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Yamamoto K, Sakaguchi M, Onishi A, Yokoyama S, Matsui Y, Yamamoto W, Onizawa H, Fujii T, Murata K, Tanaka M, Hashimoto M, Matsuda S, Morinobu A. Energy landscape analysis and time-series clustering analysis of patient state multistability related to rheumatoid arthritis drug treatment: The KURAMA cohort study. PLoS One 2024; 19:e0302308. [PMID: 38709812 PMCID: PMC11073743 DOI: 10.1371/journal.pone.0302308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 04/02/2024] [Indexed: 05/08/2024] Open
Abstract
Rheumatoid arthritis causes joint inflammation due to immune abnormalities, resulting in joint pain and swelling. In recent years, there have been considerable advancements in the treatment of this disease. However, only approximately 60% of patients achieve remission. Patients with multifactorial diseases shift between states from day to day. Patients may remain in a good or poor state with few or no transitions, or they may switch between states frequently. The visualization of time-dependent state transitions, based on the evaluation axis of stable/unstable states, may provide useful information for achieving rheumatoid arthritis treatment goals. Energy landscape analysis can be used to quantitatively determine the stability/instability of each state in terms of energy. Time-series clustering is another method used to classify transitions into different groups to identify potential patterns within a time-series dataset. The objective of this study was to utilize energy landscape analysis and time-series clustering to evaluate multidimensional time-series data in terms of multistability. We profiled each patient's state transitions during treatment using energy landscape analysis and time-series clustering. Energy landscape analysis divided state transitions into two patterns: "good stability leading to remission" and "poor stability leading to treatment dead-end." The number of patients whose disease status improved increased markedly until approximately 6 months after treatment initiation and then plateaued after 1 year. Time-series clustering grouped patients into three clusters: "toward good stability," "toward poor stability," and "unstable." Patients in the "unstable" cluster are considered to have clinical courses that are difficult to predict; therefore, these patients should be treated with more care. Early disease detection and treatment initiation are important. The evaluation of state multistability enables us to understand a patient's current state in the context of overall state transitions related to rheumatoid arthritis drug treatment and to predict future state transitions.
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Affiliation(s)
- Keiichi Yamamoto
- Division of Data Science, Center for Industrial Research and Innovation, Translational Research Institute for Medical Innovation, Osaka Dental University, Hirakata City, Osaka, Japan
| | - Masahiko Sakaguchi
- Department of Engineering Informatics, Faculty of Information and Communication Engineering, Osaka Electro-Communication University, Neyagawa City, Osaka, Japan
| | - Akira Onishi
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | | | | | - Wataru Yamamoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
- Department of Health Information Management, Kurashiki Sweet Hospital, Nakasho, Kurashiki, Kurashiki City, Okayama Prefecture, Japan
| | - Hideo Onizawa
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | - Takayuki Fujii
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | - Koichi Murata
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | - Masao Tanaka
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | - Motomu Hashimoto
- Department of Clinical Immunology, Osaka Metropolitan University Graduate School of Medicine, Osaka City, Japan
| | - Shuichi Matsuda
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
| | - Akio Morinobu
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Sakyo, Kyoto, Japan
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Peng T, Li B, Bi L, Zhang F. Iguratimod inhibits protein citrullination and inflammation by downregulating NBCe2 in patients with rheumatoid arthritis. Biomed Pharmacother 2024; 174:116551. [PMID: 38636399 DOI: 10.1016/j.biopha.2024.116551] [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: 12/13/2023] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Bicarbonate has recently been identified as a crucial factor affecting peptidylarginine deiminase (PAD) activity; however, the mechanism underlying its role in rheumatoid arthritis (RA) remains unclear. Iguratimod (IGU), a small-molecule disease-modifying anti-rheumatic drug, requires further investigation. This study aimed to explore the mechanism by which bicarbonate affects citrullination and inflammation in RA and identify new targets for IGU. METHODS We enrolled 20 patients with RA in the study. Sodium bicarbonate cotransporter 2 (NBCe2) was detected in the peripheral blood neutrophils and peripheral blood mononuclear cells (PBMCs) of these patients. The effects of varying concentrations of IGU, methotrexate (MTX), dexamethasone (DXM), and S0859 (an NBCe2 inhibitor) on NBCe2, PAD2, PAD4, and citrullinated histone H3 (cit-H3) levels in, migration ability of, and cytokine production from neutrophils and PBMCs were examined. RESULTS Our findings showed that in patients with RA, citrullinated protein production by peripheral blood neutrophils instead of PBMCs, which showed higher NBCe2 expression levels, increased with an increase in the bicarbonate concentration. In addition, tumor necrosis factor-alpha (TNF-α) promoted NBCe2 expression in neutrophils from patients with RA. Furthermore, we revealed that the inhibitory effects of IGU on neutrophil NBCe2 and cit-H3 levels, degrees of inhibition of neutrophil and PBMC migration, and suppression of interleukin 6, TNF-α, and metalloproteinase-9 secretion from neutrophil-like differentiated HL-60 cells did not substantially differ from those of MTX, DXM, and S0859 at specific doses. CONCLUSIONS Bicarbonate promotes protein citrullination and inflammation in RA via NBCe2, and IGU can downregulate NBCe2.
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Affiliation(s)
- Tiane Peng
- Department of Rheumatology and Immunology, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Bingtong Li
- Department of Rheumatology and Immunology, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Liqi Bi
- Department of Rheumatology and Immunology, China-Japan Union Hospital of Jilin University, Changchun 130033, China.
| | - Fangze Zhang
- Department of Gastroenterology/Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun 130033, China.
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Umeda A, Murata K, Murotani Y, Fujii T, Onishi A, Murakami K, Onizawa H, Otsuki B, Shimizu T, Tanaka M, Morinobu A, Matsuda S. Low Hounsfield unit values on computed tomography as a potential predictor of vertebral fracture in patients with rheumatoid arthritis: The KURAMA cohort study. Int J Rheum Dis 2024; 27:e15146. [PMID: 38661342 DOI: 10.1111/1756-185x.15146] [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: 02/01/2024] [Revised: 03/12/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVE Hounsfield units (HU) measured using computed tomography (CT) have gained considerable attention for the detection of osteoporosis. This study aimed to investigate whether opportunistic CT could predict vertebral fractures in patients with rheumatoid arthritis (RA). METHODS A total of 233 patients with RA who underwent chest CT were included in this study. The HU values of the anterior 1/3 of the vertebral bodies based on the sagittal plane at T11-L2 after reconstruction were measured. The incidence of vertebral fractures was investigated with respect to the HU value. RESULTS Vertebral fractures were identified in 32 patients during a mean follow-up period of 3.8 years. In patients who experienced vertebral fractures within 2 years of CT imaging, the HU values of the vertebral bodies (T11-L2) were lower than those in patients who did not experience fractures. Receiver operating characteristic curve analysis identified that a T11 HU value of <125 was a risk factor for vertebral fracture within 2 years. Multivariate analysis showed that a T11 HU value of <125 and the existence of prevalent vertebral fractures were significant risk factors for fracture. CONCLUSION HU measurements of the anterior 1/3 of the vertebral body are a potential predictor for vertebral fractures in patients with RA.
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Affiliation(s)
- Akane Umeda
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichi Murata
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Yoshiki Murotani
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayuki Fujii
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akira Onishi
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kosaku Murakami
- Division of Clinical Immunology and Cancer Immunotherapy, Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideo Onizawa
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Bungo Otsuki
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takayoshi Shimizu
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masao Tanaka
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shuichi Matsuda
- Department of Orthopaedic Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Wang L, Niu X. Immunoregulatory Roles of Osteopontin in Diseases. Nutrients 2024; 16:312. [PMID: 38276550 PMCID: PMC10819284 DOI: 10.3390/nu16020312] [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: 11/17/2023] [Revised: 01/07/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Osteopontin (OPN) is a multifunctional protein that plays a pivotal role in the immune system. It is involved in various biological processes, including cell adhesion, migration and survival. The study of the immunomodulatory effects of OPN is of paramount importance due to its potential therapeutic applications. A comprehensive understanding of how OPN regulates the immune response could pave the way for the development of novel treatments for a multitude of diseases, including autoimmune disorders, infectious diseases and cancer. Therefore, in the following paper, we provide a systematic overview of OPN and its immunoregulatory roles in various diseases, laying the foundation for the development of OPN-based therapies in the future.
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Affiliation(s)
- Lebei Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoyin Niu
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
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Qiu Y, Feng X, Liu C, Shi Y, Xu L, You H, Wang L, Lv C, Wang F, Tan W. Proteomic profiling identifies SPP1 associated with rapidly progressive interstitial lung disease in anti-MDA5-positive dermatomyositis. Arthritis Res Ther 2024; 26:9. [PMID: 38167532 PMCID: PMC10759429 DOI: 10.1186/s13075-023-03243-z] [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: 09/21/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Anti-melanoma differentiation-associated gene five antibody positive (MDA5+) dermatomyositis (DM) is significantly associated with rapidly progressive interstitial lung disease (RP-ILD). Early detection of RP-ILD remains a major challenge. This study aims to identify and validate prognostic factors for RP-ILD in MDA5+ DM patients. METHODS Plasma samples from 20 MDA5+ DM patients and 10 healthy controls (HC) were collected for proteomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The proteins of interest were validated in independent samples (20 HC, 20 MDA5+ DM with RP-ILD, and 20 non-RP-ILD patients) with enzyme-linked immunosorbent assay (ELISA). RESULTS A total of 413 differentially expressed proteins (DEPs) were detected between the MDA5+ DM patients and HC. When comparing DEPs between RP-ILD and non-RP-ILD patients, 79 proteins were changed in RP-ILD patients, implicating acute inflammatory response, coagulation, and complement cascades. Six candidate biomarkers were confirmed with ELISA. Secreted phosphoprotein 1 (SPP1), serum amyloid A1 (SAA1), and Kininogen 1 (KNG1) concentrations were significantly elevated in RP-ILD patients than those in non-RP-ILD patients and HC. In the different clinical subgroups, SPP1 was particularly elevated in the high-risk RP-ILD subgroup of MDA5+ DM. CONCLUSION This study provides novel insights into the pathogenesis of RP-ILD development in MDA5+ DM and suggests the plasma protein SPP1 could serve as a potential blood biomarker for RP-ILD early warning.
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Affiliation(s)
- Yulu Qiu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Xiaoke Feng
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
- Integrated Traditional Chinese and Western Medicine Institute of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chang Liu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Yumeng Shi
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Lingxiao Xu
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Hanxiao You
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Lei Wang
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Chengyin Lv
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China
| | - Fang Wang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
| | - Wenfeng Tan
- Department of Rheumatology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu Province, China.
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Stern LJ, Clement C, Galluzzi L, Santambrogio L. Non-mutational neoantigens in disease. Nat Immunol 2024; 25:29-40. [PMID: 38168954 PMCID: PMC11075006 DOI: 10.1038/s41590-023-01664-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
The ability of mammals to mount adaptive immune responses culminating with the establishment of immunological memory is predicated on the ability of the mature T cell repertoire to recognize antigenic peptides presented by syngeneic MHC class I and II molecules. Although it is widely believed that mature T cells are highly skewed towards the recognition of antigenic peptides originating from genetically diverse (for example, foreign or mutated) protein-coding regions, preclinical and clinical data rather demonstrate that novel antigenic determinants efficiently recognized by mature T cells can emerge from a variety of non-mutational mechanisms. In this Review, we describe various mechanisms that underlie the formation of bona fide non-mutational neoantigens, such as epitope mimicry, upregulation of cryptic epitopes, usage of non-canonical initiation codons, alternative RNA splicing, and defective ribosomal RNA processing, as well as both enzymatic and non-enzymatic post-translational protein modifications. Moreover, we discuss the implications of the immune recognition of non-mutational neoantigens for human disease.
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Affiliation(s)
- Lawrence J Stern
- Department of Pathology, UMass Chan Medical School, Worcester, MA, USA
- Immunology and Microbiology Program, UMass Chan Medical School, Worcester, MA, USA
| | - Cristina Clement
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA
| | - Lorenzo Galluzzi
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
| | - Laura Santambrogio
- Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York, NY, USA.
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