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Kobayashi S, Nagafuchi Y, Okubo M, Sugimori Y, Hatano H, Yamada S, Nakano M, Yoshida R, Takeshima Y, Ota M, Tsuchida Y, Iwasaki Y, Setoguchi K, Kubo K, Okamura T, Yamamoto K, Shoda H, Fujio K. Dysregulation of the gene signature of effector regulatory T cells in the early phase of systemic sclerosis. Rheumatology (Oxford) 2022; 61:4163-4174. [PMID: 35040949 DOI: 10.1093/rheumatology/keac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/11/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES We evaluated flow-cytometric and transcriptome features of peripheral blood immune cells from early-phase (disease duration < 5 years) systemic sclerosis (SSc) in comparison to late-phase SSc. METHODS Fifty Japanese patients with SSc (12 early SSc cases and 38 late SSc cases) and 50 age- and sex-matched healthy controls were enrolled. A comparison of flow-cytometric subset proportions and RNA-sequencing of 24 peripheral blood immune cell subsets was performed. We evaluated differentially expressed genes (DEGs), characterized the co-expressed gene modules, and estimated the composition of subpopulations by deconvolution based on single-cell RNA-sequencing data. As a disease control, idiopathic inflammatory myositis (IIM) patients were also evaluated. RESULTS Analyzing the data from early and late SSc, Fraction II effector regulatory T cell (Fr. II eTreg) genes showed a remarkable differential gene expression, which was enriched for genes related to oxidative phosphorylation. Although the flow-cytometric proportion of Fr. II eTregs was not changed in early SSc, deconvolution indicated expansion of the activated subpopulation. Co-expressed gene modules of Fr. II eTregs demonstrated enrichment of the DEGs of early SSc and correlation with the proportion of the activated subpopulation. These results suggested that DEGs in Fr. II eTregs from patients with early SSc were closely associated with the increased proportion of the activated subpopulation. Similar dysregulation of Fr. II eTregs was also observed in data from patients with early IIM. CONCLUSIONS RNA-seq of immune cells indicated the dysregulation of Fr. II eTregs in early SSc with increased proportion of the activated subpopulation.
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Affiliation(s)
- Satomi Kobayashi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Japan. 35-2 Sakaechou, Itabashi-ku, 173-0015, Japan, Tokyo, Tokyo
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mai Okubo
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yusuke Sugimori
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Hiroaki Hatano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Saeko Yamada
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Masahiro Nakano
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Ryochi Yoshida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yusuke Takeshima
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yumi Tsuchida
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Yukiko Iwasaki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Keigo Setoguchi
- Department of Rheumatology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Japan. 3-18-22 Honkomagome, Bunkyo-ku, 113-8677, Japan, Tokyo, Tokyo
| | - Kanae Kubo
- Department of Medicine and Rheumatology, Tokyo Metropolitan Geriatric Hospital, Japan. 35-2 Sakaechou, Itabashi-ku, 173-0015, Japan, Tokyo, Tokyo
| | - Tomohisa Okamura
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuhiko Yamamoto
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo.,Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Japan. 1-7-22 Suehiro-cho, Tsurumi-ku, Kanagawa, 230-0045, Japan, Yokohama, Yokohama
| | - Hirofumi Shoda
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Japan. 7-3-1 Hongo, Bunkyo-ku, 113-8655, Japan, Tokyo, Tokyo
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Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0373. [PMID: 27644972 PMCID: PMC5031639 DOI: 10.1098/rsta.2015.0373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 05/18/2023]
Abstract
We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Jana Jones
- Department of Ancient History, Macquarie University, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Prathiba Ravishankar
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Dylan Xavier
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Do Seon Lim
- Department of Dental Hygiene, College of Health Sciences, Eulji University, Sungnam, South Korea
| | - Dong Hoon Shin
- Department of Anatomy, Seoul National University, College of Medicine, Seoul, South Korea
| | - Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Legal Medicine Section, University of Turin, 10126 Turin, Italy UMR 7268, Laboratoire d'Anthropologie bio-culturelle, Droit, Étique and Santé (ADÉS), Faculté de Médecine de Marseille, 13344 Marseille, France
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
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