active SLE who had been prospectively enrolled in the British Isles Lupus Assessment Group (BILAG) Biologics Register. We measured autoantibodies using immunoprecipitation and enzyme-linked immunosorbent assays. We determined responses to first-cycle rituximab at 6 months from treatment start in 110 SLE patients by assessing BILAG 2004 disease activity. RESULTS Interferon gene expression scores were lower in patients of European ancestry than in all other ancestry groups. The relationship between blood interferon gene expression scores and scores annotated to plasmablasts, neutrophils, myeloid lineage, inflammation, and erythropoiesis differed between patients of European and non-European ancestries. Hierarchical clustering revealed 3 distinct non-European ancestry patient subsets with stratified responses to rituximab that were not explained by sociodemographic and clinical variables, with responses lowest in an interferon-low, neutrophil-high cluster and highest in a cluster with high expression levels across all signatures (P < 0.001). Clusters in European ancestry patients did not predict response to rituximab but segregated patients by global disease activity and renal involvement. In both ancestral groups, interferon-high clusters were associated with U1 RNP/Sm antibodies. CONCLUSION Ancestry appears central to the immunologic and clinical heterogeneity in SLE. These results suggest that ancestry, disease activity, and transcriptional signatures could each assist in predicting the effectiveness of B cell depletion therapies.
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Affiliation(s)
- Lucy M. Carter
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - Adewonuola Alase
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Zoe Wigston
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Antonios Psarras
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of LeedsLeedsUK
| | - Emily Sutton
- Centre for Epidemiology Versus Arthritis, Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Md Yuzaiful Md Yusof
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - John A. Reynolds
- Institute of Inflammation and Ageing, University of Birmingham, and Sandwell and West Birmingham NHS TrustBirminghamUK
| | | | - Neil McHugh
- Department of Pharmacy and PharmacologyUniversity of Bath, ClavertonBathUK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
| | - Miriam Wittmann
- Department of DermatologyUniversity Medical Centre, Johannes Gutenberg‐UniversityMainzGermany
| | - Ian N. Bruce
- Centre for Epidemiology Versus Arthritis, Division of Musculoskeletal and Dermatological SciencesUniversity of ManchesterManchesterUK
| | - Edward M. Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS TrustLeedsUK
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7
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Stephenson S, Doody GM. Metabolic Reprogramming During B-Cell Differentiation. Methods Mol Biol 2023; 2675:271-283. [PMID: 37258770 DOI: 10.1007/978-1-0716-3247-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
B cells engaging with antigen and secondary signals provided by T cell help, or ligands for Toll-like receptors, undergo a step-wise process of differentiation to eventually produce antibody-secreting plasma cells. During the course of this conversion, the cells transition from a resting, non-growing state to an activated B-cell state engaged in DNA synthesis and mitosis to a terminally differentiated, quiescent cell state with expanded organelles necessary for high levels of secretion. Each of these phases is accompanied by considerable changes in metabolic requirements. To facilitate evaluation of this metabolic reprogramming, methods for the in vitro differentiation of human B cells that incorporates each of the transitional stages are described.
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Affiliation(s)
- Sophie Stephenson
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Gina M Doody
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
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8
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The diverse repertoire of ISG15: more intricate than initially thought. Exp Mol Med 2022; 54:1779-1792. [PMID: 36319753 PMCID: PMC9722776 DOI: 10.1038/s12276-022-00872-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/05/2022] Open
Abstract
ISG15, the product of interferon (IFN)-stimulated gene 15, is the first identified ubiquitin-like protein (UBL), which plays multifaceted roles not only as a free intracellular or extracellular molecule but also as a post-translational modifier in the process of ISG15 conjugation (ISGylation). ISG15 has only been identified in vertebrates, indicating that the functions of ISG15 and its conjugation are restricted to higher eukaryotes and have evolved with IFN signaling. Despite the highlighted complexity of ISG15 and ISGylation, it has been suggested that ISG15 and ISGylation profoundly impact a variety of cellular processes, including protein translation, autophagy, exosome secretion, cytokine secretion, cytoskeleton dynamics, DNA damage response, telomere shortening, and immune modulation, which emphasizes the necessity of reassessing ISG15 and ISGylation. However, the underlying mechanisms and molecular consequences of ISG15 and ISGylation remain poorly defined, largely due to a lack of knowledge on the ISG15 target repertoire. In this review, we provide a comprehensive overview of the mechanistic understanding and molecular consequences of ISG15 and ISGylation. We also highlight new insights into the roles of ISG15 and ISGylation not only in physiology but also in the pathogenesis of various human diseases, especially in cancer, which could contribute to therapeutic intervention in human diseases.
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9
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Psarras A, Wittmann M, Vital EM. Emerging concepts of type I interferons in SLE pathogenesis and therapy. Nat Rev Rheumatol 2022; 18:575-590. [PMID: 36097207 DOI: 10.1038/s41584-022-00826-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 11/09/2022]
Abstract
Type I interferons have been suspected for decades to have a crucial role in the pathogenesis of systemic lupus erythematosus (SLE). Evidence has now overturned several long-held assumptions about how type I interferons are regulated and cause pathological conditions, providing a new view of SLE pathogenesis that resolves longstanding clinical dilemmas. This evidence includes data on interferons in relation to genetic predisposition and epigenetic regulation. Importantly, data are now available on the role of interferons in the early phases of the disease and the importance of non-haematopoietic cellular sources of type I interferons, such as keratinocytes, renal tubular cells, glial cells and synovial stromal cells, as well as local responses to type I interferons within these tissues. These local effects are found not only in inflamed target organs in established SLE, but also in histologically normal skin during asymptomatic preclinical phases, suggesting a role in disease initiation. In terms of clinical application, evidence relating to biomarkers to characterize the type I interferon system is complex, and, notably, interferon-blocking therapies are now licensed for the treatment of SLE. Collectively, the available data enable us to propose a model of disease pathogenesis that invokes the unique value of interferon-targeted therapies. Accordingly, future approaches in SLE involving disease reclassification and preventative strategies in preclinical phases should be investigated.
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Affiliation(s)
- Antonios Psarras
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.,Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Miriam Wittmann
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.,Department of Dermatology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Edward M Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK. .,NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
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10
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Stephenson S, Care MA, Doody GM, Tooze RM. APRIL Drives a Coordinated but Diverse Response as a Foundation for Plasma Cell Longevity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:926-937. [PMID: 36130130 PMCID: PMC7613700 DOI: 10.4049/jimmunol.2100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/29/2022] [Indexed: 01/04/2023]
Abstract
Ab-secreting cells survive in niche microenvironments, but cellular responses driven by particular niche signals are incompletely defined. The TNF superfamily member a proliferation-inducing ligand (APRIL) can support the maturation of transitory plasmablasts into long-lived plasma cells. In this study, we explore the biological programs established by APRIL in human plasmablasts. Under conditions allowing the maturation of ex vivo- or in vitro-generated plasmablasts, we find that APRIL drives activation of ERK, p38, and JNK, accompanied by a classical NF-κB response and activation of the AKT/FOXO1 pathway. Time-course gene expression data resolve coordinated transcriptional responses propagated via immediate early genes and NF-κB targets and converging onto modules of genes enriched for MYC targets and metabolism/cell growth-related pathways. This response is shared between APRIL and an alternate TNF superfamily member CD40L but is not a feature of alternative niche signals delivered by IFN-α or SDF1. However, APRIL and CD40L responses also diverge. CD40L drives expression of genes related to the activated B cell state whereas APRIL does not. Thus, APRIL establishes a broad foundation for plasma cell longevity with features of cellular refueling while being uncoupled from support of the B cell state.
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Affiliation(s)
- Sophie Stephenson
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom; and
| | - Matthew A Care
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom; and
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Gina M Doody
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom; and
| | - Reuben M Tooze
- Division of Haematology and Immunology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom; and
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11
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Melanson G, Du Bois AC, Webster C, Uniacke J. ISGylation
directly modifies hypoxia‐inducible factor‐2α and enhances its polysome association. FEBS Lett 2022; 596:2834-2850. [DOI: 10.1002/1873-3468.14476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Gaelan Melanson
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - Antonia C. Du Bois
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - Caroline Webster
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
| | - James Uniacke
- Department of Molecular and Cellular Biology University of Guelph Guelph Ontario Canada
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12
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B cells in autoimmune hepatitis: bystanders or central players? Semin Immunopathol 2022; 44:411-427. [PMID: 35488094 PMCID: PMC9256567 DOI: 10.1007/s00281-022-00937-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
Abstract
B cells are central for the adaptive immune system to mount successful immune responses not only as antibody producers but also as regulators of cellular immunity. These multifaceted features are also reflected in autoimmunity where autoreactive B cells can fuel disease by production of cytotoxic autoantibodies, presentation of autoantigens to autoreactive T cells, and secretion of cytokines and chemokines that either promote detrimental immune activation or impair regulatory T and B cells. The role of B cells and autoantibodies in autoimmune hepatitis (AIH) have been controversially discussed, with typical autoantibodies and hypergammaglobulinemia indicating a key role, while strong HLA class II association suggests T cells as key players. In this review, we summarize current knowledge on B cells in AIH and how different B cell subpopulations may drive AIH progression beyond autoantibodies. We also discuss recent findings of B cell-directed therapies in AIH.
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13
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Aringer M, Alarcón-Riquelme ME, Clowse M, Pons-Estel GJ, Vital EM, Dall’Era M. A glimpse into the future of systemic lupus erythematosus. Ther Adv Musculoskelet Dis 2022; 14:1759720X221086719. [PMID: 35368371 PMCID: PMC8972918 DOI: 10.1177/1759720x221086719] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/23/2022] [Indexed: 12/17/2022] Open
Abstract
This viewpoint article on a forecast of clinically meaningful changes in the management of systemic lupus erythematosus (SLE) in the next 10 years is based on a review of the current state of the art. The groundwork has been laid by a robust series of classification criteria and treatment recommendations that have all been published since 2019. Building on this strong foundation, SLE management predictably will take significant steps forward. Assessment for lupus arthritis will presumably include musculoskeletal sonography. Large-scale polyomics studies are likely to unravel more of the central immune mechanisms of the disease. Biomarkers predictive of therapeutic success may enter the field; the type I interferon signature, as a companion for use of anifrolumab, an antibody against the common type I interferon receptor, is one serious candidate. Besides anifrolumab for nonrenal SLE and the new calcineurin inhibitor voclosporin in lupus nephritis, both of which are already approved in the United States and likely to become available in the European Union in 2022, several other approaches are in advanced clinical trials. These include advanced B cell depletion, inhibition of costimulation via CD40 and CD40 ligand (CD40L), and Janus kinase 1 (Jak1) and Tyrosine kinase 2 (Tyk2) inhibition. At the same time, essentially all of our conventional therapeutic armamentarium will continue to be used. The ability of patients to have successful SLE pregnancies, which has become much better in the last decades, should further improve, with approaches including tumor necrosis factor blockade and self-monitoring of fetal heart rates. While we hope that the COVID-19 pandemic will soon be controlled, it has highlighted the risk of severe viral infections in SLE, with increased risk tied to certain therapies. Although there are some data that a cure might be achievable, this likely will remain a challenge beyond 10 years from now.
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Affiliation(s)
- Martin Aringer
- Professor of Medicine (Rheumatology), Division of Rheumatology, Department of Medicine III, University Medical Center and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany
| | - Marta E. Alarcón-Riquelme
- Department of Medical Genomics, GENYO, Pfizer-University of Granada-Andalusian Government Center for Genomics and Oncological Research, Granada, Spain
| | - Megan Clowse
- Division of Rheumatology & Immunology, Duke University, Durham, NC, USA
| | - Guillermo J. Pons-Estel
- Department of Rheumatology, Grupo Oroño–Centro Regional de Enfermedades Autoinmunes y Reumáticas (GO-CREAR), Rosario, Argentina
| | - Edward M. Vital
- University of Leeds and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Maria Dall’Era
- Lupus Clinic and Rheumatology Clinical Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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14
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Schultheiß C, Paschold L, Willscher E, Simnica D, Wöstemeier A, Muscate F, Wass M, Eisenmann S, Dutzmann J, Keyßer G, Gagliani N, Binder M. Maturation trajectories and transcriptional landscape of plasmablasts and autoreactive B cells in COVID-19. iScience 2021; 24:103325. [PMID: 34723157 PMCID: PMC8536484 DOI: 10.1016/j.isci.2021.103325] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/03/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
In parasite and viral infections, aberrant B cell responses can suppress germinal center reactions thereby blunting long-lived memory and may provoke immunopathology including autoimmunity. Using COVID-19 as model, we set out to identify serological, cellular, and transcriptomic imprints of pathological responses linked to autoreactive B cells at single-cell resolution. We show that excessive plasmablast expansions are prognostically adverse and correlate with autoantibody production but do not hinder the formation of neutralizing antibodies. Although plasmablasts followed interleukin-4 (IL-4) and BAFF-driven developmental trajectories, were polyclonal, and not enriched in autoreactive B cells, we identified two memory populations (CD80+/ISG15+ and CD11c+/SOX5+/T-bet+/−) with immunogenetic and transcriptional signs of autoreactivity that may be the cellular source of autoantibodies in COVID-19 and that may persist beyond recovery. Immunomodulatory interventions discouraging such adverse responses may be useful in selected patients to shift the balance from autoreactivity toward long-term memory. Plasmablast expansions correlate with disease severity and autoantibodies in COVID-19 Patients with high plasmablast levels exhibit IGHV4-34 skewing Autoreactive BCRs are enriched in atypical memory, not plasmablast populations
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Affiliation(s)
- Christoph Schultheiß
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Edith Willscher
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Donjete Simnica
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Anna Wöstemeier
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franziska Muscate
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maxi Wass
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
| | - Stephan Eisenmann
- Department of Internal Medicine I, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jochen Dutzmann
- Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Gernot Keyßer
- Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Nicola Gagliani
- I. Department of Medicine and Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Ernst-Grube-Straße 40, 06120 Halle (Saale), Germany
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15
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Thery F, Eggermont D, Impens F. Proteomics Mapping of the ISGylation Landscape in Innate Immunity. Front Immunol 2021; 12:720765. [PMID: 34447387 PMCID: PMC8383068 DOI: 10.3389/fimmu.2021.720765] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 01/12/2023] Open
Abstract
During infection, pathogen sensing and cytokine signaling by the host induce expression of antimicrobial proteins and specialized post-translational modifications. One such protein is ISG15, a ubiquitin-like protein (UBL) conserved among vertebrates. Similar to ubiquitin, ISG15 covalently conjugates to lysine residues in substrate proteins in a process called ISGylation. Mice deficient for ISGylation or lacking ISG15 are strongly susceptible to many viral pathogens and several intracellular bacterial pathogens. Although ISG15 was the first UBL discovered after ubiquitin, the mechanisms behind its protective activity are poorly understood. Largely, this stems from a lack of knowledge on the ISG15 substrate repertoire. To unravel the antiviral activity of ISG15, early studies used mass spectrometry-based proteomics in combination with ISG15 pulldown. Despite reporting hundreds of ISG15 substrates, these studies were unable to identify the exact sites of modification, impeding a clear understanding of the molecular consequences of protein ISGylation. More recently, a peptide-based enrichment approach revolutionized the study of ubiquitin allowing untargeted discovery of ubiquitin substrates, including knowledge of their exact modification sites. Shared molecular determinants between ISG15 and ubiquitin allowed to take advantage of this technology for proteome-wide mapping of ISG15 substrates and modification sites. In this review, we provide a comprehensive overview of mass spectrometry-based proteomics studies on protein ISGylation. We critically discuss the relevant literature, compare reported substrates and sites and make suggestions for future research.
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Affiliation(s)
- Fabien Thery
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Denzel Eggermont
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,VIB Proteomics Core, VIB, Ghent, Belgium
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16
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Cui M, Li T, Yan X, Wang C, Shen Q, Ren H, Li L, Zhang R. Blood Genomics Identifies Three Subtypes of Systemic Lupus Erythematosus: "IFN-High," "NE-High," and "Mixed". Mediators Inflamm 2021; 2021:6660164. [PMID: 34305454 PMCID: PMC8270691 DOI: 10.1155/2021/6660164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/29/2021] [Accepted: 06/17/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Systemic lupus erythematosus (SLE) is a systemic and multifactorial autoimmune disease, and its diverse clinical manifestations affect molecular diagnosis and drug benefits. Our study was aimed at defining the SLE subtypes based on blood transcriptome data, analyzing functional patterns, and elucidating drug benefits. METHODS Three data sets were used in this paper that were collected from the Gene Expression Omnibus (GEO) database, which contained two published data sets of pediatric and adult SLE patients (GSE65391, GSE49454) and public longitudinal data (GSE72754) from a cohort of SLE patients treated with IFN-α Kinoid (IFN-K). Based on disease activity scores and gene expression data, we defined a global SLE signature and merged three clustering algorithms to develop a single-sample subtype classifier (SSC). Systematic analysis of coexpression networks based on modules revealed the molecular mechanism for each subtype. RESULTS We identified 92 genes as a signature of the SLE subtypes and three intrinsic subsets ("IFN-high," "NE-high," and "mixed"), which varied in disease severity. We speculated that IFN-high might be due to the overproduction of interferons (IFNs) caused by viral infection, leading to the formation of autoantibodies. NE-high might primarily result from bacterial and fungal infections that stimulated neutrophils (NE) to produce neutrophil extracellular traps (NETs) and induced individual autoimmune responses. The mixed type contained both of these molecular mechanisms and showed an intrinsic connection. CONCLUSIONS Our research results indicated that identifying the molecular mechanism associated with different SLE subtypes would benefit the molecular diagnosis and stratified therapy. Moreover, repositioning of IFN-K based on subtypes also revealed an improved therapeutic effect, providing a new direction for disease treatment and drug development.
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Affiliation(s)
- Mintian Cui
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Taotao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Xinwei Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Chao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Qi Shen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Hongbiao Ren
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Liangshuang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Ruijie Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
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17
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Wang Y, Ma Q, Huo Z. Identification of hub genes, pathways, and related transcription factors in systemic lupus erythematosus: A preliminary bioinformatics analysis. Medicine (Baltimore) 2021; 100:e26499. [PMID: 34160465 PMCID: PMC8238284 DOI: 10.1097/md.0000000000026499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by multiple organ damage and the production of a variety of autoantibodies. The pathogenesis of SLE has not been fully defined, and it is difficult to treat. Our study aimed to identify candidate genes that may be used as biomarkers for the screening, diagnosis, and treatment of SLE. METHODS We used the GEO2R tool to identify the differentially expressed genes (DEGs) in SLE-related datasets retrieved from the Gene Expression Omnibus (GEO). In addition, we also identified the biological functions of the DEGs by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Additionally, we constructed protein-protein interaction (PPI) networks to identify hub genes, as well as the regulatory network of transcription factors related to DEGs. RESULTS Two datasets were identified for use from the GEO (GSE50772, GSE4588), and 34 up-regulated genes and 4 down-regulated genes were identified by GEO2R. Pathway analysis of the DEGs revealed enrichment of the interferon alpha/beta signaling pathway; GO analysis was mainly enriched in response to interferon alpha, regulation of ribonuclease activity. PPIs were constructed through the STRING database and 14 hub genes were selected and 1 significant module (score = 12.923) was obtained from the PPI network. Additionally, 11 key transcription factors that interacted closely with the 14 hub DEGs were identified from the gene transcription factor network. CONCLUSIONS Bioinformatic analysis is an effective tool for screening the original genomic data in the GEO database, and a large number of SLE-related DEGs were identified. The identified hub DEGs may be potential biomarkers of SLE.
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18
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Al Ali F, Marr AK, Tatari-Calderone Z, Alfaki M, Toufiq M, Roelands J, Syed Ahamed Kabeer B, Bedognetti D, Marr N, Garand M, Rinchai D, Chaussabel D. Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers. F1000Res 2021. [DOI: 10.12688/f1000research.36395.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.
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19
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Xie X, Shrimpton J, Doody GM, Conaghan PG, Ponchel F. B-cell capacity for differentiation changes with age. Aging Cell 2021; 20:e13341. [PMID: 33711204 PMCID: PMC8045946 DOI: 10.1111/acel.13341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/18/2021] [Accepted: 02/21/2021] [Indexed: 01/17/2023] Open
Abstract
Background Age‐related immune deficiencies are thought to be responsible for increased susceptibility to infection in older adults, with alterations in lymphocyte populations becoming more prevalent over time. The loss of humoral immunity in ageing was attributed to the diminished numbers of B cells and the reduced ability to generate immunoglobulin. Aims To compare the intrinsic B‐cell capacity for differentiation into mature plasma cells (PCs), between young and old donors, using in vitro assays, providing either effective T‐cell help or activation via TLR engagement. Methods B cells were isolated from healthy individuals, in younger (30–38 years) and older (60–64 years) donors. An in vitro model system of B‐cell differentiation was used, analysing 5 differentiation markers by flow cytometry, under T‐dependent (TD: CD40/BCR stimulation) or T‐independent (TI: TLR7/BCR activation) conditions. Antibody secretion was measured by ELISA and gene expression using qPCR. Results TI and TD differentiation resulted in effective proliferation of B cells followed by their differentiation into PC. B‐cell‐executed TI differentiation was faster, all differentiation marker and genes being expressed earlier than under TD differentiation (day 6), although generating less viable cells and lower antibody levels (day 13). Age‐related differences in B‐cell capacity for differentiation were minimal in TD differentiation. In contrast, in TI differentiation age significantly affected proliferation, viability, differentiation, antibody secretion and gene expression, older donors being more efficient. Conclusion Altogether, B‐cell differentiation into PC appeared similar between age groups when provided with T‐cell help, in contrast to TI differentiation, where multiple age‐related changes suggest better capacities in older donors. These new findings may help explain the emergence of autoantibodies in ageing.
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Affiliation(s)
- Xuanxiao Xie
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
| | - Jennifer Shrimpton
- Division of Haematology and Immunology Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Gina M. Doody
- Division of Haematology and Immunology Leeds Institute of Medical Research University of Leeds Leeds UK
| | - Philip G. Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Leeds Biomedical Research Centre University of Leeds Leeds UK
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20
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Gupta S, Kaplan MJ. Bite of the wolf: innate immune responses propagate autoimmunity in lupus. J Clin Invest 2021; 131:144918. [PMID: 33529160 PMCID: PMC7843222 DOI: 10.1172/jci144918] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The etiopathogenesis of systemic lupus erythematosus (SLE), a clinically heterogeneous multisystemic syndrome that derives its name from the initial characterization of facial lesions that resemble the bite of a wolf, is considered a complex, multifactorial interplay between underlying genetic susceptibility factors and the environment. Prominent pathogenic factors include the induction of aberrant cell death pathways coupled with defective cell death clearance mechanisms that promote excessive externalization of modified cellular and nuclear debris with subsequent loss of tolerance to a wide variety of autoantigens and innate and adaptive immune dysregulation. While abnormalities in adaptive immunity are well recognized and are key to the pathogenesis of SLE, recent findings have emphasized fundamental roles of the innate immune system in the initiation and propagation of autoimmunity and the development of organ damage in this disease. This Review focuses on recent discoveries regarding the role of components of the innate immune system, specifically neutrophils and interferons, in promoting various aspects of lupus pathogenesis, with potential implications for novel therapeutic strategies.
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21
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Wang J, Sui J, Mao C, Li X, Chen X, Liang C, Wang X, Wang SH, Jia C. Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats. Genes (Basel) 2021; 12:genes12020180. [PMID: 33513983 PMCID: PMC7911279 DOI: 10.3390/genes12020180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 12/13/2022] Open
Abstract
The development of hair follicle in cashmere goats shows significant periodic change, as with mice and humans. However, for cashmere goat with double-coat, the periodic change may be due to other regulatory molecules and signal pathways. To understand the mechanism of periodic development of hair follicle, we performed a weighted gene coexpression network analysis (WGCNA) to mine key genes and establish an interaction network by utilizing the NCBI public dataset. Ten coexpression modules, including 7689 protein-coding genes, were constructed by WGCNA, six of which are considered to be significantly related to the development of the hair follicle cycle. A functional enrichment analysis for each model showed that they are closely related to ECM- receptor interaction, focal adhesion, PI3K-Akt signaling pathway, estrogen signaling pathway, and so on. Combined with the analysis of differential expressed genes, 12 hub genes from coexpression modules were selected as candidate markers, i.e., COL1A1, C1QTNF6, COL1A2, AQP3, KRTAP3-1, KRTAP11-1, FA2H, NDUFS5, DERL2, MRPL14, ANTKMT and XAB2, which might be applied to improve cashmere production.
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22
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Carrillo-Vázquez DA, Jardón-Valadez E, Torres-Ruiz J, Juárez-Vega G, Maravillas-Montero JL, Meza-Sánchez DE, Domínguez-López ML, Varela JCA, Gómez-Martín D. Conformational changes in myeloperoxidase induced by ubiquitin and NETs containing free ISG15 from systemic lupus erythematosus patients promote a pro-inflammatory cytokine response in CD4 + T cells. J Transl Med 2020; 18:429. [PMID: 33176801 PMCID: PMC7659105 DOI: 10.1186/s12967-020-02604-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/05/2020] [Indexed: 12/29/2022] Open
Abstract
Background Neutrophil extracellular traps (NETs) from patients with systemic lupus erythematosus (SLE) are characterized by lower ubiquitylation and myeloperoxidase (MPO) as a substrate. The structural and functional effect of such modification and if there are additional post-translational modifications (PTMs) are unknown. Methods To assess the expression and functional role of PTMs in NETs of patients with SLE; reactivation, proliferation and cytokine production was evaluated by flow cytometry using co-cultures with dendritic cells (DC) and CD4+ from SLE patients and healthy controls. The impact of ubiquitylation on MPO was assessed by molecular dynamics. The expression of ISG15 in NETs was evaluated by immunofluorescence and Western Blot. Results Fifteen patients with SLE and ten healthy controls were included. In the co-cultures of CD4+ lymphocytes with DC stimulated with ubiquitylated MPO or recombinant MPO, a higher expression of IFNγ and IL-17A was found in CD4+ from SLE patients (p < 0.05). Furthermore, with DC stimulated with ubiquitylated MPO a trend towards increased expression of CD25 and Ki67 was found in lupus CD4+ lymphocytes, while the opposite was documented in controls (p < 0.05). Through molecular dynamics we found the K129-K488-K505 residues of MPO as susceptible to ubiquitylation. Ubiquitylation affects the hydration status of the HEME group depending on the residue to which it is conjugated. R239 was found near by the HEME group when the ubiquitin was in K488-K505. In addition, we found greater expression of ISG15 in the SLE NETs vs controls (p < 0.05), colocalization with H2B (r = 0.81) only in SLE samples and increased production of IFNγ in PBMCs stimulated with lupus NETs compared to healthy controls NETs. Conclusion The ubiquitylated MPO has a differential effect on the induction of reactivation of CD4+ lymphocytes in patients with SLE, which may be related to structural changes by ubiquitylation at the catalytic site of MPO. Besides a lower ubiquitylation pattern, NETs of patients with SLE are characterized by the expression of ISG15, and the induction of IFNγ by Th1 cells.
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Affiliation(s)
- Daniel Alberto Carrillo-Vázquez
- Department of Internal Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico.,Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico.,Department of Immunology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Eduardo Jardón-Valadez
- Earth Resources Department, Universidad Autónoma Metropolitana, 52005, Lerma, Estado de Mexico, Mexico
| | - Jiram Torres-Ruiz
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico.,Emergency Medicine Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico
| | - Guillermo Juárez-Vega
- Red de Apoyo a La Investigación, Coordinación de Investigación Científica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Luis Maravillas-Montero
- Red de Apoyo a La Investigación, Coordinación de Investigación Científica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - David Eduardo Meza-Sánchez
- Red de Apoyo a La Investigación, Coordinación de Investigación Científica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - María Lilia Domínguez-López
- Department of Immunology, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Jorge Carlos Alcocer Varela
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico
| | - Diana Gómez-Martín
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Tlalpan, 14080, Mexico City, Mexico. .,Red de Apoyo a La Investigación, Coordinación de Investigación Científica, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Abstract
B cells serve as a key weapon against infectious diseases. They also contribute to multiple autoimmune diseases, including multiple sclerosis (MS) where depletion of B cells is a highly effective therapy. We describe a comprehensive profile of central nervous system (CNS)-specific transcriptional B cell phenotypes in MS at single-cell resolution with paired immune repertoires. We reveal a polyclonal immunoglobulin M (IgM) and IgG1 cerebrospinal fluid B cell expansion polarized toward an inflammatory, memory and plasmablast/plasma cell phenotype, with differential up-regulation of specific proinflammatory pathways. We did not find evidence that CNS B cells harbor a neurotropic virus. These data support the targeting of activated resident B cells in the CNS as a potentially effective strategy for control of treatment-resistant chronic disease. Central nervous system B cells have several potential roles in multiple sclerosis (MS): secretors of proinflammatory cytokines and chemokines, presenters of autoantigens to T cells, producers of pathogenic antibodies, and reservoirs for viruses that trigger demyelination. To interrogate these roles, single-cell RNA sequencing (scRNA-Seq) was performed on paired cerebrospinal fluid (CSF) and blood from subjects with relapsing-remitting MS (RRMS; n = 12), other neurologic diseases (ONDs; n = 1), and healthy controls (HCs; n = 3). Single-cell immunoglobulin sequencing (scIg-Seq) was performed on a subset of these subjects and additional RRMS (n = 4), clinically isolated syndrome (n = 2), and OND (n = 2) subjects. Further, paired CSF and blood B cell subsets (RRMS; n = 7) were isolated using fluorescence activated cell sorting for bulk RNA sequencing (RNA-Seq). Independent analyses across technologies demonstrated that nuclear factor kappa B (NF-κB) and cholesterol biosynthesis pathways were activated, and specific cytokine and chemokine receptors were up-regulated in CSF memory B cells. Further, SMAD/TGF-β1 signaling was down-regulated in CSF plasmablasts/plasma cells. Clonally expanded, somatically hypermutated IgM+ and IgG1+ CSF B cells were associated with inflammation, blood–brain barrier breakdown, and intrathecal Ig synthesis. While we identified memory B cells and plasmablast/plasma cells with highly similar Ig heavy-chain sequences across MS subjects, similarities were also identified with ONDs and HCs. No viral transcripts, including from Epstein–Barr virus, were detected. Our findings support the hypothesis that in MS, CSF B cells are driven to an inflammatory and clonally expanded memory and plasmablast/plasma cell phenotype.
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Hao Shi, Yan KK, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience 2020; 23:101354. [PMID: 32717640 PMCID: PMC7390880 DOI: 10.1016/j.isci.2020.101354] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.
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Affiliation(s)
- Hao Shi
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Koon-Kiu Yan
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chenxi Qian
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Nicolaou O, Sokratous K, Makowska Z, Morell M, De Groof A, Montigny P, Hadjisavvas A, Michailidou K, Oulas A, Spyrou GM, Demetriou C, Alarcón-Riquelme ME, Psarellis S, Kousios A, Lauwerys B, Kyriacou K. Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis. Arthritis Res Ther 2020; 22:147. [PMID: 32552896 PMCID: PMC7301983 DOI: 10.1186/s13075-020-02236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Approximately 50% of systemic lupus erythematosus (SLE) patients develop nephritis, which is among the most severe and frequent complications of the disease and a leading cause of morbidity and mortality. Despite intensive research, there are still no reliable lupus nephritis (LN) markers in clinical use that can assess renal damage and activity with a high sensitivity and specificity. To this end, the aim of this study was to identify new clinically relevant tissue-specific protein biomarkers and possible underlying molecular mechanisms associated with renal involvement in SLE, using mass spectrometry (MS)-based proteomics. METHODS Kidneys were harvested from female triple congenic B6.NZMsle1/sle2/sle3 lupus mice model, and the respective sex- and age-matched C57BL/6 control mice at 12, 24 and 36 weeks of age, representing pre-symptomatic, established and end-stage LN, respectively. Proteins were extracted from kidneys, purified, reduced, alkylated and digested by trypsin. Purified peptides were separated by liquid chromatography and analysed by high-resolution MS. Data were processed by the Progenesis QIp software, and functional annotation analysis was performed using DAVID bioinformatics resources. Immunofluorescence and multiple reaction monitoring (MRM) MS methods were used to confirm prospective biomarkers in SLE mouse strains as well as human serum samples. RESULTS Proteomic profiling of kidney tissues from SLE and control mice resulted in the identification of more than 3800 unique proteins. Pathway analysis revealed a number of dysregulated molecular pathways that may be mechanistically involved in renal pathology, including phagosome and proximal tubule bicarbonate reclamation pathways. Proteomic analysis supported by human transcriptomic data and pathway analysis revealed Coronin-1A, Ubiquitin-like protein ISG15, and Rho GDP-dissociation inhibitor 2, as potential LN biomarkers. These results were further validated in other SLE mouse strains using MRM-MS. Most importantly, experiments in humans showed that measurement of Coronin-1A in human sera using MRM-MS can segregate LN patients from SLE patients without nephritis with a high sensitivity (100%) and specificity (100%). CONCLUSIONS These preliminary findings suggest that serum Coronin-1A may serve as a promising non-invasive biomarker for LN and, upon validation in larger cohorts, may be employed in the future as a screening test for renal disease in SLE patients.
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Affiliation(s)
- Orthodoxia Nicolaou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kleitos Sokratous
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Present Address: OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE, UK
| | | | - María Morell
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Aurélie De Groof
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Pauline Montigny
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- CHU UCL Namur, Yvoir, Belgium
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anastasis Oulas
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M Spyrou
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus
- Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christiana Demetriou
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
| | - Marta E Alarcón-Riquelme
- Genomic Medicine Department, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
- Unit of Immunology and Chronic Disease, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Savvas Psarellis
- Department of Rheumatology, Nicosia General Hospital, Nicosia, Cyprus
| | - Andreas Kousios
- Renal and Transplant Centre Hammersmith Hospital Imperial College Healthcare NHS Trust, London, UK
| | - Bernard Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
- Department of Rheumatology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
- Cyprus School of Molecular Medicine, Iroon Avenue 6, Agios Dometios, 2371, P.O. Box 23462 / 1683, Nicosia, Cyprus.
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26
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El-Sherbiny YM, Md Yusof MY, Psarras A, Hensor EMA, Kabba KZ, Dutton K, Mohamed AAA, Elewaut D, McGonagle D, Tooze R, Doody G, Wittmann M, Emery P, Vital EM. B Cell Tetherin: A Flow Cytometric Cell-Specific Assay for Response to Type I Interferon Predicts Clinical Features and Flares in Systemic Lupus Erythematosus. Arthritis Rheumatol 2020; 72:769-779. [PMID: 31804007 PMCID: PMC8653884 DOI: 10.1002/art.41187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/03/2019] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Type I interferon (IFN) responses are broadly associated with autoimmune diseases, including systemic lupus erythematosus (SLE). Given the cardinal role of autoantibodies in SLE, this study was undertaken to investigate whether the findings of a B cell-specific IFN assay correlate with SLE activity. METHODS B cells and peripheral blood mononuclear cells (PBMCs) were stimulated with type I IFN and type II IFN. Gene expression was analyzed, and the expression of pathway-related membrane proteins was determined. A flow cytometry assay for tetherin (CD317), an IFN-induced protein ubiquitously expressed on leukocytes, was validated in vitro and then clinically against SLE diagnosis, plasmablast expansion, and the British Isles Lupus Assessment Group (BILAG) 2004 score in a discovery cohort (n = 156 SLE patients, 30 rheumatoid arthritis [RA] patients, and 25 healthy controls). A second, longitudinal validation cohort of 80 SLE patients was also evaluated for flare prediction. RESULTS In vitro, a close cell-specific and dose-response relationship between type I IFN-responsive genes and cell surface tetherin was observed in all immune cell subsets. Tetherin expression on multiple cell subsets was selectively responsive to stimulation with type I IFN compared to types II and III IFNs. In patient samples from the discovery cohort, memory B cell tetherin showed the strongest associations with diagnosis (SLE:healthy control effect size 0.11 [P = 0.003]; SLE:RA effect size 0.17 [P < 0.001]), plasmablast numbers in rituximab-treated patients (R = 0.38, P = 0.047), and BILAG 2004. These associations were equivalent to or stronger than those for IFN score or monocyte tetherin. Memory B cell tetherin was found to be predictive of future clinical flares in the validation cohort (hazard ratio 2.29 [95% confidence interval 1.01-4.64]; P = 0.022). CONCLUSION Our findings indicate that memory B cell surface tetherin, a B cell-specific IFN assay, is associated with SLE diagnosis and disease activity, and predicts flares better than tetherin on other cell subsets or whole blood assays, as determined in an independent validation cohort.
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Affiliation(s)
- Yasser M El-Sherbiny
- University of Leeds, Leeds, UK, Nottingham Trent University School of Science and Technology, Nottingham, UK, and Mansoura University, Mansoura, Egypt
| | - Md Yuzaiful Md Yusof
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Antonios Psarras
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Elizabeth M A Hensor
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Katherine Dutton
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alaa A A Mohamed
- University of Leeds, Leeds, UK, and Assiut University, Assiut, Egypt
| | | | - Dennis McGonagle
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | | | - Miriam Wittmann
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Emery
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Edward M Vital
- University of Leeds, Leeds, UK, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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27
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Zarei Ghobadi M, Mozhgani SH, Farzanehpour M, Behzadian F. Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis. Virol J 2019; 16:124. [PMID: 31665046 PMCID: PMC6819563 DOI: 10.1186/s12985-019-1231-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Background Despite the high yearly prevalence of Influenza, the pathogenesis mechanism and involved genes have not been fully known. Finding the patterns and mapping the complex interactions between different genes help us to find the possible biomarkers and treatment targets. Methods Herein, weighted gene co-expression network analysis (WGCNA) was employed to construct a co-expression network among genes identified by microarray analysis of the pediatric influenza-infected samples. Results Three of the 38 modules were found as the most related modules to influenza infection. At a functional level, we found that the genes in these modules regulate the immune responses, protein targeting, and defense to virus. Moreover, the analysis of differentially expressed genes disclosed 719 DEGs between the normal and infected subjects. The comprehensive investigation of genes in the module involved in immune system and viral defense (yellow module) revealed that SP110, HERC5, SAMD9L, RTP4, C19orf66, HELZ2, EPSTI1, and PHF11 which were also identified as DEGs (except C19orf66) have the potential to be as the biomarkers and also drug targeting for the treatment of pediatric influenza. Conclusions The WGCN analysis revealed co-expressed genes which were involved in the innate immune system and defense to virus. The differentially expressed genes in the identified modules can be considered for designing drug targets. Moreover, modules can help to find pathogenesis routes in the future.
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Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdieh Farzanehpour
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran
| | - Farida Behzadian
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Iran.
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28
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Yuan Y, Ma H, Ye Z, Jing W, Jiang Z. Interferon-stimulated gene 15 expression in systemic lupus erythematosus : Diagnostic value and association with lymphocytopenia. Z Rheumatol 2019; 77:256-262. [PMID: 28204879 DOI: 10.1007/s00393-017-0274-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND The aim of this study was to (a) assess the relationship between interferon-stimulated gene 15 (ISG15) expression and clinical manifestations of systemic lupus erythematosus (SLE) and (b) investigate the diagnostic value of ISG15 in SLE. PATIENTS AND METHODS The study comprised 28 patients newly diagnosed with SLE, 10 patients with undifferentiated connective tissue disease, and 22 healthy volunteers. Of the SLE patients, 14 were chosen randomly to be followed up for 4 weeks. ISG15 expression in whole blood cells was determined by quantitative polymerase chain reaction. Clinical and laboratory parameters were recorded at baseline and after treatment. RESULTS The ISG15 mRNA level was higher in whole blood cell counts of SLE patients when compared with the disease control and healthy control groups. Moreover, it was correlated with SLE disease activity as assessed via the SLE disease activity index, serositis, and anemia at baseline. ISG15 expression correlated with lymphocytopenia in active SLE patients before treatment. On receiver operating characteristic curve analysis, the area under the curve for ISG15 expression was 0.826 (p = 0.000015). CONCLUSION ISG15 expression is relatively high in SLE patients and correlates with disease activity before treatment. ISG15 expression is higher in SLE patients with lymphocytopenia before treatment.
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Affiliation(s)
- Y Yuan
- Department of Rheumatology and Immunology, the First Hospital, Jilin University, 130021, Changchun, China
| | - H Ma
- Department of Rheumatology and Immunology, the First Hospital, Jilin University, 130021, Changchun, China
| | - Z Ye
- Department of Rheumatology and Immunology, the First Hospital, Jilin University, 130021, Changchun, China
| | - W Jing
- Department of Gerontology, the First Hospital, Jilin University, 130021, Changchun, China
| | - Z Jiang
- Department of Rheumatology and Immunology, the First Hospital, Jilin University, 130021, Changchun, China.
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29
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Crow MK, Ronnblom L. Type I interferons in host defence and inflammatory diseases. Lupus Sci Med 2019; 6:e000336. [PMID: 31205729 PMCID: PMC6541752 DOI: 10.1136/lupus-2019-000336] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022]
Abstract
Type I interferons (IFN) can have dual and opposing roles in immunity, with effects that are beneficial or detrimental to the individual depending on whether IFN pathway activation is transient or sustained. Determinants of IFN production and its functional consequences include the nature of the microbial or nucleic acid stimulus, the type of nucleic acid sensor involved in inducing IFN, the predominant subtype of type I IFN produced and the immune ecology of the tissue at the time of IFN expression. When dysregulated, the type I IFN system drives many autoimmune and non-autoimmune inflammatory diseases, including SLE and the tissue inflammation associated with chronic infection. The type I IFN system may also contribute to outcomes for patients affected by solid cancers or myocardial infarction. Significantly more research is needed to discern the mechanisms of induction and response to type I IFNs across these diseases, and patient endophenotyping may help determine whether the cytokine is acting as 'friend' or 'foe', within a particular patient, and at the time of treatment. This review summarises key concepts and discussions from the second International Summit on Interferons in Inflammatory Diseases, during which expert clinicians and scientists evaluated the evidence for the role of type I IFNs in autoimmune and other inflammatory diseases.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, Weill Cornell Medical College, New York City, New York, USA
| | - Lars Ronnblom
- Section of Rheumatology, Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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30
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Ramadani F, Bowen H, Gould HJ, Fear DJ. Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway. Front Immunol 2019; 10:402. [PMID: 30915071 PMCID: PMC6421273 DOI: 10.3389/fimmu.2019.00402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
IgE is secreted by plasma cells (PCs) and is central to allergic disease. Using an ex vivo tonsil B cell culture system, which mimics the Th2 responses in vivo, we have recently characterized the development pathway of human IgE-expressing PCs. In this system, as in mice, we reported the predisposition of IgE-expressing B cells to differentiate into PCs. To gain a comprehensive understanding of the molecular events involved in the differentiation of human IgE+ B cells into PCs we have used the Illumina HumanHT-12 v4 Expression BeadChip array to analyse the gene expression profile of ex vivo generated human IgE+ B cells at various stages of their differentiation into PCs. We also compared the transcription profiles of IgE+ and IgG1+ cells to discover isotype-specific patterns. Comparisons of IgE+ and IgG1+ cell transcriptional profiles revealed molecular signatures specific for IgE+ cells, which diverge from their IgG1+ cell counterparts upon differentiation into PCs. At the germinal center (GC) stage of development, unlike in some mouse studies of IgE biology, we observed similar rates of apoptosis and no significant differences in the expression of apoptosis-associated genes between the IgE+ and IgG1+ B cells. We identified a gene interaction network associated with early growth response 1 (EGR1) that, together with the up-regulated IRF4, may account for the predisposition of IgE+ B cells to differentiate into PCs. However, despite their swifter rates of PC differentiation, the transcription profile of IgE+ PCs is more closely related to IgE+ and IgG1+ plasmablasts (PBs) than to IgG1+ PCs, suggesting that the terminal differentiation of IgE+ cells is impeded. We also show that IgE+ PCs have increased levels of apoptosis suggesting that the IgE+ PCs generated in our in vitro tonsil B cell cultures, as in mice, are short-lived. We identified gene regulatory networks as well as cell cycle and apoptosis signatures that may explain the diverging PC differentiation programme of these cells. Overall, our study provides a detailed analysis of the transcriptional pathways underlying the differentiation of human IgE-expressing B cells and points to molecular signatures that regulate IgE+ PC differentiation and function.
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Affiliation(s)
- Faruk Ramadani
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, United Kingdom.,Asthma UK Centre, Allergic Mechanisms in Asthma, King's College London, London, United Kingdom
| | - Holly Bowen
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, United Kingdom.,Asthma UK Centre, Allergic Mechanisms in Asthma, King's College London, London, United Kingdom
| | - Hannah J Gould
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, United Kingdom.,Asthma UK Centre, Allergic Mechanisms in Asthma, King's College London, London, United Kingdom
| | - David J Fear
- Asthma UK Centre, Allergic Mechanisms in Asthma, King's College London, London, United Kingdom.,Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, United Kingdom
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31
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Stephenson S, Care MA, Fan I, Zougman A, Westhead DR, Doody GM, Tooze RM. Growth Factor-like Gene Regulation Is Separable from Survival and Maturation in Antibody-Secreting Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1287-1300. [PMID: 30642980 PMCID: PMC6360259 DOI: 10.4049/jimmunol.1801407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/05/2018] [Indexed: 12/23/2022]
Abstract
Recurrent mutational activation of the MAP kinase pathway in plasma cell myeloma implicates growth factor-like signaling responses in the biology of Ab-secreting cells (ASCs). Physiological ASCs survive in niche microenvironments, but how niche signals are propagated and integrated is poorly understood. In this study, we dissect such a response in human ASCs using an in vitro model. Applying time course expression data and parsimonious gene correlation network analysis (PGCNA), a new approach established by our group, we map expression changes that occur during the maturation of proliferating plasmablast to quiescent plasma cell under survival conditions including the potential niche signal TGF-β3. This analysis demonstrates a convergent pattern of differentiation, linking unfolded protein response/endoplasmic reticulum stress to secretory optimization, coordinated with cell cycle exit. TGF-β3 supports ASC survival while having a limited effect on gene expression including upregulation of CXCR4. This is associated with a significant shift in response to SDF1 in ASCs with amplified ERK1/2 activation, growth factor-like immediate early gene regulation and EGR1 protein expression. Similarly, ASCs responding to survival conditions initially induce partially overlapping sets of immediate early genes without sustaining the response. Thus, in human ASCs growth factor-like gene regulation is transiently imposed by niche signals but is not sustained during subsequent survival and maturation.
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Affiliation(s)
- Sophie Stephenson
- Section of Experimental Haematology, Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Matthew A Care
- Section of Experimental Haematology, Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Im Fan
- Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals National Health Service Trust, St. James's University Hospital, Leeds LS9 7TF, United Kingdom; and
| | - Alexandre Zougman
- Section of Biomarkers and Therapy, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - David R Westhead
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gina M Doody
- Section of Experimental Haematology, Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom
| | - Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds LS9 7TF, United Kingdom;
- Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals National Health Service Trust, St. James's University Hospital, Leeds LS9 7TF, United Kingdom; and
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32
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Al-Maskari M, Care MA, Robinson E, Cocco M, Tooze RM, Doody GM. Site-1 protease function is essential for the generation of antibody secreting cells and reprogramming for secretory activity. Sci Rep 2018; 8:14338. [PMID: 30254311 PMCID: PMC6156501 DOI: 10.1038/s41598-018-32705-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 09/11/2018] [Indexed: 01/08/2023] Open
Abstract
The unfolded protein response (UPR) and activation of XBP1 is necessary for high secretory efficiency and functional differentiation of antibody secreting cells (ASCs). The UPR additionally includes a branch in which membrane-bound transcription factors, exemplified by ATF6, undergo intramembrane-proteolysis by the sequential action of site-1 (MBTPS1/S1P) and site-2 proteases (MBTPS2/S2P) and release of the cytoplasmic domain as an active transcription factor. Such regulation is shared with a family of CREB3-related transcription factors and sterol regulatory element-binding proteins (SREBPs). Of these, we identify that the CREB3 family member CREB3L2 is strongly induced and activated during the transition from B-cell to plasma cell state. Inhibition of site-1 protease leads to a profound reduction in plasmablast number linked to induction of autophagy. Plasmablasts generated in the presence of site-1 protease inhibitor segregated into CD38high and CD38low populations, the latter characterized by a marked reduction in the capacity to secrete IgG. Site-1 protease inhibition is accompanied by a distinctive change in gene expression associated with amino acid, steroid and fatty acid synthesis pathways. These results demonstrate that transcriptional control of metabolic programs necessary for secretory activity can be targeted via site-1 protease inhibition during ASC differentiation.
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Affiliation(s)
- Muna Al-Maskari
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Matthew A Care
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Emily Robinson
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Mario Cocco
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom
| | - Gina M Doody
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, United Kingdom.
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33
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El-Sherbiny YM, Psarras A, Md Yusof MY, Hensor EMA, Tooze R, Doody G, Mohamed AAA, McGonagle D, Wittmann M, Emery P, Vital EM. A novel two-score system for interferon status segregates autoimmune diseases and correlates with clinical features. Sci Rep 2018; 8:5793. [PMID: 29643425 PMCID: PMC5895784 DOI: 10.1038/s41598-018-24198-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/23/2018] [Indexed: 11/10/2022] Open
Abstract
Measurement of type I interferon (IFN-I) has potential to diagnose and stratify autoimmune diseases, but existing results have been inconsistent. Interferon-stimulated-gene (ISG) based methods may be affected by the modularity of the ISG transcriptome, cell-specific expression, response to IFN-subtypes and bimodality of expression. We developed and clinically validated a 2-score system (IFN-Score-A and -B) using Factor Analysis of 31 ISGs measured by TaqMan selected from 3-IFN-annotated modules. We evaluated these scores using in-vitro IFN stimulation as well as in sorted cells then clinically validated in a cohort of 328 autoimmune disease patients and healthy controls. ISGs varied in response to IFN-subtypes and both scores varied between cell subsets. IFN-Score-A differentiated Systemic Lupus Erythematosus (SLE) from both Rheumatoid Arthritis (RA) and Healthy Controls (HC) (both p < 0.001), while IFN-Score-B differentiated SLE and RA from HC (both p < 0.001). In SLE, both scores were associated with cutaneous and hematological (all p < 0.05) but not musculoskeletal disease activity. Comparing with bimodal (IFN-high/low) classification, significant differences in IFN-scores were found between diagnostic groups within the IFN-high group. Our continuous 2-score system is more clinically relevant than a simple bimodal classification of IFN status. This system should allow improvement in diagnosis, stratification, and therapy in IFN-mediated autoimmunity.
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Affiliation(s)
- Y M El-Sherbiny
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - A Psarras
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - M Y Md Yusof
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - E M A Hensor
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - R Tooze
- Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - G Doody
- Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - A A A Mohamed
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Department of Rheumatology and Rehabilitation, Faculty of Medicine, Assiut University, Asyut, Egypt
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - D McGonagle
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - M Wittmann
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - P Emery
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - E M Vital
- National Institute of Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.
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Wu C, Zhao Y, Lin Y, Yang X, Yan M, Min Y, Pan Z, Xia S, Shao Q. Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. Mol Med Rep 2017; 17:3591-3598. [PMID: 29257335 PMCID: PMC5802164 DOI: 10.3892/mmr.2017.8293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/17/2017] [Indexed: 12/20/2022] Open
Abstract
DNA microarray and high-throughput sequencing have been widely used to identify the differentially expressed genes (DEGs) in systemic lupus erythematosus (SLE). However, the big data from gene microarrays are also challenging to work with in terms of analysis and processing. The presents study combined data from the microarray expression profile (GSE65391) and bioinformatics analysis to identify the key genes and cellular pathways in SLE. Gene ontology (GO) and cellular pathway enrichment analyses of DEGs were performed to investigate significantly enriched pathways. A protein-protein interaction network was constructed to determine the key genes in the occurrence and development of SLE. A total of 310 DEGs were identified in SLE, including 193 upregulated genes and 117 downregulated genes. GO analysis revealed that the most significant biological process of DEGs was immune system process. Kyoto Encyclopedia of Genes and Genome pathway analysis showed that these DEGs were enriched in signaling pathways associated with the immune system, including the RIG-I-like receptor signaling pathway, intestinal immune network for IgA production, antigen processing and presentation and the toll-like receptor signaling pathway. The current study screened the top 10 genes with higher degrees as hub genes, which included 2′-5′-oligoadenylate synthetase 1, MX dynamin like GTPase 2, interferon induced protein with tetratricopeptide repeats 1, interferon regulatory factor 7, interferon induced with helicase C domain 1, signal transducer and activator of transcription 1, ISG15 ubiquitin-like modifier, DExD/H-box helicase 58, interferon induced protein with tetratricopeptide repeats 3 and 2′-5′-oligoadenylate synthetase 2. Module analysis revealed that these hub genes were also involved in the RIG-I-like receptor signaling, cytosolic DNA-sensing, toll-like receptor signaling and ribosome biogenesis pathways. In addition, these hub genes, from different probe sets, exhibited significant co-expressed tendency in multi-experiment microarray datasets (P<0.01). In conclusion, these key genes and cellular pathways may improve the current understanding of the underlying mechanism of development of SLE. These key genes may be potential biomarkers of diagnosis, therapy and prognosis for SLE.
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Affiliation(s)
- Chengjiang Wu
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yangjing Zhao
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yu Lin
- Center for Computational Science, University of Miami, Coral Gables, FL 33146, USA
| | - Xinxin Yang
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Meina Yan
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Yujiao Min
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Zihui Pan
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Sheng Xia
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
| | - Qixiang Shao
- Department of Immunology, Key Laboratory for Laboratory Medicine of Jiangsu Province, Jiangsu University Medical School, Zhenjiang, Jiangsu 212013, P.R. China
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Romão VC, Vital EM, Fonseca JE, Buch MH. Right drug, right patient, right time: aspiration or future promise for biologics in rheumatoid arthritis? Arthritis Res Ther 2017; 19:239. [PMID: 29065909 PMCID: PMC5655983 DOI: 10.1186/s13075-017-1445-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Individualising biologic disease-modifying anti-rheumatic drugs (bDMARDs) to maximise outcomes and deliver safe and cost-effective care is a key goal in the management of rheumatoid arthritis (RA). Investigation to identify predictive tools of bDMARD response is a highly active and prolific area of research. In addition to clinical phenotyping, cellular and molecular characterisation of synovial tissue and blood in patients with RA, using different technologies, can facilitate predictive testing. This narrative review will summarise the literature for the available bDMARD classes and focus on where progress has been made. We will also look ahead and consider the increasing use of 'omics' technologies, the potential they hold as well as the challenges, and what is needed in the future to fully realise our ambition of personalised bDMARD treatment.
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Affiliation(s)
- Vasco C. Romão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Edward M. Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - João Eurico Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Department of Rheumatology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Av. Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Maya H. Buch
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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36
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Psarras A, Emery P, Vital EM. Type I interferon-mediated autoimmune diseases: pathogenesis, diagnosis and targeted therapy. Rheumatology (Oxford) 2017; 56:1662-1675. [PMID: 28122959 DOI: 10.1093/rheumatology/kew431] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Indexed: 12/21/2022] Open
Abstract
Type I interferons (IFN-Is) are a group of molecules with pleiotropic effects on the immune system forming a crucial link between innate and adaptive immune responses. Apart from their important role in antiviral immunity, IFN-Is are increasingly recognized as key players in autoimmune CTDs such as SLE. Novel therapies that target IFN-I appear effective in SLE in early trials, but effectiveness is related to the presence of IFN-I biomarkers. IFN-I biomarkers may also act as positive or negative predictors of response to other biologics. Despite the high failure rate of clinical trials in SLE, subgroups of patients often respond better. Fully optimizing the potential of these agents is therefore likely to require stratification of patients using IFN-I and other biomarkers. This suggests the unified concept of type I IFN-mediated autoimmune diseases as a grouping including patients with a variety of different traditional diagnoses.
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Affiliation(s)
- Antonios Psarras
- Leeds Teaching Hospitals NHS Trust, NIHR Leeds Biomedical Research Unit.,Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Paul Emery
- Leeds Teaching Hospitals NHS Trust, NIHR Leeds Biomedical Research Unit.,Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Edward M Vital
- Leeds Teaching Hospitals NHS Trust, NIHR Leeds Biomedical Research Unit.,Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
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37
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Ikeda K, Hayakawa K, Fujishiro M, Kawasaki M, Hirai T, Tsushima H, Miyashita T, Suzuki S, Morimoto S, Tamura N, Takamori K, Ogawa H, Sekigawa I. JAK inhibitor has the amelioration effect in lupus-prone mice: the involvement of IFN signature gene downregulation. BMC Immunol 2017; 18:41. [PMID: 28830352 PMCID: PMC5568047 DOI: 10.1186/s12865-017-0225-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/13/2017] [Indexed: 11/10/2022] Open
Abstract
Background We previously reported that JAK–STAT-pathway mediated regulation of IFN-regulatory factor genes could play an important role in SLE pathogenesis. Here, we evaluated the efficacy of the JAK inhibitor tofacitinib (TOFA) for controlling IFN signalling via the JAK–STAT pathway and as a therapeutic for SLE. Results We treated NZB/NZW F1 mice with TOFA and assessed alterations in their disease, pathological, and immunological conditions. Gene-expression results obtained from CD4+ T cells (SLE mice) and CD3+ T cells (human SLE patients) were measured by DNA microarray and qRT-PCR. TOFA treatment resulted in reduced levels of anti-dsDNA antibodies, decreased proteinuria, and amelioration of nephritis as compared with those observed in control animals. Moreover, we observed the rebalance in the populations of naïve CD4+ T cells and effector/memory cells in TOFA-treated mice; however, treatment with a combination of TOFA and dexamethasone (DEXA) elicited a stronger inhibitory effect toward the effector/memory cells than did TOFA or DEXA monotherapy. We also detected decreased expression of several IFN-signature genes Ifit3 and Isg15 in CD4+ from SLE-prone mice following TOFA and DEXA treatment, and IFIT3 in CD3+ T cells from human patients following immunosuppressant therapy including steroid, respectively. Conclusion Modulation of type I IFN signalling via JAK–STAT inhibition may exert a beneficial effect in SLE patients, and our results suggest that TOFA could be utilised for the development of new SLE-specific therapeutic strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12865-017-0225-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keigo Ikeda
- Department of Internal Medicine and Rheumatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka Urayasu-shi, Chiba, 279-0021, Japan. .,Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan.
| | - Kunihiro Hayakawa
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Maki Fujishiro
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Mikiko Kawasaki
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Takuya Hirai
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Hiroshi Tsushima
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomoko Miyashita
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Satoshi Suzuki
- Department of Internal Medicine and Rheumatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka Urayasu-shi, Chiba, 279-0021, Japan
| | - Shinji Morimoto
- Department of Internal Medicine and Rheumatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka Urayasu-shi, Chiba, 279-0021, Japan.,Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Naoto Tamura
- Department of Internal Medicine and Rheumatology, Juntendo University School of Medicine, Tokyo, Japan
| | - Kenji Takamori
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Hideoki Ogawa
- Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Iwao Sekigawa
- Department of Internal Medicine and Rheumatology, Juntendo University Urayasu Hospital, 2-1-1 Tomioka Urayasu-shi, Chiba, 279-0021, Japan.,Institutes for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
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38
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Sanz I. New Perspectives in Rheumatology: May You Live in Interesting Times: Challenges and Opportunities in Lupus Research. Arthritis Rheumatol 2017; 69:1552-1559. [PMID: 28371318 DOI: 10.1002/art.40109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/21/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Iñaki Sanz
- Emory University School of Medicine, Atlanta, Georgia
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39
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Arumugakani G, Stephenson SJ, Newton DJ, Rawstron A, Emery P, Doody GM, McGonagle D, Tooze RM. Early Emergence of CD19-Negative Human Antibody-Secreting Cells at the Plasmablast to Plasma Cell Transition. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2017; 198:4618-4628. [PMID: 28490574 PMCID: PMC5458329 DOI: 10.4049/jimmunol.1501761] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
Abstract
Long-lived human plasma cells (PCs) play central roles in immunity and autoimmunity and are enriched among the subpopulation of CD19neg human PCs. However, whether human CD19neg PCs are necessarily aged cells that have gradually lost CD19 expression is not known. Assessing peripheral blood samples at steady-state and during the acute response to influenza vaccination in healthy donors, we identify the presence of phenotypic CD19neg plasmablasts, the proliferative precursor state to mature PCs, and demonstrate by ELISPOT that these are Ab-secreting cells (ASCs). During the acute response to influenza vaccination, CD19pos, CD19low, and CD19neg ASCs secrete vaccine-specific Abs and show linked IGHV repertoires. To address precursor/product relationships, we use in vitro models that mimic T-dependent and T-independent differentiation, finding that the CD19neg state can be established at the plasmablast to PC transition, that CD19neg PCs increase as a percentage of surviving PCs in vitro, and that CD19neg and CD19pos PCs can be maintained independently. These data provide proof-of-principle for the view that newly generated ASCs can acquire a mature PC phenotype that is accompanied by loss of CD19 expression at an early stage of differentiation and that aging is not an obligate requirement for a CD19neg state to be established.
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Affiliation(s)
- Gururaj Arumugakani
- Section of Experimental Musculoskeletal Medicine, Leeds Institute of Rheumatic and Musculoskeletal Medicine, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Sophie J Stephenson
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom; and
| | - Darren J Newton
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom; and
| | - Andy Rawstron
- Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Paul Emery
- Section of Experimental Musculoskeletal Medicine, Leeds Institute of Rheumatic and Musculoskeletal Medicine, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Gina M Doody
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom; and
| | - Dennis McGonagle
- Section of Experimental Musculoskeletal Medicine, Leeds Institute of Rheumatic and Musculoskeletal Medicine, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Reuben M Tooze
- Section of Experimental Haematology, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom; and
- Haematological Malignancy Diagnostic Service, Leeds Teaching Hospitals National Health Service Trust, St James's University Hospital, Leeds LS9 7TF, United Kingdom
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40
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Wong YY, Johnson B, Friedrich TC, Trepanier LA. Hepatic expression profiles in retroviral infection: relevance to drug hypersensitivity risk. Pharmacol Res Perspect 2017; 5:e00312. [PMID: 28603631 PMCID: PMC5464341 DOI: 10.1002/prp2.312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/11/2022] Open
Abstract
HIV‐infected patients show a markedly increased risk of delayed hypersensitivity (HS) reactions to potentiated sulfonamide antibiotics (trimethoprim/sulfamethoxazole or TMP/SMX). Some studies have suggested altered SMX biotransformation in HIV infection, but hepatic biotransformation pathways have not been evaluated directly. Systemic lupus erythematosus (SLE) is another chronic inflammatory disease with a higher incidence of sulfonamide HS, but it is unclear whether retroviral infection and SLE share risk factors for drug HS. We hypothesized that retroviral infection would lead to dysregulation of hepatic pathways of SMX biotransformation, as well as pathway alterations in common with SLE that could contribute to drug HS risk. We characterized hepatic expression profiles and enzymatic activities in an SIV‐infected macaque model of retroviral infection, and found no evidence for dysregulation of sulfonamide drug biotransformation pathways. Specifically, NAT1,NAT2,CYP2C8,CYP2C9,CYB5R3,MARC1/2, and glutathione‐related genes (GCLC,GCLM,GSS,GSTM1, and GSTP1) were not differentially expressed in drug naïve SIVmac239‐infected male macaques compared to age‐matched controls, and activities for SMX N‐acetylation and SMX hydroxylamine reduction were not different. However, multiple genes that are reportedly over‐expressed in SLE patients were also up‐regulated in retroviral infection, to include enhanced immunoproteasomal processing and presentation of antigens as well as up‐regulation of gene clusters that may be permissive to autoimmunity. These findings support the hypothesis that pathways downstream from drug biotransformation may be primarily important in drug HS risk in HIV infection.
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Affiliation(s)
- Yat Yee Wong
- Department of Medical Sciences School of Veterinary Medicine Madison Wisconsin
| | - Brian Johnson
- Molecular and Environmental Toxicology Center School of Medicine and Public Health University of Wisconsin-Madison Madison Wisconsin
| | - Thomas C Friedrich
- Department of Pathobiological Sciences School of Veterinary Medicine Madison Wisconsin.,AIDS Vaccine Research Laboratory Wisconsin National Primate Research Center Madison Wisconsin
| | - Lauren A Trepanier
- Department of Medical Sciences School of Veterinary Medicine Madison Wisconsin
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Dos Santos PF, Mansur DS. Beyond ISGlylation: Functions of Free Intracellular and Extracellular ISG15. J Interferon Cytokine Res 2017; 37:246-253. [PMID: 28467275 DOI: 10.1089/jir.2016.0103] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
ISG15 is a ubiquitin-like type I IFN-stimulated protein of 15 kDa and is one of the most prominently expressed proteins in viral infections. ISG15 is widely known to be involved in a process called ISGylation, where it binds to over 150 targets from a variety of classes of proteins including central immune signaling pathways such as those mediated by NFκB, JNK, and IRF-3. However, ISG15 also exists in a free form that can act intra- or extracellularly. In vitro and in vivo evidences suggest that free ISG15 play different roles in several cellular processes, from cancer and defense against viral infections to activation of immune cells such as lymphocytes, monocytes, and NK cells. This review discusses the roles of free intracellular and secreted ISG15 approaching questions yet to be answered about the mechanism of action of this protein.
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Affiliation(s)
- Paula Fernandes Dos Santos
- Departament of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina , Santa Catarina, Brazil
| | - Daniel Santos Mansur
- Departament of Microbiology, Immunology and Parasitology, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina , Santa Catarina, Brazil
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