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Xu Y, Yang Z, Wang T, Hu L, Jiao S, Zhou J, Dai T, Feng Z, Li S, Meng Q. From molecular subgroups to molecular targeted therapy in rheumatoid arthritis: A bioinformatics approach. Heliyon 2024; 10:e35774. [PMID: 39220908 PMCID: PMC11365346 DOI: 10.1016/j.heliyon.2024.e35774] [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: 10/13/2023] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/04/2024] Open
Abstract
1Background Rheumatoid Arthritis (RA) is a heterogeneous autoimmune disease with multiple unidentified pathogenic factors. The inconsistency between molecular subgroups poses challenges for early diagnosis and personalized treatment strategies. In this study, we aimed to accurately distinguish RA patients at the transcriptome level using bioinformatics methods. 2Methods We collected a total of 362 transcriptome datasets from RA patients in three independent samples from the GEO database. Consensus clustering was performed to identify molecular subgroups, and clinical features were assessed. Differential analysis was employed to annotate the biological functions of specifically upregulated genes between subgroups. 3Results Based on consensus clustering of RA samples, we identified three robust molecular subgroups, with Subgroup III representing the high-risk subgroup and Subgroup II exhibiting a milder phenotype, possibly associated with relatively higher levels of autophagic ability. Subgroup I showed biological functions mainly related to viral infections, cellular metabolism, protein synthesis, and inflammatory responses. Subgroup II involved autophagy of mitochondria and organelles, protein localization, and organelle disassembly pathways, suggesting heterogeneity in the autophagy process of mitochondria that may play a protective role in inflammatory diseases. Subgroup III represented a high-risk subgroup with pathological processes including abnormal amyloid precursor protein activation, promotion of inflammatory response, and cell proliferation. 4Conclusion The classification of the RA dataset revealed pathological heterogeneity among different subgroups, providing new insights and a basis for understanding the molecular mechanisms of RA, identifying potential therapeutic targets, and developing personalized treatment approaches.
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Affiliation(s)
- Yangyang Xu
- Guizhou Medical University, Guiyang City, Guizhou Province, China
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
| | - Zhenyu Yang
- Jinan University, Guangzhou, Guangdong Province, China
- Xuzhou New Health Hospital, North Hospital of Xuzhou Cancer Hospital, Xuzhou City, Jiangsu Province, China
| | - Tengyan Wang
- Guizhou Hospital of The First Affiliated Hospital, Sun Yat-Sen University, Guiyang City, Guizhou Province, China
| | - Liqiong Hu
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
| | - Songsong Jiao
- Jinan University, Guangzhou, Guangdong Province, China
| | - Jiangfei Zhou
- Jinan University, Guangzhou, Guangdong Province, China
| | - Tianming Dai
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
| | - Zhencheng Feng
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
| | - Siming Li
- Guizhou Medical University, Guiyang City, Guizhou Province, China
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
| | - Qinqqi Meng
- Guangzhou Red Cross Hospital Affiliated of Jinan University, Guangzhou, Guangdong Province, China
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Wang Y, Yan H, Zhao L, He XL, Bao TRG, Sun XD, Yang YC, Zhu SY, Gao XX, Wang AH, Jia JM. An integrated network pharmacology approach reveals that Darutigenol reduces inflammation and cartilage degradation in a mouse collagen-induced arthritis model by inhibiting the JAK-STAT3 pathway. JOURNAL OF ETHNOPHARMACOLOGY 2023; 314:116574. [PMID: 37160212 DOI: 10.1016/j.jep.2023.116574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/27/2023] [Accepted: 05/01/2023] [Indexed: 05/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Darutigenol (DL) is a natural active product derived from the Chinese herbal medicine Sigesbeckia glabrescens (Makino) Makino. It is administered as a traditional Chinese medicine (TCM) to dispel rheumatism, benefit the joints, and detoxify. However, its potential mechanism in the treatment of rheumatoid arthritis (RA) remains unknown. AIMS OF THE STUDY The objectives of this research were to determine the effects and elucidate the modes of action of DL on RA-related joint inflammation. MATERIALS AND METHODS Network pharmacology and molecular docking were used to screen and validate candidate DL targets for RA treatment, respectively. A DBA/1 mouse rheumatoid arthritis model was induced with bovine type II collagen. Intragastric DL administration was followed by the calculation of the clinical arthritis index. A section of the ankle joint was excised and stained and the pathological changes in it were observed. Enzyme-linked immunosorbent assays (ELISA) and western blotting (WB) were used to clarify the mechanisms of DL in RA treatment. RESULTS DL effectively attenuated the inflammation, mitigated the articular cartilage degradation, and bone erosion, and alleviated the inflammatory joints associated with RA. Network pharmacology screened six key targets of DL while molecular docking revealed that it docked well with its protein targets. The DL treatment group presented with significantly less ankle joint redness and swelling, a lower arthritis index scores and serum and bone marrow supernatant IL-6 levels, more complete ankle joint surfaces, and less synovial inflammation, cartilage degradation, and bone erosion than the collagen-induced arthritis (CIA) group. The DL treatment also substantially downregulated the Janus kinase (JAK)1, JAK3, matrix metalloproteinase (MMP)2, MMP9, and phospho-signal transducer and activator of transcription (p-STAT)3 proteins in the joints. CONCLUSIONS To the best of our knowledge, the present work was the first to demonstrate that DL has significant anti-inflammatory efficacy and reduces cartilage degradation and bone erosion. It also demonstrated that the anti-RA effect of DL may be explained by its ability to inhibit joint inflammation and reduce articular cartilage degradation through the interleukin (IL)-6/JAK1,3/STAT3 axis and downregulate MMP2 and MMP9. Hence, DL might play a therapeutic role in a mouse RA model.
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Affiliation(s)
- Yong Wang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Hui Yan
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Long Zhao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xue-Lai He
- School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan, 442000, People's Republic of China; Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Shiyan, 442000, People's Republic of China
| | - Te-Ri-Gen Bao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xian-Duo Sun
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Yong-Cheng Yang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Shu-Yi Zhu
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xiao-Xu Gao
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - An-Hua Wang
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Jing-Ming Jia
- Teaching and Research Department of Chinese Materia Medica Resources, College of Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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Alam A, Abubaker Bagabir H, Sultan A, Siddiqui MF, Imam N, Alkhanani MF, Alsulimani A, Haque S, Ishrat R. An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases. Front Pharmacol 2022; 12:770762. [PMID: 35153741 PMCID: PMC8829040 DOI: 10.3389/fphar.2021.770762] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/27/2021] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent. The estimated total global TB deaths in 2019 were 1.4 million. The decline in TB incidence rate is very slow, while the burden of noncommunicable diseases (NCDs) is exponentially increasing in low- and middle-income countries, where the prevention and treatment of TB disease remains a great burden, and there is enough empirical evidence (scientific evidence) to justify a greater research emphasis on the syndemic interaction between TB and NCDs. The current study was proposed to build a disease-gene network based on overlapping TB with NCDs (overlapping means genes involved in TB and other/s NCDs), such as Parkinson’s disease, cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and lung cancer. We compared the TB-associated genes with genes of its overlapping NCDs to determine the gene-disease relationship. Next, we constructed the gene interaction network of disease-genes by integrating curated and experimentally validated interactions in humans and find the 13 highly clustered modules in the network, which contains a total of 86 hub genes that are commonly associated with TB and its overlapping NCDs, which are largely involved in the Inflammatory response, cellular response to cytokine stimulus, response to cytokine, cytokine-mediated signaling pathway, defense response, response to stress and immune system process. Moreover, the identified hub genes and their respective drugs were exploited to build a bipartite network that assists in deciphering the drug-target interaction, highlighting the influential roles of these drugs on apparently unrelated targets and pathways. Targeting these hub proteins by using drugs combination or drug repurposing approaches will improve the clinical conditions in comorbidity, enhance the potency of a few drugs, and give a synergistic effect with better outcomes. Thus, understanding the Mycobacterium tuberculosis (Mtb) infection and associated NCDs is a high priority to contain its short and long-term effects on human health. Our network-based analysis opens a new horizon for more personalized treatment, drug-repurposing opportunities, investigates new targets, multidrug treatment, and can uncover several side effects of unrelated drugs for TB and its overlapping NCDs.
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Affiliation(s)
- Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Hala Abubaker Bagabir
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Armiya Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | | | - Nikhat Imam
- Department of Mathematics, Institute of Computer Science and Information Technology, Magadh University, Bodh Gaya, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Marsh LJ, Kemble S, Reis Nisa P, Singh R, Croft AP. Fibroblast pathology in inflammatory joint disease. Immunol Rev 2021; 302:163-183. [PMID: 34096076 DOI: 10.1111/imr.12986] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis is an immune-mediated inflammatory disease in which fibroblasts contribute to both joint damage and inflammation. Fibroblasts are a major cell constituent of the lining of the joint cavity called the synovial membrane. Under resting conditions, fibroblasts have an important role in maintaining joint homeostasis, producing extracellular matrix and joint lubricants. In contrast, during joint inflammation, fibroblasts contribute to disease pathology by producing pathogenic levels of inflammatory mediators that drive the recruitment and retention of inflammatory cells within the joint. Recent advances in single-cell profiling techniques have transformed our ability to examine fibroblast biology, leading to the identification of specific fibroblast subsets, defining a previously underappreciated heterogeneity of disease-associated fibroblast populations. These studies are challenging the previously held dogma that fibroblasts are homogeneous and are providing unique insights into their role in inflammatory joint pathology. In this review, we discuss the recent advances in our understanding of how fibroblast heterogeneity contributes to joint pathology in rheumatoid arthritis. Finally, we address how these insights could lead to the development of novel therapies that directly target selective populations of fibroblasts in the future.
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Affiliation(s)
- Lucy-Jayne Marsh
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Samuel Kemble
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Patricia Reis Nisa
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Ruchir Singh
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
| | - Adam P Croft
- Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), Queen Elizabeth Hospital, University of Birmingham, Birmingham, UK
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