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Estupiñán-Moreno E, Hernández-Rodríguez J, Li T, Ciudad L, Andrés-León E, Terron-Camero LC, Prieto-González S, Espígol-Frigolé G, Cid MC, Márquez A, Martin J, Ballestar E, Ortiz-Fernández L. Decoding CD4 + T cell transcriptome in giant cell arteritis: Novel pathways and altered cross-talk with monocytes. J Autoimmun 2024; 146:103240. [PMID: 38754238 DOI: 10.1016/j.jaut.2024.103240] [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: 02/05/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Giant cell arteritis (GCA) is an immune-mediated large-vessels vasculitis with complex etiology. Although the pathogenic mechanisms remain poorly understood, a central role for CD4+ T cells has been demonstrated. In this context, understanding the transcriptome dysregulation in GCA CD4+ T cells will yield new insights into its pathogenesis. METHODS Transcriptome analysis was conducted on CD4+ T cells from 70 patients with GCA with different disease activity and treatment status (active patients before treatment and patients in remission with and without glucocorticoid treatment), and 28 healthy controls. The study also evaluated potential impacts of DNA methylation on gene expression alterations and assessed cross-talk with CD14+ monocytes. RESULTS This study has uncovered a substantial number of genes and pathways potentially contributing to the pathogenicity of CD4+ T cells in GCA. Specifically, CD4+ T cells from GCA patients with active disease exhibited altered expression levels of genes involved in multiple immune-related processes, including various interleukins (IL) signaling pathways. Notably, IL-2, a decisive interleukin for regulatory T cells homeostasis, was among the most significant. Additionally, impaired apoptotic pathways appear crucial in GCA development. Our findings also suggest that histone-related epigenetic pathways may be implicated in promoting an inflammatory phenotype in GCA active patients. Finally, our study observed altered signaling communication, such as the Jagged-Notch signaling, between CD4+ T cells and monocytes that could have pathogenic relevance in GCA. CONCLUSIONS Our study suggests the participation of novel cytokines and pathways and the occurrence of a disruption of monocyte-T cell crosstalk driving GCA pathogenesis.
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Affiliation(s)
- Elkyn Estupiñán-Moreno
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - José Hernández-Rodríguez
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Eduardo Andrés-León
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Laura Carmen Terron-Camero
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Sergio Prieto-González
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Georgina Espígol-Frigolé
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria C Cid
- Vasculitis Research Unit. Department of Autoimmune Diseases, Hospital Clinic, Universitat de Barcelona, Institut D'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ana Márquez
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain
| | - Javier Martin
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain.
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.
| | - Lourdes Ortiz-Fernández
- Institute of Parastitology and Biomedicine López-Neyra (IPBLN), Spanish National Research Council (CSIC), Granada, Spain.
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2
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Khajavi L, Nguyen XH, Queriault C, Chabod M, Barateau L, Dauvilliers Y, Zytnicki M, Liblau R. The transcriptomics profiling of blood CD4 and CD8 T-cells in narcolepsy type I. Front Immunol 2023; 14:1249405. [PMID: 38077397 PMCID: PMC10702585 DOI: 10.3389/fimmu.2023.1249405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023] Open
Abstract
Background Narcolepsy Type I (NT1) is a rare, life-long sleep disorder arising as a consequence of the extensive destruction of orexin-producing hypothalamic neurons. The mechanisms involved in the destruction of orexin neurons are not yet elucidated but the association of narcolepsy with environmental triggers and genetic susceptibility (strong association with the HLA, TCRs and other immunologically-relevant loci) implicates an immuno-pathological process. Several studies in animal models and on human samples have suggested that T-cells are the main pathogenic culprits. Methods RNA sequencing was performed on four CD4 and CD8 T-cell subsets (naive, effector, effector memory and central memory) sorted by flow cytometry from peripheral blood mononuclear cells (PBMCs) of NT1 patients and HLA-matched healthy donors as well as (age- and sex-) matched individuals suffering from other sleep disorders (OSD). The RNAseq analysis was conducted by comparing the transcriptome of NT1 patients to that of healthy donors and other sleep disorder patients (collectively referred to as the non-narcolepsy controls) in order to identify NT1-specific genes and pathways. Results We determined NT1-specific differentially expressed genes, several of which are involved in tubulin arrangement found in CD4 (TBCB, CCT5, EML4, TPGS1, TPGS2) and CD8 (TTLL7) T cell subsets, which play a role in the immune synapse formation and TCR signaling. Furthermore, we identified genes (GZMB, LTB in CD4 T-cells and NLRP3, TRADD, IL6, CXCR1, FOXO3, FOXP3 in CD8 T-cells) and pathways involved in various aspects of inflammation and inflammatory response. More specifically, the inflammatory profile was identified in the "naive" subset of CD4 and CD8 T-cell. Conclusion We identified NT1-specific differentially expressed genes, providing a cell-type and subset specific catalog describing their functions in T-cells as well as their potential involvement in NT1. Several genes and pathways identified are involved in the formation of the immune synapse and TCR activation as well as inflammation and the inflammatory response. An inflammatory transcriptomic profile was detected in both "naive" CD4 and CD8 T-cell subsets suggesting their possible involvement in the development or progression of the narcoleptic process.
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Affiliation(s)
- Leila Khajavi
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique (CNRS), L'Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paul-Sabatier de Toulouse (UPS), Toulouse, France
- Applied Mathematics and Informatics Unit of Toulouse (MIAT), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Toulouse, France
| | - Xuan-Hung Nguyen
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique (CNRS), L'Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paul-Sabatier de Toulouse (UPS), Toulouse, France
- Vinmec Institute of Applied Science and Regenerative Medicine, Vinmec Healthcare System and College of Health Sciences, VinUniveristy, Hanoi, Vietnam
| | - Clémence Queriault
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique (CNRS), L'Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paul-Sabatier de Toulouse (UPS), Toulouse, France
| | - Marianne Chabod
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique (CNRS), L'Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paul-Sabatier de Toulouse (UPS), Toulouse, France
| | - Lucie Barateau
- National Reference Center for Orphan Diseases, Narcolepsy, Idiopathic Hypersomnia and Kleine-Levin Syndrome, Department of Neurology, Gui-de-Chauliac Hospital, Centre Hospitalier Universitaire (CHU) de Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Montpellier, France
| | - Yves Dauvilliers
- National Reference Center for Orphan Diseases, Narcolepsy, Idiopathic Hypersomnia and Kleine-Levin Syndrome, Department of Neurology, Gui-de-Chauliac Hospital, Centre Hospitalier Universitaire (CHU) de Montpellier, Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Montpellier, France
| | - Matthias Zytnicki
- Applied Mathematics and Informatics Unit of Toulouse (MIAT), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), Toulouse, France
| | - Roland Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique (CNRS), L'Institut National de la Sante et de la Recherche Medicale (INSERM), Universite Paul-Sabatier de Toulouse (UPS), Toulouse, France
- Department of Immunology, Toulouse University Hospital, Toulouse, France
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Schäfer VS, Brossart P, Warrington KJ, Kurts C, Sendtner GW, Aden CA. The role of autoimmunity and autoinflammation in giant cell arteritis: A systematic literature review. Autoimmun Rev 2023; 22:103328. [PMID: 36990133 DOI: 10.1016/j.autrev.2023.103328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Giant cell arteritis is the most common form of large vessel vasculitis and preferentially involves large and medium-sized arteries in patients over the age of 50. Aggressive wall inflammation, neoangiogenesis and consecutive remodeling processes are the hallmark of the disease. Though etiology is unknown, cellular and humoral immunopathological processes are well understood. Matrix metalloproteinase-9 mediated tissue infiltration occurs through lysis of basal membranes in adventitial vessels. CD4+ cells attain residency in immunoprotected niches, differentiate into vasculitogenic effector cells and enforce further leukotaxis. Signaling pathways involve the NOTCH1-Jagged1 pathway opening vessel infiltration, CD28 mediated T-cell overstimulation, lost PD-1/PD-L1 co-inhibition and JAK/STAT signaling in interferon dependent responses. From a humoral perspective, IL-6 represents a classical cytokine and potential Th-cell differentiator whereas interferon-γ (IFN- γ) has been shown to induce chemokine ligands. Current therapies involve glucocorticoids, tocilizumab and methotrexate application. However, new agents, most notably JAK/STAT inhibitors, PD-1 agonists and MMP-9 blocking substances, are being evaluated in ongoing clinical trials.
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Matsumoto K, Suzuki K, Yoshida H, Magi M, Kaneko Y, Takeuchi T. Longitudinal monitoring of circulating immune cell phenotypes in large vessel vasculitis. Autoimmun Rev 2022; 21:103160. [PMID: 35926769 DOI: 10.1016/j.autrev.2022.103160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022]
Abstract
Giant cell arteritis (GCA) and Takayasu arteritis (TAK) are two types of primary large vessel vasculitis (LVV). LVV is an intractable, rare disease with a high relapse rate. Disease progression in asymptomatic patients is an important issue in the clinical management of LVV. Useful biomarkers associated with clinical phenotypes, disease activity, and prognosis may be present in peripheral blood. In this review, we focused on peripheral leukocyte counts, surface markers, functions, and gene expression in LVV patients. In particular, we explored longitudinal changes in circulating immune cell phenotypes during the active phase of the disease and during treatment. The numbers and phenotypes of leukocytes in the peripheral blood were different between LVV and healthy controls, GCA and TAK, LVV in active versus treatment phases, and LVV in treatment responders versus non-responders. Therefore, biomarkers obtained from peripheral blood immune cells may be useful for longitudinal monitoring of disease activity in LVV.
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Affiliation(s)
- Kotaro Matsumoto
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Katsuya Suzuki
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | - Mayu Magi
- Chugai Pharmaceutical Co. Ltd., Kanagawa, Japan
| | - Yuko Kaneko
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
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Kabeerdoss J, Danda D, Goel R, Mohan H, Danda S, Scofield RH. Genome-Wide DNA Methylation Profiling in CD8 T-Cells and Gamma Delta T-Cells of Asian Indian Patients With Takayasu Arteritis. Front Cell Dev Biol 2022; 10:843413. [PMID: 35813204 PMCID: PMC9259853 DOI: 10.3389/fcell.2022.843413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Takayasu’s Arteritis (TA) is a chronic inflammatory disease that affects aorta and its main branches at their origin. Genetic, pathological and functional studies have shown that CD8 and Gamma delta (γ/δ) T-lymphocytes are involved in inflammatory processes in affected regions of arteries causing vascular damage. The molecular function of these lymphocytes remains unclear and currently no epigenetic studies are available in TA. We primarily performed genome wide methylation analysis in CD8 T cells and γδ T cells of patients with TA and compared with healthy controls. Methods: We recruited 12 subjects in each group namely TA patient and healthy controls. Blood samples were collected after obtaining informed written consent. CD8 T cells and γδ T cells were separated from whole blood. DNA extracted from these cells and were subjected to bisulfite treatment. Finally, bisulfite treated DNA was loaded in Infinium Methylation EPIC array. Bioinformatics analysis was used to identify differential methylation regions which were then mapped to genes. Results: Interleukin (IL)-32 and Lymphotoxin-A were genes significantly hypomethylated in CD8 T-cells. Anti-inflammatory cytokine genes, IL-10, IL-1RN and IL-27 were hypomethylated in γδ T cells of TA patients as compared to healthy controls. Gene enrichment analysis using Gene Ontology (GO) database and Kyoto Encyclopaedia of Genes and Genomes (KEGG) identified that genes involved in T-cell receptor signalling pathways were hypomethylated in CD8 T-cells and hypermethylated in γδ T cells of TA patients. Conclusion: CD8 T-cells might play a major role in immunopathogenesis of inflammation in TA, whereas γδ T cells may play a regulatory role.
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Affiliation(s)
- Jayakanthan Kabeerdoss
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, India
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
- *Correspondence: Debashish Danda, ; Jayakanthan Kabeerdoss,
| | - Debashish Danda
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, India
- *Correspondence: Debashish Danda, ; Jayakanthan Kabeerdoss,
| | - Ruchika Goel
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, India
| | - Hindhumathi Mohan
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, India
| | - Sumita Danda
- Department of Medical Genetics, Christian Medical College, Vellore, India
| | - R. Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Department of Veterans Affairs, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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6
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Matsumoto K, Suzuki K, Yoshimoto K, Ishigaki S, Yoshida H, Magi M, Matsumoto Y, Kaneko Y, Takeuchi T. Interleukin-1 pathway in active large vessel vasculitis patients with a poor prognosis: a longitudinal transcriptome analysis. Clin Transl Immunology 2021; 10:e1307. [PMID: 34249359 PMCID: PMC8251870 DOI: 10.1002/cti2.1307] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/14/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
Objectives Large vessel vasculitis (LVV) is characterised by a high relapse rate. Because accurate assessment of the LVV disease status can be difficult, an accurate prognostic marker for initial risk stratification is required. We conducted a comprehensive longitudinal investigation of next‐generation RNA‐sequencing data for patients with LVV to explore useful biomarkers associated with clinical characteristics. Methods Key molecular pathways relevant to LVV pathogenesis were identified by examining the whole blood RNA from patients with LVV and healthy controls (HCs). The data were examined by pathway analysis and weighted gene correlation network analysis (WGCNA) to identify functional gene sets that were differentially expressed between LVV patients and HCs, and associated with clinical features. We then compared the expression of the selected genes during week 0, week 6, remission and relapse. Results The whole‐transcriptome gene expression data for 108 samples obtained from LVV patients (n = 27) and HCs (n = 12) were compared. The pathway analysis and WGCNA revealed that molecular pathway related to interleukin (IL)‐1 was significantly upregulated in LVV patients compared with HCs, which correlated with the positron emission tomography vascular activity score, a disease‐extent score based on the distribution of affected arteries. Further analysis revealed that the expression levels of genes in the IL‐1 signalling pathway remained high after conventional treatment and were associated with disease relapse. Conclusion Upregulation of the IL‐1 signalling pathway was a characteristic of LVV patients and was associated with the extent of disease and a poor prognosis.
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Affiliation(s)
- Kotaro Matsumoto
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
| | - Katsuya Suzuki
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
| | - Keiko Yoshimoto
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
| | - Sho Ishigaki
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
| | | | - Mayu Magi
- Chugai Pharmaceutical Co. Ltd Kanagawa Japan
| | | | - Yuko Kaneko
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
| | - Tsutomu Takeuchi
- Division of Rheumatology Department of Internal Medicine Keio University School of Medicine Tokyo Japan
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Reitsema RD, Boots AMH, van der Geest KSM, Sandovici M, Heeringa P, Brouwer E. CD8+ T Cells in GCA and GPA: Bystanders or Active Contributors? Front Immunol 2021; 12:654109. [PMID: 33815414 PMCID: PMC8015776 DOI: 10.3389/fimmu.2021.654109] [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: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 12/28/2022] Open
Abstract
Vasculitis refers to inflammation of blood vessels and can cause a variety of serious complications depending on which vessels are affected. Two different forms of vasculitis are Giant Cell Arteritis (GCA) and Granulomatosis with Polyangiitis (GPA). GCA is the most common form of vasculitis in adults affecting the large arteries and can lead to visual impairment and development of aneurysms. GPA affects small- and medium-sized blood vessels predominantly in the lungs and kidneys resulting in organ failure. Both diseases can potentially be fatal. Although the pathogenesis of GCA and GPA are incompletely understood, a prominent role for CD4+ T cells has been implicated in both diseases. More recently, the role of CD8+ T cells has gained renewed interest. CD8+ T cells are important players in the adaptive immune response against intracellular microorganisms. After a general introduction on the different forms of vasculitis and their association with infections and CD8+ T cells, we review the current knowledge on CD8+ T-cell involvement in the immunopathogenesis of GCA and GPA focusing on phenotypic and functional features of circulating and lesional CD8+ T cells. Furthermore, we discuss to which extent aging is associated with CD8+ T-cell phenotype and function in GCA and GPA.
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Affiliation(s)
- Rosanne D Reitsema
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Annemieke M H Boots
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Kornelis S M van der Geest
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Maria Sandovici
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Peter Heeringa
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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8
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Oh VKS, Li RW. Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data. Genes (Basel) 2021; 12:352. [PMID: 33673721 PMCID: PMC7997275 DOI: 10.3390/genes12030352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Affiliation(s)
- Vera-Khlara S. Oh
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
- Department of Computer Science and Statistics, College of Natural Sciences, Jeju National University, Jeju City 63243, Korea
| | - Robert W. Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
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9
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Robinette ML, Rao DA, Monach PA. The Immunopathology of Giant Cell Arteritis Across Disease Spectra. Front Immunol 2021; 12:623716. [PMID: 33717128 PMCID: PMC7946968 DOI: 10.3389/fimmu.2021.623716] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
Giant cell arteritis (GCA) is a granulomatous systemic vasculitis of large- and medium-sized arteries that affects the elderly. In recent years, advances in diagnostic imaging have revealed a greater degree of large vessel involvement than previously recognized, distinguishing classical cranial- from large vessel (LV)- GCA. GCA often co-occurs with the poorly understood inflammatory arthritis/bursitis condition polymyalgia rheumatica (PMR) and has overlapping features with other non-infectious granulomatous vasculitides that affect the aorta, namely Takayasu Arteritis (TAK) and the more recently described clinically isolated aortitis (CIA). Here, we review the literature focused on the immunopathology of GCA on the background of the three settings in which comparisons are informative: LV and cranial variants of GCA; PMR and GCA; the three granulomatous vasculitides (GCA, TAK, and CIA). We discuss overlapping and unique features between these conditions across clinical presentation, epidemiology, imaging, and conventional histology. We propose a model of GCA where abnormally activated circulating cells, especially monocytes and CD4+ T cells, enter arteries after an unknown stimulus and cooperate to destroy it and review the evidence for how this mechanistically occurs in active disease and improves with treatment.
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Affiliation(s)
- Michelle L. Robinette
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Paul A. Monach
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
- Rheumatology Section, VA Boston Healthcare System, Boston, MA, United States
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10
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Akiyama M, Ohtsuki S, Berry GJ, Liang DH, Goronzy JJ, Weyand CM. Innate and Adaptive Immunity in Giant Cell Arteritis. Front Immunol 2021; 11:621098. [PMID: 33717054 PMCID: PMC7947610 DOI: 10.3389/fimmu.2020.621098] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022] Open
Abstract
Autoimmune diseases can afflict every organ system, including blood vessels that are critically important for host survival. The most frequent autoimmune vasculitis is giant cell arteritis (GCA), which causes aggressive wall inflammation in medium and large arteries and results in vaso-occlusive wall remodeling. GCA shares with other autoimmune diseases that it occurs in genetically predisposed individuals, that females are at higher risk, and that environmental triggers are suspected to beget the loss of immunological tolerance. GCA has features that distinguish it from other autoimmune diseases and predict the need for tailored diagnostic and therapeutic approaches. At the core of GCA pathology are CD4+ T cells that gain access to the protected tissue niche of the vessel wall, differentiate into cytokine producers, attain tissue residency, and enforce macrophages differentiation into tissue-destructive effector cells. Several signaling pathways have been implicated in initiating and sustaining pathogenic CD4+ T cell function, including the NOTCH1-Jagged1 pathway, the CD28 co-stimulatory pathway, the PD-1/PD-L1 co-inhibitory pathway, and the JAK/STAT signaling pathway. Inadequacy of mechanisms that normally dampen immune responses, such as defective expression of the PD-L1 ligand and malfunction of immunosuppressive CD8+ T regulatory cells are a common theme in GCA immunopathology. Recent studies are providing a string of novel mechanisms that will permit more precise pathogenic modeling and therapeutic targeting in GCA and will fundamentally inform how abnormal immune responses in blood vessels lead to disease.
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Affiliation(s)
- Mitsuhiro Akiyama
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Shozo Ohtsuki
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - David H Liang
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Jörg J Goronzy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Cornelia M Weyand
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Schwartz DM, Burma AM, Kitakule MM, Luo Y, Mehta NN. T Cells in Autoimmunity-Associated Cardiovascular Diseases. Front Immunol 2020; 11:588776. [PMID: 33117403 PMCID: PMC7576936 DOI: 10.3389/fimmu.2020.588776] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/21/2020] [Indexed: 12/24/2022] Open
Abstract
T cells are indisputably critical mediators of atherosclerotic cardiovascular disease (CVD), where they secrete pro-inflammatory cytokines that promote vascular pathology. Equally well-established is the fact that autoimmune diseases, which are mediated by autoreactive T cells, substantially increase the risk of developing CVD. Indeed, as immunomodulatory treatments have become more effective at treating end-organ pathology, CVD has become a leading cause of death in patients with autoimmune diseases. Despite this, investigators have only recently begun to probe the mechanisms by which autoreactive T cells promote CVD in the context of autoimmune diseases. T cells are best-studied in the pathogenesis of systemic vasculitides, where they react to self-antigen in the vessel wall. However, newer studies indicate that T cells also contribute to the increased CVD risk associated with lupus and rheumatoid arthritis. Given the central role of T-cell-derived cytokines in the pathogenesis of psoriasis, the role of these factors in psoriatic CVD is also under investigation. In the future, T cells are likely to represent major targets for the prevention and treatment of CVD in patients with autoimmune diseases.
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Affiliation(s)
- Daniella Muallem Schwartz
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Aarohan M. Burma
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Moses M. Kitakule
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yiming Luo
- Rheumatology Fellowship Program, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Nehal N. Mehta
- Section of Inflammation and Cardiometabolic Diseases, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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Watanabe R, Berry GJ, Liang DH, Goronzy JJ, Weyand CM. Cellular Signaling Pathways in Medium and Large Vessel Vasculitis. Front Immunol 2020; 11:587089. [PMID: 33072134 PMCID: PMC7544845 DOI: 10.3389/fimmu.2020.587089] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Autoimmune and autoinflammatory diseases of the medium and large arteries, including the aorta, cause life-threatening complications due to vessel wall destruction but also by wall remodeling, such as the formation of wall-penetrating microvessels and lumen-stenosing neointima. The two most frequent large vessel vasculitides, giant cell arteritis (GCA) and Takayasu arteritis (TAK), are HLA-associated diseases, strongly suggestive for a critical role of T cells and antigen recognition in disease pathogenesis. Recent studies have revealed a growing spectrum of effector functions through which T cells participate in the immunopathology of GCA and TAK; causing the disease-specific patterning of pathology and clinical outcome. Core pathogenic features of disease-relevant T cells rely on the interaction with endothelial cells, dendritic cells and macrophages and lead to vessel wall invasion, formation of tissue-damaging granulomatous infiltrates and induction of the name-giving multinucleated giant cells. Besides antigen, pathogenic T cells encounter danger signals in their immediate microenvironment that they translate into disease-relevant effector functions. Decisive signaling pathways, such as the AKT pathway, the NOTCH pathway, and the JAK/STAT pathway modify antigen-induced T cell activation and emerge as promising therapeutic targets to halt disease progression and, eventually, reset the immune system to reestablish the immune privilege of the arterial wall.
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Affiliation(s)
- Ryu Watanabe
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - David H Liang
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Jörg J Goronzy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Cornelia M Weyand
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
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Strunk D, Schmidt-Pogoda A, Beuker C, Milles LS, Korsukewitz C, Meuth SG, Minnerup J. Biomarkers in Vasculitides of the Nervous System. Front Neurol 2019; 10:591. [PMID: 31244756 PMCID: PMC6562258 DOI: 10.3389/fneur.2019.00591] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/20/2019] [Indexed: 12/13/2022] Open
Abstract
Besides being affected by the rare and severe primary angiitis of the central nervous system (PACNS) the nervous system is also affected by primary systemic vasculitides (PSV). In contrast to PACNS, PSV affect not only the central but also the peripheral nervous system, resulting in a large array of potential symptoms. Given the high burden of disease, difficulties in distinguishing between differential diagnoses, and incomplete pathophysiological insights, there is an urgent need for additional precise diagnostic tools to enable an earlier diagnosis and initiation of effective treatments. Methods available to date, such as inflammatory markers, antibodies, cerebrospinal fluid (CSF) analysis, imaging, and biopsy, turn out to be insufficient to meet all current challenges. We highlight the use of biomarkers as an approach to extend current knowledge and, ultimately, improve patient management. Biomarkers are considered to be useful for disease diagnosis and monitoring, for predicting response to treatment, and for prognosis in clinical practice, as well as for establishing outcome parameters in clinical trials. In this article, we review the recent literature on biomarkers which have been applied in the context of different types of nervous system vasculitides including PACNS, giant-cell arteritis, Takayasu's arteritis, polyarteritis nodosa, ANCA (anti-neutrophil cytoplasm antibody)-associated vasculitides, cryoglobulinemic vasculitis, IgA vasculitis, and Behçet's disease. Overall, the majority of biomarkers is not specific for vasculitides of the nervous system.
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Affiliation(s)
- Daniel Strunk
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Antje Schmidt-Pogoda
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Carolin Beuker
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Lennart S Milles
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Catharina Korsukewitz
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Sven G Meuth
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
| | - Jens Minnerup
- Department of Neurology, Institute for Translational Neurology, University of Münster, Münster, Germany
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