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Kumar S, Orcales F, Shih BB, Fang X, Yin C, Yates A, Dimitrion P, Neuhaus I, Johnson C, Adrianto I, Wiala A, Hamzavi I, Zhou L, Naik H, Posch C, Mi QS, Liao W. Cellular indexing of transcriptomes and epitopes (CITE-Seq) in hidradenitis suppurativa identifies dysregulated cell types in peripheral blood and facilitates diagnosis via machine learning. RESEARCH SQUARE 2024:rs.3.rs-4791069. [PMID: 39315268 PMCID: PMC11419166 DOI: 10.21203/rs.3.rs-4791069/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition characterized by painful nodules, abscesses, and scarring, predominantly affecting intertriginous regions and it is often underdiagnosed. This study aimed to utilize single cell RNA and cell-surface protein sequencing (CITE-Seq) to delineate the immune composition of circulating cells in Hidradenitis suppurativa (HS) peripheral blood compared to healthy controls. CITE-Seq was used to analyze the gene and protein expression profiles of peripheral blood mononuclear cells (PBMCs) from 9 HS and 29 healthy controls. The study identified significant differences cell composition between HS patients and healthy controls, including increased proportions of CD14+ and CD16+ monocytes, cDC2, plasmablasts, and proliferating CD4+ T cells in HS patients. Differential expression analysis revealed upregulation of inflammatory markers such as TNF, IL1B, and NF-κB in monocytes, as well as chemokines and cell adhesion molecules involved in immune cell recruitment and tissue infiltration. Pathway enrichment analysis highlighted the involvement of IL-17, IL-26 and TNF signaling pathways in HS pathogenesis. Machine learning identified key markers for diagnostics and therapeutic development. The findings also support the potential for machine learning models to aid in the diagnosis of HS based on immune cell markers. These insights may inform future therapeutic strategies targeting specific immune pathways in HS.
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Affiliation(s)
- Sugandh Kumar
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Faye Orcales
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Bobby B Shih
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Xiaohui Fang
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Congcong Yin
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
| | - Ashley Yates
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Peter Dimitrion
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- School of Medicine, Wayne State University, Detroit, MI, USA
| | - Isaac Neuhaus
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Chandler Johnson
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Indra Adrianto
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- Center for Bioinformatics, Department of Public Health Sciences, Henry Ford Health, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Antonia Wiala
- Clinic Landstrasse, Department of Dermatology, 1030 Vienna, Austria
| | - Iltefat Hamzavi
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
| | - Li Zhou
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- School of Medicine, Wayne State University, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Haley Naik
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
| | - Christian Posch
- Clinic Landstrasse, Department of Dermatology, 1030 Vienna, Austria
- School of Medicine, Sigmund Freud University, 1020 Vienna, Austria
| | - Qing-Sheng Mi
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI, USA
- School of Medicine, Wayne State University, Detroit, MI, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, USA
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA
- Henry Ford Health + Michigan State University Health Sciences, Detroit, MI, USA
| | - Wilson Liao
- Department of Dermatology, University of California at San Francisco, San Francisco, CA, USA
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Nakajima S, Tsuchiya H, Fujio K. Unraveling immune cell heterogeneity in autoimmune arthritis: insights from single-cell RNA sequencing. Immunol Med 2024:1-13. [PMID: 39120105 DOI: 10.1080/25785826.2024.2388343] [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: 06/11/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of immune-mediated arthritis, which comprises rheumatoid arthritis and spondyloarthritis. This review outlines the key findings and advancements in scRNA-seq studies focused on the pathogenesis of autoimmune arthritis and its clinical application. In rheumatoid arthritis, scRNA-seq has elucidated the heterogeneity among synovial fibroblasts and immune cell subsets in inflammatory sites, offering insights into disease mechanisms and the differences in treatment responses. Various studies have identified distinct synovial fibroblast subpopulations, such as THY1+ inflammatory and THY1- destructive fibroblasts. Furthermore, scRNA-seq has revealed diverse T cell profiles in the synovium, including peripheral helper T cells and clonally expanded CD8+ T cells, shedding light on potential therapeutic targets and predictive markers of treatment response. Similarly, in spondyloarthritis, particularly psoriatic arthritis and ankylosing spondylitis, scRNA-seq studies have identified distinct cellular profiles associated with disease pathology. Challenges such as cost and sample size limitations persist, but collaborative efforts and utilization of public databases hold promise for overcoming these obstacles. Overall, scRNA-seq emerges as a powerful tool for dissecting cellular heterogeneity and driving precision medicine in immune-mediated arthritis.
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Affiliation(s)
- Sotaro Nakajima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruka Tsuchiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Chiñas M, Fernandez-Salinas D, Aguiar VRC, Nieto-Caballero VE, Lefton M, Nigrovic PA, Ermann J, Gutierrez-Arcelus M. Functional genomics implicates natural killer cells in the pathogenesis of ankylosing spondylitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.21.23295912. [PMID: 37808698 PMCID: PMC10557806 DOI: 10.1101/2023.09.21.23295912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Objective Multiple lines of evidence indicate that ankylosing spondylitis (AS) is a lymphocyte-driven disease. However, which lymphocyte populations are critical in AS pathogenesis is not known. In this study, we aimed to identify the key cell types mediating the genetic risk in AS using an unbiased functional genomics approach. Methods We integrated genome-wide association study (GWAS) data with epigenomic and transcriptomic datasets of human immune cells. To quantify enrichment of cell type-specific open chromatin or gene expression in AS risk loci, we used three published methods that have successfully identified relevant cell types in other diseases. We performed co-localization analyses between GWAS risk loci and genetic variants associated with gene expression (eQTL) to find putative target genes. Results Natural killer (NK) cell-specific open chromatin regions are significantly enriched in heritability for AS, compared to other immune cell types such as T cells, B cells, and monocytes. This finding was consistent between two AS GWAS. Using RNA-seq data, we validated that genes in AS risk loci are enriched in NK cell-specific gene expression. Using the human Space-Time Gut Cell Atlas, we also found significant upregulation of AS-associated genes predominantly in NK cells. Co-localization analysis revealed four AS risk loci affecting regulation of candidate target genes in NK cells: two known loci, ERAP1 and TNFRSF1A, and two under-studied loci, ENTR1 (aka SDCCAG3) and B3GNT2. Conclusion Our findings suggest that NK cells may play a crucial role in AS development and highlight four putative target genes for functional follow-up in NK cells.
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Affiliation(s)
- Marcos Chiñas
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniela Fernandez-Salinas
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Licenciatura en Ciencias Genomicas, Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
| | - Vitor R. C. Aguiar
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Victor E. Nieto-Caballero
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Licenciatura en Ciencias Genomicas, Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México (UNAM), Morelos 62210, Mexico
| | - Micah Lefton
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Peter A. Nigrovic
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Joerg Ermann
- Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Maria Gutierrez-Arcelus
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Ren Z, Li C, Wang J, Sui J, Ma Y. Single-cell transcriptome revealed dysregulated RNA-binding protein expression patterns and functions in human ankylosing spondylitis. Front Med (Lausanne) 2024; 11:1369341. [PMID: 38770048 PMCID: PMC11104332 DOI: 10.3389/fmed.2024.1369341] [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: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 05/22/2024] Open
Abstract
Objective To explore the expression characteristics and regulatory patterns of RBPs in different immune cell types of AS, and to clarify the potential key role of RBPs in the occurrence and development of AS disease. Methods PBMC sample data from scRNA-seq (HC*29, AS*10) and bulk RNA-seq (NC*3, AS*5) were selected for correlation analysis. Results (1) Compared with the HC group, the numbers of B, DC (dendritic cells), CD14+ Mono and CD8+ T cells were increased in AS group, while the numbers of platelet (platelets), CD8+ NKT, CD16+ Mono (non-classical monocytes), Native CD4+ T and NK were decreased. (2) Through the analysis of RBP genes in B cells, some RBPs were found to play an important role in B cell differentiation and function, such as DDX3X, SFPQ, SRRM1, UPF2. (3) It may be related to B-cell receptor, IgA immunity, NOD-like receptor and other signaling pathways; Through the analysis of RBP genes in CD8+ T cells, some RBPs that play an important role in the immune regulation of CD8+ T were found, such as EIF2S3, EIF4B, HSPA5, MSL3, PABPC1 and SRSF7; It may be related to T cell receptor, TNF, IL17 and other signaling pathways. (4) Based on bulk RNA-seq, it was found that compared with HC and AS patients, differentially expressed variable splicing genes (RASGs) may play an important role in the occurrence and development of AS by participating in transcriptional regulation, protein phosphorylation and ubiquitination, DNA replication, angiogenesis, intracellular signal transduction and other related pathways. Conclusion RBPs has specific expression characteristics in different immune cell types of AS patients, and has important regulatory functions. Its abnormal expression and regulation may be closely related to the occurrence and development of AS.
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Affiliation(s)
- Zheng Ren
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Chenyang Li
- Microsurgery Unit, The Third People’s Hospital of Xinjiang, Ürümqi, Xinjiang, China
| | - Jing Wang
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Jiangtao Sui
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Yuan Ma
- Xinjiang Institute of Spinal Surgery, Sixth Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
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Dhall S, Vaish A, Vaishya R. Machine learning and deep learning for the diagnosis and treatment of ankylosing spondylitis- a scoping review. J Clin Orthop Trauma 2024; 52:102421. [PMID: 38708092 PMCID: PMC11063901 DOI: 10.1016/j.jcot.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/10/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
Background and objectives Machine Learning (ML) and Deep Learning (DL) are novel technologies that can facilitate early diagnosis of Ankylosing Spondylitis (AS) and predict better patient-specific treatments. We aim to provide the current update on their use at different stages of AS diagnosis and treatment, describe different types of techniques used, dataset descriptions, contributions and limitations of existing work and ed to identify gaps in current knowledge for future works. Methods We curated the data of this review from the PubMed database. We searched the full-text articles related to the use of ML/DL in the diagnosis and treatment of AS, for the period 2013-2023. Each article was manually scrutinized to be included or excluded for this review as per its relevance. Results This review revealed that ML/DL technology is useful to assist and promote early diagnosis through AS patient characteristic profile creation, and identification of new AS-related biomarkers. They can help in forecasting the progression of AS and predict treatment responses to aid patient-specific treatment planning. However, there was a lack of sufficient-sized datasets sourced from multi-centres containing different types of diagnostic parameters. Also, there is less research on ML/DL-based AS treatment as compared to ML/DL-based AS diagnosis. Conclusion ML/DL can facilitate an early diagnosis and patient-tailored treatment for effective handling of AS. Benefits are especially higher in places with a lack of diagnostic resources and human experts. The use of ML/DL-trained models for AS diagnosis and treatment can provide the necessary support to the otherwise overwhelming healthcare systems in a cost-effective and timely way.
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Affiliation(s)
- Sakshi Dhall
- Department of Mathematics, Jamia Millia Islamia, Delhi, 110025, India
| | - Abhishek Vaish
- Department of Orthopaedics and Joint Replacement Surgery, Indraprastha Apollo Hospitals, Sarita Vihar, New Delhi, 110076, India
| | - Raju Vaishya
- Department of Orthopaedics and Joint Replacement Surgery, Indraprastha Apollo Hospitals, Sarita Vihar, New Delhi, 110076, India
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Furst A, Gill T. Exploring the role of gut microbes in spondyloarthritis: Implications for pathogenesis and therapeutic strategies. Best Pract Res Clin Rheumatol 2024; 38:101961. [PMID: 38851970 DOI: 10.1016/j.berh.2024.101961] [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: 03/13/2024] [Revised: 05/11/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
The gut microbiota plays a pivotal role in regulating host immunity, and dysregulation of this interaction is implicated in autoimmune and inflammatory diseases, including spondyloarthritis (SpA). This review explores microbial dysbiosis and altered metabolic function observed in various forms of SpA, such as ankylosing spondylitis (AS), psoriatic arthritis (PsA), acute anterior uveitis (AAU), and SpA-associated gut inflammation. Studies on animal models and clinical samples highlight the association between gut microbial dysbiosis, metabolic perturbations and immune dysregulation in SpA pathogenesis. These studies have received impetus through next-generation sequencing methods, which have enabled the characterization of gut microbial composition and function, and host gene expression. Microbial/metabolomic studies have revealed potential biomarkers and therapeutic targets, such as short-chain fatty acids, and tryptophan metabolites, offering insights into disease mechanisms and treatment approaches. Further studies on microbial function and its modulation of the immune response have uncovered molecular mechanisms underlying various SpA. Understanding the complex interplay between microbial community structure and function holds promise for improved diagnosis and management of SpA and other autoimmune disorders.
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Affiliation(s)
- Alec Furst
- School of Medicine, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Tejpal Gill
- Division of Arthritis and Rheumatic Diseases, Oregon Health and Science University, Portland, OR, 97239, USA.
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Ermann J, Lefton M, Wei K, Gutierrez-Arcelus M. Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell Profiling. Curr Rheumatol Rep 2024; 26:144-154. [PMID: 38227172 DOI: 10.1007/s11926-023-01132-7] [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] [Accepted: 12/28/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE OF REVIEW Single-cell profiling, either in suspension or within the tissue context, is a rapidly evolving field. The purpose of this review is to outline recent advancements and emerging trends with a specific focus on studies in spondyloarthritis. RECENT FINDINGS The introduction of sequencing-based approaches for the quantification of RNA, protein, or epigenetic modifications at single-cell resolution has provided a major boost to discovery-driven research. Fluorescent flow cytometry, mass cytometry, and image-based cytometry continue to evolve. Spatial transcriptomics and imaging mass cytometry have extended high-dimensional analysis to cells in tissues. Applications in spondyloarthritis include the indexing and functional characterization of cells, discovery of disease-associated cell states, and identification of signatures associated with therapeutic responses. Single-cell TCR-seq has provided evidence for clonal expansion of CD8+ T cells in spondyloarthritis. The use of single-cell profiling approaches in spondyloarthritis research is still in its early stages. Challenges include high cost and limited availability of diseased tissue samples. To harness the full potential of the rapidly expanding technical capabilities, large-scale collaborative efforts are imperative.
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Affiliation(s)
- Joerg Ermann
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Micah Lefton
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Maria Gutierrez-Arcelus
- Harvard Medical School, Boston, MA, USA
- Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Martini V, Silvestri Y, Ciurea A, Möller B, Danelon G, Flamigni F, Jarrossay D, Kwee I, Foglierini M, Rinaldi A, Cecchinato V, Uguccioni M. Patients with ankylosing spondylitis present a distinct CD8 T cell subset with osteogenic and cytotoxic potential. RMD Open 2024; 10:e003926. [PMID: 38395454 PMCID: PMC10895246 DOI: 10.1136/rmdopen-2023-003926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVES Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease affecting mainly the axial skeleton. Peripheral involvement (arthritis, enthesitis and dactylitis) and extra-musculoskeletal manifestations, including uveitis, psoriasis and bowel inflammation, occur in a relevant proportion of patients. AS is responsible for chronic and severe back pain caused by local inflammation that can lead to osteoproliferation and ultimately spinal fusion. The association of AS with the human leucocyte antigen-B27 gene, together with elevated levels of chemokines, CCL17 and CCL22, in the sera of patients with AS, led us to study the role of CCR4+ T cells in the disease pathogenesis. METHODS CD8+CCR4+ T cells isolated from the blood of patients with AS (n=76) or healthy donors were analysed by multiparameter flow cytometry, and gene expression was evaluated by RNA sequencing. Patients with AS were stratified according to the therapeutic regimen and current disease score. RESULTS CD8+CCR4+ T cells display a distinct effector phenotype and upregulate the inflammatory chemokine receptors CCR1, CCR5, CX3CR1 and L-selectin CD62L, indicating an altered migration ability. CD8+CCR4+ T cells expressing CX3CR1 present an enhanced cytotoxic profile, expressing both perforin and granzyme B. RNA-sequencing pathway analysis revealed that CD8+CCR4+ T cells from patients with active disease significantly upregulate genes promoting osteogenesis, a core process in AS pathogenesis. CONCLUSIONS Our results shed light on a new molecular mechanism by which T cells may selectively migrate to inflammatory loci, promote new bone formation and contribute to the pathological ossification process observed in AS.
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Affiliation(s)
- Veronica Martini
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Ylenia Silvestri
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Adrian Ciurea
- Department of Rheumatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Burkhard Möller
- Department of Rheumatology and Immunology, Inselspital-University Hospital Bern, University of Bern, Bern, Switzerland
| | - Gabriela Danelon
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Flavio Flamigni
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - David Jarrossay
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
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Li JX, Wu X, Lee YH, Xu H. West meets East in genetics of ankylosing spondylitis. Int J Rheum Dis 2023; 26:2122-2126. [PMID: 37910030 DOI: 10.1111/1756-185x.14846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 11/03/2023]
Affiliation(s)
- Jing-Xing Li
- Department of General Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
- Graduate Institute of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Xin Wu
- Department of Rheumatology and Immunology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yung-Heng Lee
- Department of Senior Services Industry Management, Minghsin University of Science and Technology, Hsinchu, Taiwan
- Department of Recreation and Sport Management, Shu-Te University, Kaohsiung, Taiwan
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
- Department of Orthopedics, Cishan Hospital, Ministry of Health and Welfare, Kaohsiung, Taiwan
| | - Huji Xu
- Department of Rheumatology and Immunology, Changzheng Hospital, Naval Medical University, Shanghai, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
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Hwang M, Assassi S, Zheng J, Castillo J, Chavez R, Vanarsa K, Mohan C, Reveille J. Quantitative proteomic screening uncovers candidate diagnostic and monitoring serum biomarkers of ankylosing spondylitis. Arthritis Res Ther 2023; 25:57. [PMID: 37041650 PMCID: PMC10088143 DOI: 10.1186/s13075-023-03044-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/30/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND We sought to discover serum biomarkers of ankylosing spondylitis (AS) for diagnosis and monitoring disease activity. METHODS We studied biologic-treatment-naïve AS and healthy control (HC) patients' sera. Eighty samples matched by age, gender, and race (1:1:1 ratio) for AS patients with active disease, inactive disease, and HC were analyzed with SOMAscan™, an aptamer-based discovery platform. T-tests tests were performed for high/low-disease activity AS patients versus HCs (diagnosis) and high versus low disease activity (Monitoring) in a 2:1 and 1:1 ratio, respectively, to identify differentially expressed proteins (DEPs). We used the Cytoscape Molecular Complex Detection (MCODE) plugin to find clusters in protein-protein interaction networks and Ingenuity Pathway Analysis (IPA) for upstream regulators. Lasso regression analysis was performed for diagnosis. RESULTS Of the 1317 proteins detected in our diagnosis and monitoring analyses, 367 and 167 (317 and 59, FDR-corrected q < .05) DEPs, respectively, were detected. MCODE identified complement, IL-10 signaling, and immune/interleukin signaling as the top 3 diagnosis PPI clusters. Complement, extracellular matrix organization/proteoglycans, and MAPK/RAS signaling were the top 3 monitoring PPI clusters. IPA showed interleukin 23/17 (interleukin 22, interleukin 23A), TNF (TNF receptor-associated factor 3), cGAS-STING (cyclic GMP-AMP synthase, Stimulator of Interferon Gene 1), and Jak/Stat (Signal transducer and activator of transcription 1), signaling in predicted upstream regulators. Lasso regression identified a Diagnostic 13-protein model predictive of AS. This model had a sensitivity of 0.75, specificity of 0.90, a kappa of 0.59, and overall accuracy of 0.80 (95% CI: 0.61-0.92). The AS vs HC ROC curve was 0.79 (95% CI: 0.61-0.96). CONCLUSION We identified multiple candidate AS diagnostic and disease activity monitoring serum biomarkers using a comprehensive proteomic screen. Enrichment analysis identified key pathways in AS diagnosis and monitoring. Lasso regression identified a multi-protein panel with modest predictive ability.
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Affiliation(s)
- Mark Hwang
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA.
| | - Shervin Assassi
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
| | - Jim Zheng
- School of Biomedical Informatics, UTHealth Houston, Houston, TX, USA
| | | | - Reyna Chavez
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
| | - Kamala Vanarsa
- Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Chandra Mohan
- Biomedical Engineering, University of Houston, Houston, TX, USA
| | - John Reveille
- McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin MSB.5270, TX, 77030, Houston, USA
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Jung S, Lee JS. Single-Cell Genomics for Investigating Pathogenesis of Inflammatory Diseases. Mol Cells 2023; 46:120-129. [PMID: 36859476 PMCID: PMC9982059 DOI: 10.14348/molcells.2023.0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 03/03/2023] Open
Abstract
Recent technical advances have enabled unbiased transcriptomic and epigenetic analysis of each cell, known as "single-cell analysis". Single-cell analysis has a variety of technical approaches to investigate the state of each cell, including mRNA levels (transcriptome), the immune repertoire (immune repertoire analysis), cell surface proteins (surface proteome analysis), chromatin accessibility (epigenome), and accordance with genome variants (eQTLs; expression quantitative trait loci). As an effective tool for investigating robust immune responses in coronavirus disease 2019 (COVID-19), many researchers performed single-cell analysis to capture the diverse, unbiased immune cell activation and differentiation. Despite challenges elucidating the complicated immune microenvironments of chronic inflammatory diseases using existing experimental methods, it is now possible to capture the simultaneous immune features of different cell types across inflamed tissues using various single-cell tools. In this review, we introduce patient-based and experimental mouse model research utilizing single-cell analyses in the field of chronic inflammatory diseases, as well as multi-organ atlas targeting immune cells.
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Affiliation(s)
- Seyoung Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jeong Seok Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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Ning D, Garg K, Mayer B, Schick B, Bracht H, Barth E, Weiss M, Li C, Schneider J, Schneider EM. Monocyte subtype expression patterns in septic patients with diabetes are distinct from patterns observed in obese patients. Front Med (Lausanne) 2023; 9:1026298. [PMID: 36687421 PMCID: PMC9849690 DOI: 10.3389/fmed.2022.1026298] [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: 08/23/2022] [Accepted: 11/29/2022] [Indexed: 01/06/2023] Open
Abstract
Background Sepsis causes a high rate of mortality and long-term morbidity, associated with an imbalance of innate immunity against infections and inflammation. Obesity and diabetes increase the risk for disease severity. Monocyte dysfunction plays a major role and justify further investigations. Objective To investigate the distribution and inflammatory phenotypes in circulating monocyte subsets in patients manifesting with sepsis including septic shock with and without obesity and diabetes. Methods A total of 235 blood samples were tested from critically ill adult patients registered at the intensive care unit (ICU). The cohorts were divided into non-diabetic groups with or without obesity and diabetic groups with or without obesity, suffering from sepsis or septic shock. We determined frequencies of total monocytes and of monocyte subsets in the circulation and density expression levels of functional markers, including CD14, CD16, HLA-DR, CD33, CD163, CD206, and arginase-1 by flow cytometric analysis. Results When progressing to septic shock in non-diabetic and diabetic patients, the percentages of total monocytes among the leukocyte population and of CD33+ and CD14+ monocytes among the monocyte population were consistently down-regulated compared to non-sepsis in non-diabetic and diabetic patients, respectively. Non-diabetic sepsis patients further presented with decreased CD33 and up-regulated CD163 expression density, which was absent in diabetic patients. We subsequently addressed obesity-related changes of monocytes in non-diabetic and diabetic septic patients. Obese septic patients with diabetes were unique in displaying increased monocytic CD16 and CD163 expression. However, obese septic patients without diabetes solely presented with lower amounts of non-classical monocytes. Body mass index (BMI) dependent changes were restricted to diabetic septic patients, with a significantly higher diminution of the classical monocyte subset and concomitantly increased CD16 expression densities. Conclusion Distribution and phenotypes of monocyte subsets were differentially modulated in critically ill patients with and without metabolic disease when progressing to sepsis or septic shock. Only diabetic septic patients displayed decline of classical monocytes and increase of CD16 expression densities. Therefore, diabetes but not obesity appears to promote the inflammatory phenotype of circulating monocytes in critically ill patients.
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Affiliation(s)
- Dan Ning
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Kunal Garg
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Benjamin Mayer
- Faculty of Medicine, Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Benedikt Schick
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Hendrik Bracht
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Eberhard Barth
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Manfred Weiss
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Chen Li
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - Julian Schneider
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany
| | - E. Marion Schneider
- Clinic for Anaesthesiology and Intensive Care Medicine, Ulm University Hospital, Ulm, Germany,*Correspondence: E. Marion Schneider,
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Hart DA. Sex differences in musculoskeletal injury and disease risks across the lifespan: Are there unique subsets of females at higher risk than males for these conditions at distinct stages of the life cycle? Front Physiol 2023; 14:1127689. [PMID: 37113695 PMCID: PMC10126777 DOI: 10.3389/fphys.2023.1127689] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Sex differences have been reported for diseases of the musculoskeletal system (MSK) as well as the risk for injuries to tissues of the MSK system. For females, some of these occur prior to the onset of puberty, following the onset of puberty, and following the onset of menopause. Therefore, they can occur across the lifespan. While some conditions are related to immune dysfunction, others are associated with specific tissues of the MSK more directly. Based on this life spectrum of sex differences in both risk for injury and onset of diseases, a role for sex hormones in the initiation and progression of this risk is somewhat variable. Sex hormone receptor expression and functioning can also vary with life events such as the menstrual cycle in females, with different tissues being affected. Furthermore, some sex hormone receptors can affect gene expression independent of sex hormones and some transitional events such as puberty are accompanied by epigenetic alterations that can further lead to sex differences in MSK gene regulation. Some of the sex differences in injury risk and the post-menopausal disease risk may be "imprinted" in the genomes of females and males during development and sex hormones and their consequences only modulators of such risks later in life as the sex hormone milieu changes. The purpose of this review is to discuss some of the relevant conditions associated with sex differences in risks for loss of MSK tissue integrity across the lifespan, and further discuss several of the implications of their variable relationship with sex hormones, their receptors and life events.
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Zhu J, Lu Q, Liang T, Li H, Zhou C, Wu S, Chen T, Chen J, Deng G, Yao Y, Liao S, Yu C, Huang S, Sun X, Chen L, Chen W, Ye Z, Guo H, Chen W, Jiang W, Fan B, Tao X, Zhan X, Liu C. Development and Validation of a Machine Learning-Based Nomogram for Prediction of Ankylosing Spondylitis. Rheumatol Ther 2022; 9:1377-1397. [PMID: 35932360 PMCID: PMC9510083 DOI: 10.1007/s40744-022-00481-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/21/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Ankylosing spondylitis (AS) is a chronic progressive inflammatory disease of the spine and its affiliated tissues. AS mainly affects the axial bone, sacroiliac joint, hip joint, spinal facet, and adjacent ligaments. We used machine learning (ML) methods to construct diagnostic models based on blood routine examination, liver function test, and kidney function test of patients with AS. This method will help clinicians enhance diagnostic efficiency and allow patients to receive systematic treatment as soon as possible. Methods We consecutively screened 348 patients with AS through complete blood routine examination, liver function test, and kidney function test at the First Affiliated Hospital of Guangxi Medical University according to the modified New York criteria (diagnostic criteria for AS). By using random sampling, the patients were randomly divided into training and validation cohorts. The training cohort included 258 patients with AS and 247 patients without AS, and the validation cohort included 90 patients with AS and 113 patients without AS. We used three ML methods (LASSO, random forest, and support vector machine recursive feature elimination) to screen feature variables and then took the intersection to obtain the prediction model. In addition, we used the prediction model on the validation cohort. Results Seven factors—erythrocyte sedimentation rate (ESR), red blood cell count (RBC), mean platelet volume (MPV), albumin (ALB), aspartate aminotransferase (AST), and creatinine (Cr)—were selected to construct a nomogram diagnostic model through ML. In the training cohort, the C value and area under the curve (AUC) value of this nomogram was 0.878 and 0.8779462, respectively. The C value and AUC value of the nomogram in the validation cohort was 0.823 and 0.8232055, respectively. Calibration curves in the training and validation cohorts showed satisfactory agreement between nomogram predictions and actual probabilities. The decision curve analysis showed that the nonadherence nomogram was clinically useful when intervention was decided at the nonadherence possibility threshold of 1%. Conclusion Our ML model can satisfactorily predict patients with AS. This nomogram can help orthopedic surgeons devise more personalized and rational clinical strategies. Supplementary Information The online version contains supplementary material available at 10.1007/s40744-022-00481-6. AS is a chronic progressive inflammatory disease of the spine and its affiliated tissues. AS starts gradually, and its early symptoms are mild. Some hospitals lack HLA-B27 and related imaging instruments to assist in the diagnosis of AS. There are relatively few studies on liver function and kidney function of patients with AS. We used ML methods to construct diagnostic models. Our model can satisfactorily predict patients with AS. This diagnostic model can help orthopedic surgeons devise more personalized and rational clinical strategies.
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Affiliation(s)
- Jichong Zhu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Qing Lu
- The First Affiliated Hospital of Guangxi, University of Science and Technology, Liuzhou, 540000, People's Republic of China
| | - Tuo Liang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Hao Li
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Chenxin Zhou
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Shaofeng Wu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Tianyou Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Jiarui Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Guobing Deng
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Yuanlin Yao
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Shian Liao
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Chaojie Yu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Shengsheng Huang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xuhua Sun
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Liyi Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Wenkang Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Zhen Ye
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Hao Guo
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Wuhua Chen
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Wenyong Jiang
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Binguang Fan
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xiang Tao
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China
| | - Xinli Zhan
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China.
| | - Chong Liu
- The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, People's Republic of China.
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