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Mu KL, Ran F, Peng LQ, Zhou LL, Wu YT, Shao MH, Chen XG, Guo CM, Luo QM, Wang TJ, Liu YC, Liu G. Identification of diagnostic biomarkers of rheumatoid arthritis based on machine learning-assisted comprehensive bioinformatics and its correlation with immune cells. Heliyon 2024; 10:e35511. [PMID: 39170142 PMCID: PMC11336745 DOI: 10.1016/j.heliyon.2024.e35511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by inflammatory cell infiltration, which can lead to chronic disability, joint destruction and loss of function. At present, the pathogenesis of RA is still unclear. The purpose of this study is to explore the potential biomarkers and immune molecular mechanisms of rheumatoid arthritis through machine learning-assisted bioinformatics analysis, in order to provide reference for the early diagnosis and treatment of RA disease. Methods RA gene chips were screened from the public gene GEO database, and batch correction of different groups of RA gene chips was performed using Strawberry Perl. DEGs were obtained using the limma package of R software, and functional enrichment analysis such as gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), disease ontology (DO), and gene set (GSEA) were performed. Three machine learning methods, least absolute shrinkage and selection operator regression (LASSO), support vector machine recursive feature elimination (SVM-RFE) and random forest tree (Random Forest), were used to identify potential biomarkers of RA. The validation group data set was used to verify and further confirm its expression and diagnostic value. In addition, CIBERSORT algorithm was used to evaluate the infiltration of immune cells in RA and control samples, and the correlation between confirmed RA diagnostic biomarkers and immune cells was analyzed. Results Through feature screening, 79 key DEGs were obtained, mainly involving virus response, Parkinson's pathway, dermatitis and cell junction components. A total of 29 hub genes were screened by LASSO regression, 34 hub genes were screened by SVM-RFE, and 39 hub genes were screened by Random Forest. Combined with the three algorithms, a total of 12 hub genes were obtained. Through the expression and diagnostic value verification in the validation group data set, 7 genes that can be used as diagnostic biomarkers for RA were preliminarily confirmed. At the same time, the correlation analysis of immune cells found that γδT cells, CD4+ memory activated T cells, activated dendritic cells and other immune cells were positively correlated with multiple RA diagnostic biomarkers, CD4+ naive T cells, regulatory T cells and other immune cells were negatively correlated with multiple RA diagnostic biomarkers. Conclusions The results of novel characteristic gene analysis of RA showed that KYNU, EVI2A, CD52, C1QB, BATF, AIM2 and NDC80 had good diagnostic and clinical value for the diagnosis of RA, and were closely related to immune cells. Therefore, these seven DEGs may become new diagnostic markers and immunotherapy markers for RA.
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Affiliation(s)
| | | | - Le-qiang Peng
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Ling-li Zhou
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Yu-tong Wu
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Ming-hui Shao
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Xiang-gui Chen
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Chang-mao Guo
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Qiu-mei Luo
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Tian-jian Wang
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Yu-chen Liu
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
| | - Gang Liu
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou, China
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Borcherding N, Brestoff JR. The power and potential of mitochondria transfer. Nature 2023; 623:283-291. [PMID: 37938702 DOI: 10.1038/s41586-023-06537-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/14/2023] [Indexed: 11/09/2023]
Abstract
Mitochondria are believed to have originated through an ancient endosymbiotic process in which proteobacteria were captured and co-opted for energy production and cellular metabolism. Mitochondria segregate during cell division and differentiation, with vertical inheritance of mitochondria and the mitochondrial DNA genome from parent to daughter cells. However, an emerging body of literature indicates that some cell types export their mitochondria for delivery to developmentally unrelated cell types, a process called intercellular mitochondria transfer. In this Review, we describe the mechanisms by which mitochondria are transferred between cells and discuss how intercellular mitochondria transfer regulates the physiology and function of various organ systems in health and disease. In particular, we discuss the role of mitochondria transfer in regulating cellular metabolism, cancer, the immune system, maintenance of tissue homeostasis, mitochondrial quality control, wound healing and adipose tissue function. We also highlight the potential of targeting intercellular mitochondria transfer as a therapeutic strategy to treat human diseases and augment cellular therapies.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA.
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Zhang W, Zhang Y, Zhang J, Deng C, Zhang C. Naringenin ameliorates collagen-induced arthritis through activating AMPK-mediated autophagy in macrophages. Immun Inflamm Dis 2023; 11:e983. [PMID: 37904715 PMCID: PMC10588338 DOI: 10.1002/iid3.983] [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: 01/31/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Naringenin is widely recognized for its notable attributes, including anti-inflammatory, anti-cancer, and immunomodulatory activities. However, its specific implications for rheumatoid arthritis (RA) and the underlying mechanisms remain to be explored. This study aimed to investigate the therapeutic efficacy and pharmacological mechanism of Naringenin in the treatment of collagen-induced arthritis (CIA). METHODS A CIA model was established in DBA/1 mice, and various doses of Naringenin were administered orally to assess its impact on RA. The study also involved lipopolysaccharides (LPS)-induced RAW264.7 cells to further evaluate the effects of Naringenin. Mechanistic studies were conducted to elucidate the signaling pathways involved in Naringenin's actions. RESULTS Naringenin significantly alleviated foot inflammation in DBA/1 CIA mice and attenuated the levels of pro-inflammatory cytokines in serum. It also enhanced antioxidant capacity in the CIA model. In vitro studies with LPS-induced RAW264.7 cells demonstrated that Naringenin attenuated pro-inflammatory cytokines and reactive oxygen species (ROS) levels. Mechanistic studies confirmed that Naringenin activated autophagy and increased autophagic flux. Blocking autophagy, either by silencing Atg5 or inhibiting autophagolysosome using chloroquine, effectively counteracted the impact of Naringenin on pro-inflammatory cytokines. Further exploration revealed that Naringenin activated the AMPK/ULK1 signaling pathway, and inhibition of AMPK reversed the initiation of autophagy and reduced pro-inflammatory cytokine secretion induced by Naringenin. CONCLUSIONS This study unveils a novel mechanism by which Naringenin may be used to treat RA. It demonstrates the therapeutic efficacy of Naringenin in a CIA model by reducing inflammation, modulating cytokine levels, and enhancing antioxidant capacity. Moreover, the activation of autophagy through the AMPK/ULK1 signaling pathway appears to play a critical role in Naringenin's anti-inflammatory effects. These findings suggest potential strategies for the development of anti-rheumatic medications based on Naringenin.
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Affiliation(s)
- Wei Zhang
- Department of OrthopedicAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
| | - Yuan Zhang
- Department of OrthopedicAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
| | - Jianguang Zhang
- Department of OrthopedicAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
| | - Chunbiao Deng
- Department of OrthopedicAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
| | - Chao Zhang
- Department of OrthopedicAffiliated Hospital of North Sichuan Medical CollegeNanchongChina
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Jing W, Liu C, Su C, Liu L, Chen P, Li X, Zhang X, Yuan B, Wang H, Du X. Role of reactive oxygen species and mitochondrial damage in rheumatoid arthritis and targeted drugs. Front Immunol 2023; 14:1107670. [PMID: 36845127 PMCID: PMC9948260 DOI: 10.3389/fimmu.2023.1107670] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease characterized by synovial inflammation, pannus formation, and bone and cartilage damage. It has a high disability rate. The hypoxic microenvironment of RA joints can cause reactive oxygen species (ROS) accumulation and mitochondrial damage, which not only affect the metabolic processes of immune cells and pathological changes in fibroblastic synovial cells but also upregulate the expression of several inflammatory pathways, ultimately promoting inflammation. Additionally, ROS and mitochondrial damage are involved in angiogenesis and bone destruction, thereby accelerating RA progression. In this review, we highlighted the effects of ROS accumulation and mitochondrial damage on inflammatory response, angiogenesis, bone and cartilage damage in RA. Additionally, we summarized therapies that target ROS or mitochondria to relieve RA symptoms and discuss the gaps in research and existing controversies, hoping to provide new ideas for research in this area and insights for targeted drug development in RA.
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Affiliation(s)
- Weiyao Jing
- Department of Acupuncture-Moxibustion and Tuina, Gansu University of Chinese Medicine, Lanzhou, China
| | - Cui Liu
- Department of Acupuncture-Moxibustion and Tuina, Gansu University of Chinese Medicine, Lanzhou, China
| | - Chenghong Su
- Department of Acupuncture-Moxibustion and Tuina, Gansu University of Chinese Medicine, Lanzhou, China
| | - Limei Liu
- Department of Acupuncture-Moxibustion and Tuina, Gansu University of Chinese Medicine, Lanzhou, China
| | - Ping Chen
- Department of Rheumatic and Bone Disease, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Xiangjun Li
- Department of Rheumatic and Bone Disease, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Xinghua Zhang
- Department of Acupuncture, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, China
| | - Bo Yuan
- Department of Acupuncture and Pain, Affiliated Hospital of Gansu University of Traditional Chinese Medicine, Lanzhou, China
| | - Haidong Wang
- Department of Rheumatic and Bone Disease, Gansu Provincial Hospital of Traditional Chinese Medicine, Lanzhou, China,*Correspondence: Haidong Wang, ; Xiaozheng Du,
| | - Xiaozheng Du
- Department of Acupuncture-Moxibustion and Tuina, Gansu University of Chinese Medicine, Lanzhou, China,*Correspondence: Haidong Wang, ; Xiaozheng Du,
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Borcherding N, Jia W, Giwa R, Field RL, Moley JR, Kopecky BJ, Chan MM, Yang BQ, Sabio JM, Walker EC, Osorio O, Bredemeyer AL, Pietka T, Alexander-Brett J, Morley SC, Artyomov MN, Abumrad NA, Schilling J, Lavine K, Crewe C, Brestoff JR. Dietary lipids inhibit mitochondria transfer to macrophages to divert adipocyte-derived mitochondria into the blood. Cell Metab 2022; 34:1499-1513.e8. [PMID: 36070756 PMCID: PMC9547954 DOI: 10.1016/j.cmet.2022.08.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/06/2022] [Accepted: 08/15/2022] [Indexed: 02/06/2023]
Abstract
Adipocytes transfer mitochondria to macrophages in white and brown adipose tissues to maintain metabolic homeostasis. In obesity, adipocyte-to-macrophage mitochondria transfer is impaired, and instead, adipocytes release mitochondria into the blood to induce a protective antioxidant response in the heart. We found that adipocyte-to-macrophage mitochondria transfer in white adipose tissue is inhibited in murine obesity elicited by a lard-based high-fat diet, but not a hydrogenated-coconut-oil-based high-fat diet, aging, or a corn-starch diet. The long-chain fatty acids enriched in lard suppress mitochondria capture by macrophages, diverting adipocyte-derived mitochondria into the blood for delivery to other organs, such as the heart. The depletion of macrophages rapidly increased the number of adipocyte-derived mitochondria in the blood. These findings suggest that dietary lipids regulate mitochondria uptake by macrophages locally in white adipose tissue to determine whether adipocyte-derived mitochondria are released into systemic circulation to support the metabolic adaptation of distant organs in response to nutrient stress.
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Affiliation(s)
- Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
| | - Wentong Jia
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Rocky Giwa
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Rachael L Field
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John R Moley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Benjamin J Kopecky
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Mandy M Chan
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Bin Q Yang
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jessica M Sabio
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Emma C Walker
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Omar Osorio
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Andrea L Bredemeyer
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Terri Pietka
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jennifer Alexander-Brett
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Sharon Celeste Morley
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Nada A Abumrad
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Joel Schilling
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kory Lavine
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Clair Crewe
- Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA; Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Jonathan R Brestoff
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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