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Li C, Liu H, Yang L, Liu R, Yin G, Xie Q. Immune-mediated necrotizing myopathy: A comprehensive review of the pathogenesis, clinical features, and treatments. J Autoimmun 2024; 148:103286. [PMID: 39033686 DOI: 10.1016/j.jaut.2024.103286] [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: 03/16/2024] [Revised: 07/10/2024] [Accepted: 07/13/2024] [Indexed: 07/23/2024]
Abstract
Immune-mediated necrotizing myopathy (IMNM) is a rare and newly recognized autoimmune disease within the spectrum of idiopathic inflammatory myopathies. It is characterized by myositis-specific autoantibodies, elevated serum creatine kinase levels, inflammatory infiltrate, and weakness. IMNM can be classified into three subtypes based on the presence or absence of specific autoantibodies: anti-signal recognition particle myositis, anti-3-hydroxy-3-methylglutaryl-coenzyme A reductase myositis, and seronegative IMNM. In recent years, IMNM has gained increasing attention and emerged as a research hotspot. Recent studies have suggested that the pathogenesis of IMNM is linked to aberrant activation of immune system, including immune responses mediated by antibodies, complement, and immune cells, particularly macrophages, as well as abnormal release of inflammatory factors. Non-immune mechanisms such as autophagy and endoplasmic reticulum stress also participate in this process. Additionally, genetic variations associated with IMNM have been identified, providing new insights into the genetic mechanisms of the disease. Progress has also been made in IMNM treatment research, including the use of immunosuppressants and the development of biologics. Despite the challenges in understanding the etiology and treatment of IMNM, the latest research findings offer important guidance and insights for delving deeper into the disease's pathogenic mechanisms and identifying new therapeutic strategies.
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Affiliation(s)
- Changpei Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Hongjiang Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Leiyi Yang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Ruiting Liu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Geng Yin
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Qibing Xie
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China.
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Searle B, Shannon A, Teodorescu R, Song NJ, Heil L, Jacob C, Remes P, Li Z, Rubinstein M. Rapid assay development for low input targeted proteomics using a versatile linear ion trap. RESEARCH SQUARE 2024:rs.3.rs-4702746. [PMID: 39070662 PMCID: PMC11275998 DOI: 10.21203/rs.3.rs-4702746/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Advances in proteomics and mass spectrometry enable the study of limited cell populations, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive low-mass accuracy measurements, these instruments are effectively restricted to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. Here, we describe a workflow using a new hybrid quadrupole-LIT instrument that rapidly develops targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Using an automated software approach for scheduling parallel reaction monitoring assays (PRM), we show consistent quantification across three orders of magnitude in a matched-matrix background. We demonstrate measuring low-level proteins such as transcription factors and cytokines with quantitative linearity below two orders of magnitude in a 1 ng background proteome without requiring stable isotope-labeled standards. From a 1 ng sample, we found clear consistency between proteins in subsets of CD4+ and CD8+ T cells measured using high dimensional flow cytometry and LIT-based proteomics. Based on these results, we believe hybrid quadrupole-LIT instruments represent an economical solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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Affiliation(s)
| | | | | | | | | | | | | | - Zihai Li
- The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
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3
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Reyes-Huerta RF, Mandujano-López V, Velásquez-Ortiz MG, Alcalá-Carmona B, Ostos-Prado MJ, Reyna-Juárez Y, Meza-Sánchez DE, Juárez-Vega G, Mejía-Domínguez NR, Torres-Ruiz J, Gómez-Martín D, Maravillas-Montero JL. Novel B-cell subsets as potential biomarkers in idiopathic inflammatory myopathies: insights into disease pathogenesis and disease activity. J Leukoc Biol 2024; 116:84-94. [PMID: 38554062 DOI: 10.1093/jleuko/qiae083] [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: 10/31/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Idiopathic inflammatory myopathies are a heterogeneous group of rare autoimmune disorders characterized by progressive muscle weakness and the histopathologic findings of inflammatory infiltrates in muscle tissue. Although their pathogenesis remains indefinite, the association of autoantibodies with clinical manifestations and the evidence of high effectiveness of depleting therapies suggest that B cells could be implicated. Therefore, we explored the landscape of peripheral B cells in this disease by multiparametric flow cytometry, finding significant numerical decreases in memory and double-negative subsets, as well as an expansion of the naive compartment relative to healthy controls, that contribute to defining disease-associated B-cell subset signatures and correlating with different clinical features of patients. Additionally, we determined the potential value of these subsets as diagnostic biomarkers, thus positioning B cells as neglected key elements possibly participating in idiopathic inflammatory myopathy onset or development.
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Affiliation(s)
- Raúl F Reyes-Huerta
- B cell Immunology Laboratory, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica S/N, CU, Coyoacán, Mexico City 04510, Mexico
- Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, CU, Coyoacán, Mexico City 04510, Mexico
| | - Vladimir Mandujano-López
- B cell Immunology Laboratory, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica S/N, CU, Coyoacán, Mexico City 04510, Mexico
| | - Ma Guadalupe Velásquez-Ortiz
- B cell Immunology Laboratory, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica S/N, CU, Coyoacán, Mexico City 04510, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, CU, Coyoacán, Mexico City 04510, Mexico
| | - Beatriz Alcalá-Carmona
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - María J Ostos-Prado
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Yatzil Reyna-Juárez
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - David E Meza-Sánchez
- B cell Immunology Laboratory, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica S/N, CU, Coyoacán, Mexico City 04510, Mexico
- Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán y Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Guillermo Juárez-Vega
- Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán y Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Nancy R Mejía-Domínguez
- Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán y Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Jiram Torres-Ruiz
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - Diana Gómez-Martín
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
- Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán y Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
| | - José L Maravillas-Montero
- B cell Immunology Laboratory, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica S/N, CU, Coyoacán, Mexico City 04510, Mexico
- Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán y Universidad Nacional Autónoma de México, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, Mexico City 14080, Mexico
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Shannon AE, Teodorescu RN, Soon N, Heil LR, Jacob CC, Remes PM, Rubinstein MP, Searle BC. A workflow for targeted proteomics assay development using a versatile linear ion trap. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596891. [PMID: 38853838 PMCID: PMC11160733 DOI: 10.1101/2024.05.31.596891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Advances in proteomics and mass spectrometry have enabled the study of limited cell populations, such as single-cell proteomics, where high-mass accuracy instruments are typically required. While triple quadrupoles offer fast and sensitive nominal resolution measurements, these instruments are effectively limited to targeted proteomics. Linear ion traps (LITs) offer a versatile, cost-effective alternative capable of both targeted and global proteomics. We demonstrate a workflow using a newly released, hybrid quadrupole-LIT instrument for developing targeted proteomics assays from global data-independent acquisition (DIA) measurements without needing high-mass accuracy. Gas-phase fraction-based DIA enables rapid target library generation in the same background chemical matrix as each quantitative injection. Using a new software tool embedded within EncyclopeDIA for scheduling parallel reaction monitoring assays, we show consistent quantification across three orders of magnitude of input material. Using this approach, we demonstrate measuring peptide quantitative linearity down to 25x dilution in a background of only a 1 ng proteome without requiring stable isotope labeled standards. At 1 ng total protein on column, we found clear consistency between immune cell populations measured using flow cytometry and immune markers measured using LIT-based proteomics. We believe hybrid quadrupole-LIT instruments represent an economic solution to democratizing mass spectrometry in a wide variety of laboratory settings.
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Ricco C, Eldaboush A, Liu ML, Werth VP. Extracellular Vesicles in the Pathogenesis, Clinical Characterization, and Management of Dermatomyositis: A Narrative Review. Int J Mol Sci 2024; 25:1967. [PMID: 38396646 PMCID: PMC10889219 DOI: 10.3390/ijms25041967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Extracellular vesicles (EVs) are lipid-bilayer particles secreted from cells that primarily assist in cell-to-cell communication through the content of their cargo, such as proteins and RNA. EVs have been implicated in the pathogenesis of various autoimmune diseases, including dermatomyositis (DM), an inflammatory autoimmune disease characterized by distinct cutaneous manifestations, myopathy, and lung disease. We sought to review the role of EVs in DM and understand how they contribute to the pathogenesis and clinical characterization of the disease. We summarized the research progress on EVs in dermatomyositis based on recent publications. EV cargoes, such as double-stranded DNA, microRNA, and proteins, contribute to DM pathogenesis and mediate the proinflammatory response and cytokine release through signaling pathways such as the stimulator of interferon genes (STING) pathway. These nucleic acids and proteins have been proposed as disease-specific, stable biomarkers to monitor disease activity and responses to therapy. They also correlate with clinical parameters, inflammatory markers, and disease severity scores. Furthermore, some markers show an association with morbidities of DM, such as muscle weakness and interstitial lung disease. The continued study of EVs will help us to further elucidate our understanding of dermatomyositis.
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Affiliation(s)
- Cristina Ricco
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; (C.R.); (A.E.); (M.-L.L.)
- Department of Dermatology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ahmed Eldaboush
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; (C.R.); (A.E.); (M.-L.L.)
- Department of Dermatology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ming-Lin Liu
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; (C.R.); (A.E.); (M.-L.L.)
- Department of Dermatology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Victoria P. Werth
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA; (C.R.); (A.E.); (M.-L.L.)
- Department of Dermatology, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Giloteaux L, Glass KA, Germain A, Franconi CJ, Zhang S, Hanson MR. Dysregulation of extracellular vesicle protein cargo in female myalgic encephalomyelitis/chronic fatigue syndrome cases and sedentary controls in response to maximal exercise. J Extracell Vesicles 2024; 13:e12403. [PMID: 38173127 PMCID: PMC10764978 DOI: 10.1002/jev2.12403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/27/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
In healthy individuals, physical exercise improves cardiovascular health and muscle strength, alleviates fatigue and reduces the risk of chronic diseases. Although exercise is suggested as a lifestyle intervention to manage various chronic illnesses, it negatively affects people with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), who suffer from exercise intolerance. We hypothesized that altered extracellular vesicle (EV) signalling in ME/CFS patients after an exercise challenge may contribute to their prolonged and exacerbated negative response to exertion (post-exertional malaise). EVs were isolated by size exclusion chromatography from the plasma of 18 female ME/CFS patients and 17 age- and BMI-matched female sedentary controls at three time points: before, 15 min, and 24 h after a maximal cardiopulmonary exercise test. EVs were characterized using nanoparticle tracking analysis and their protein cargo was quantified using Tandem Mass Tag-based (TMT) proteomics. The results show that exercise affects the EV proteome in ME/CFS patients differently than in healthy individuals and that changes in EV proteins after exercise are strongly correlated with symptom severity in ME/CFS. Differentially abundant proteins in ME/CFS patients versus controls were involved in many pathways and systems, including coagulation processes, muscle contraction (both smooth and skeletal muscle), cytoskeletal proteins, the immune system and brain signalling.
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Affiliation(s)
- Ludovic Giloteaux
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Katherine A. Glass
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Arnaud Germain
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Carl J. Franconi
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of BiotechnologyCornell UniversityIthacaNew YorkUSA
| | - Maureen R. Hanson
- Department of Molecular Biology and GeneticsCornell UniversityIthacaNew YorkUSA
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Abyadeh M, Alikhani M, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomics provides insights into the theranostic potential of extracellular vesicles. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:101-133. [PMID: 38220422 DOI: 10.1016/bs.apcsb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Alikhani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Xu S, Hu X, Wang J, Xu Q, Han Z, Zhou H, Gao M. Polymyositis and dermatomyositis biomarkers. Clin Chim Acta 2023; 547:117443. [PMID: 37329941 DOI: 10.1016/j.cca.2023.117443] [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: 04/04/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/19/2023]
Abstract
Polymyositis (PM) and dermatomyositis (DM) are the two subtypes of idiopathic inflammatory myositis and are characterized as symmetrical progressive muscle weakness in the proximal extremities. PM/DM affect multiple organs and systems, including the cardiovascular, respiratory and digestive tract systems. An in-depth understanding of PM/DM biomarkers will facilitate development of simple and accurate strategies for diagnosis, treatment, and prognosis prediction. This review summarized the classic biomarkers of PM/DM, including anti-aminoacyl tRNA synthetases (ARS) antibody, anti-Mi-2 antibody, anti-melanoma differentiation-associated gene 5 (MDA5) antibody, anti-transcription intermediary factor 1-γ (TIF1-γ) antibody, anti-nuclear matrix protein 2 (NXP2) antibody, among others. Among them, anti-aminoacyl tRNA synthetases antibody is the most classic. In addition, many potential novel biomarkers were also discussed in this review, including anti-HSC70 antibody, YKL-40, interferons, myxovirus resistance protein 2, regenerating islet-derived protein 3-α, interleukin (IL)-17, IL-35, microRNA (miR)-1 and so on. Among the biomarkers of PM/DM described in this review, classic biomarkers have become the mainstream biomarkers to assist clinicians in diagnosis due to their early discovery, in-depth research, and widespread application. The novel biomarkers also have potential and broad research prospects, which will make immeasurable contributions to exploring biomarker-based classification standards and expanding their application value.
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Affiliation(s)
- Shuyue Xu
- Wuxi No. 2 People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Xiaowei Hu
- Xinwu District Center for Disease Control and Prevention, Wuxi, China
| | - Jing Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Qiangwei Xu
- Department of Rheumatology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Zhijun Han
- Wuxi No. 2 People's Hospital Affiliated to Nanjing Medical University, Wuxi, China; Department of Clinical Research Center, Jiangnan University Medical Center, Wuxi, China
| | - Haiyan Zhou
- Department of Cardiovascular Medicine, The Affiliated Hospital of Guizhou Medical University, Guiyang, China.
| | - Mingzhu Gao
- Department of Clinical Research Center, Jiangnan University Medical Center, Wuxi, China; Wuxi No. 2 People's Hospital Affiliated to Nanjing Medical University, Wuxi, China.
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