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Gumkowska-Sroka O, Kotyla K, Kotyla P. Immunogenetics of Systemic Sclerosis. Genes (Basel) 2024; 15:586. [PMID: 38790215 PMCID: PMC11121022 DOI: 10.3390/genes15050586] [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: 04/07/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Systemic sclerosis (SSc) is a rare autoimmune connective tissue disorder characterized by massive fibrosis, vascular damage, and immune imbalance. Advances in rheumatology and immunology over the past two decades have led to a redefinition of systemic sclerosis, shifting from its initial perception as primarily a "hyperfibrotic" state towards a recognition of systemic sclerosis as an immune-mediated disease. Consequently, the search for genetic markers has transitioned from focusing on fibrotic mechanisms to exploring immune regulatory pathways. Immunogenetics, an emerging field at the intersection of immunology, molecular biology, and genetics has provided valuable insights into inherited factors that influence immunity. Data from genetic studies conducted thus far indicate that alterations in genetic messages can significantly impact disease risk and progression. While certain genetic variations may confer protective effects, others may exacerbate disease susceptibility. This paper presents a comprehensive review of the most relevant genetic changes that influence both the risk and course of systemic sclerosis. Special emphasis is placed on factors regulating the immune response, recognizing their pivotal role in the pathogenesis of the disease.
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Affiliation(s)
| | | | - Przemysław Kotyla
- Department of Rheumatology and Clinical Immunology, Medical University of Silesia, Voivodeship Hospital No. 5, 41-200 Sosnowiec, Poland; (O.G.-S.); (K.K.)
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Hum RM, Sharma SD, Stadler M, Viatte S, Ho P, Nair N, Shi C, Yap CF, Soomro M, Plant D, Humphreys JH, MacGregor A, Yates M, Verstappen S, Barton A, Bowes J. Using Polygenic Risk Scores to Aid Diagnosis of Patients With Early Inflammatory Arthritis: Results From the Norfolk Arthritis Register. Arthritis Rheumatol 2024; 76:696-703. [PMID: 38010198 DOI: 10.1002/art.42760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 09/29/2023] [Accepted: 10/10/2023] [Indexed: 11/29/2023]
Abstract
OBJECTIVE There is growing evidence that genetic data are of benefit in the rheumatology outpatient setting by aiding early diagnosis. A genetic probability tool (G-PROB) has been developed to aid diagnosis has not yet been tested in a real-world setting. Our aim was to assess whether G-PROB could aid diagnosis in the rheumatology outpatient setting using data from the Norfolk Arthritis Register (NOAR), a prospective observational cohort of patients presenting with early inflammatory arthritis. METHODS Genotypes and clinician diagnoses were obtained from patients from NOAR. Six G-probabilities (0%-100%) were created for each patient based on known disease-associated odds ratios of published genetic risk variants, each corresponding to one disease of rheumatoid arthritis, systemic lupus erythematosus, psoriatic arthritis, spondyloarthropathy, gout, or "other diseases." Performance of the G-probabilities compared with clinician diagnosis was assessed. RESULTS We tested G-PROB on 1,047 patients. Calibration of G-probabilities with clinician diagnosis was high, with regression coefficients of 1.047, where 1.00 is ideal. G-probabilities discriminated clinician diagnosis with pooled areas under the curve (95% confidence interval) of 0.85 (0.84-0.86). G-probabilities <5% corresponded to a negative predictive value of 96.0%, for which it was possible to suggest >2 unlikely diseases for 94% of patients and >3 for 53.7% of patients. G-probabilities >50% corresponded to a positive predictive value of 70.4%. In 55.7% of patients, the disease with the highest G-probability corresponded to clinician diagnosis. CONCLUSION G-PROB converts complex genetic information into meaningful and interpretable conditional probabilities, which may be especially helpful at eliminating unlikely diagnoses in the rheumatology outpatient setting.
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Affiliation(s)
- Ryan M Hum
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Seema D Sharma
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Michael Stadler
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Sebastien Viatte
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Pauline Ho
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Nisha Nair
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Chenfu Shi
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Chuan Fu Yap
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Mehreen Soomro
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Darren Plant
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Jenny H Humphreys
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | | | - Max Yates
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Suzanne Verstappen
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - Anne Barton
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Musculoskeletal Research, NIHR Manchester Biomedical Research Centre, Lydia Becker Institute of Immunology and Inflammation, The University of Manchester, Manchester, UK
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Li C, Xiao M, Geng S, Wang Y, Zeng L, Lai P, Gong Y, Chen X. Comprehensive analysis of human monocyte subsets using full-spectrum flow cytometry and hierarchical marker clustering. Front Immunol 2024; 15:1405249. [PMID: 38742110 PMCID: PMC11089106 DOI: 10.3389/fimmu.2024.1405249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction Exploring monocytes' roles within the tumor microenvironment is crucial for crafting targeted cancer treatments. Methods This study unveils a novel methodology utilizing four 20-color flow cytometry panels for comprehensive peripheral immune system phenotyping, specifically targeting classical, intermediate, and non-classical monocyte subsets. Results By applying advanced dimensionality reduction techniques like t-distributed stochastic neighbor embedding (tSNE) and FlowSom analysis, we performed an extensive profiling of monocytes, assessing 50 unique cell surface markers related to a wide range of immunological functions, including activation, differentiation, and immune checkpoint regulation. Discussion This in-depth approach significantly refines the identification of monocyte subsets, directly supporting the development of personalized immunotherapies and enhancing diagnostic precision. Our pioneering panel for monocyte phenotyping marks a substantial leap in understanding monocyte biology, with profound implications for the accuracy of disease diagnostics and the success of checkpoint-inhibitor therapies. Key findings include revealing distinct marker expression patterns linked to tumor progression and providing new avenues for targeted therapeutic interventions.
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Affiliation(s)
- Chao Li
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Maozhi Xiao
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Suxia Geng
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yulian Wang
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Lingji Zeng
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Peilong Lai
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ying Gong
- Department of Laboratory Medicine, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaomei Chen
- Department of Hematology, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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Villanueva-Martin G, Acosta-Herrera M, Carmona EG, Kerick M, Ortego-Centeno N, Callejas-Rubio JL, Mages N, Klages S, Börno S, Timmermann B, Bossini-Castillo L, Martin J. Non-classical circulating monocytes expressing high levels of microsomal prostaglandin E2 synthase-1 tag an aberrant IFN-response in systemic sclerosis. J Autoimmun 2023; 140:103097. [PMID: 37633117 DOI: 10.1016/j.jaut.2023.103097] [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: 05/18/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/28/2023]
Abstract
Systemic sclerosis (SSc) is a complex disease that affects the connective tissue, causing fibrosis. SSc patients show altered immune cell composition and activation in the peripheral blood (PB). PB monocytes (Mos) are recruited into tissues where they differentiate into macrophages, which are directly involved in fibrosis. To understand the role of CD14+ PB Mos in SSc, a single-cell transcriptome analysis (scRNA-seq) was conducted on 8 SSc patients and 8 controls. Using unsupervised clustering methods, CD14+ cells were assigned to 11 clusters, which added granularity to the known monocyte subsets: classical (cMos), intermediate (iMos) and non-classical Mos (ncMos) or type 2 dendritic cells. NcMos were significantly overrepresented in SSc patients and showed an active IFN-signature and increased expression levels of PTGES, in addition to monocyte motility and adhesion markers. We identified a SSc-related cluster of IRF7+ STAT1+ iMos with an aberrant IFN-response. Finally, a depletion of M2 polarised cMos in SSc was observed. Our results highlighted the potential of PB Mos as biomarkers for SSc and provided new possibilities for putative drug targets for modulating the innate immune response in SSc.
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Affiliation(s)
- Gonzalo Villanueva-Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Elio G Carmona
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain; Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain; Department of Medicine, University of Granada, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Jose Luis Callejas-Rubio
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Norbert Mages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Lara Bossini-Castillo
- Department of Genetics and Biotechnology Institute, Biomedical Research Centre (CIBM), University of Granada, 18100, Granada, Spain; Advanced Therapies and Biomedical Technologies (TEC-14), Biosanitary Research Institute Ibs. GRANADA, 18016, Granada, Spain.
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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Davidson C, Wordsworth BP, Cohen CJ, Knight JC, Vecellio M. Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis. Front Genet 2023; 14:1129207. [PMID: 36760998 PMCID: PMC9905691 DOI: 10.3389/fgene.2023.1129207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Ankylosing Spondylitis (AS) is a chronic inflammatory arthritis of the spine exhibiting a strong genetic background. The mechanistic and functional understanding of the AS-associated genomic loci, identified with Genome Wide Association Studies (GWAS), remains challenging. Chromosome conformation capture (3C) and derivatives are recent techniques which are of great help in elucidating the spatial genome organization and of enormous support in uncover a mechanistic explanation for disease-associated genetic variants. The perturbation of three-dimensional (3D) genome hierarchy may lead to a plethora of human diseases, including rheumatological disorders. Here we illustrate the latest approaches and related findings on the field of genome organization, highlighting how the instability of 3D genome conformation may be among the causes of rheumatological disease phenotypes. We suggest a new perspective on the inclusive potential of a 3C approach to inform GWAS results in rheumatic diseases. 3D genome organization may ultimately lead to a more precise and comprehensive functional interpretation of AS association, which is the starting point for emerging and more specific therapies.
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Affiliation(s)
- Connor Davidson
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Carla J. Cohen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C. Knight
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- Centro Ricerche Fondazione Italiana Ricerca Sull’Artrite (FIRA), Fondazione Pisana x la Scienza ONLUS, San Giuliano Terme, Italy
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