1
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Peng Y, Zhang M, Hu J. Non-coding RNAs involved in fibroblast-like synoviocyte functioning in arthritis rheumatoid: From pathogenesis to therapy. Cytokine 2024; 173:156418. [PMID: 37952312 DOI: 10.1016/j.cyto.2023.156418] [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: 10/15/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Rheumatoid arthritis (RA) is a polygenic autoimmune disorder with an uncertain etiology, primarily impacting the joints. Moreover, the disease may manifest beyond articular involvement, leading to extra-articular manifestations. Fibroblast-like synoviocytes (FLS) are cells of mesenchymal origin that possess crucial physiological significance within the synovium, contributing to the synthesis of specific constituents found in the synovial fluid and articular cartilage. Consequently, there has been a growing focus on FLS as a potential therapeutic target in the context of RA. Recent investigations have revealed that non-coding RNAs (ncRNAs) serve as pivotal regulators of FLS function, with their dysregulated expression patterns being detected within FLS populations. NcRNAs, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), assume essential functions as regulators of gene expression at both the post-transcriptional and transcriptional levels, and also serve as guiding molecules for chromatin-modifying complexes. Majority of these ncRNAs contribute to various FLS activities including metastasis, proliferation, and cytokine production. In the current work, we comprehensively review the existing literature on ncRNAs, which play pivotal roles in FLS activity and the pathogenesis of RA. Furthermore, this study provides a comprehensive summary and description of the lncRNA/circRNA-miRNA-mRNA regulatory axes in FLS activity, along with potential implications for the RA development. As well, in the final section, we illustrated that therapeutic agents including herbal medicine, and exosomes by modulating ncRNAs regulate FLS activity.
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Affiliation(s)
- Yuwei Peng
- Rheumatology and Immunology, PingXiangPeople's Hospital, No. 8, Wugongshangzhong Avenue, Anyuan District, PiangXiang City, Jiangxi Province, 337000, China
| | - Meng Zhang
- Rheumatology and Immunology, PingXiangPeople's Hospital, No. 8, Wugongshangzhong Avenue, Anyuan District, PiangXiang City, Jiangxi Province, 337000, China
| | - Jiangkang Hu
- Rheumatology and Immunology, PingXiangPeople's Hospital, No. 8, Wugongshangzhong Avenue, Anyuan District, PiangXiang City, Jiangxi Province, 337000, China.
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2
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Han L, Zhang L. CCL21/CCR7 axis as a therapeutic target for autoimmune diseases. Int Immunopharmacol 2023; 121:110431. [PMID: 37331295 DOI: 10.1016/j.intimp.2023.110431] [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: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023]
Abstract
Chemokine receptor 7 (CCR7) is a G protein-coupled receptor containing 7 transmembrane domains that is expressed on various cells, such as naive T/B cells, central memory T cells, regulatory T cells, immature/mature dendritic cells (DCs), natural killer cells, and a minority of tumor cells. Chemokine ligand 21 (CCL21) is the known high-affinity ligand that binds to CCR7 and drives cell migration in tissues. CCL21 is mainly produced by stromal cells and lymphatic endothelial cells, and its expression is significantly increased under inflammatory conditions. Genome-wide association studies (GWAS) have shown a strong association between CCL21/CCR7 axis and disease severity in patients with rheumatoid arthritis, sjogren's syndrome, systemic lupus erythematosus, polymyositis, ankylosing spondylitis, and asthma. Disrupting CCL21/CCR7 interaction with antibodies or inhibitors prevents the migration of CCR7-expressing immune and non-immune cells at the site of inflammation and reduces disease severity. This review emphasizes the importance of the CCL21 /CCR7 axis in autoimmune diseases and evaluates its potential as a novel therapeutic target for these conditions.
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Affiliation(s)
- Le Han
- Department of Pharmacy, The Affiliated Jiangyin Hospital of Southeast University Medical College, Jiangyin 214400, China
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-Inflammatory and Immune Medicine, Ministry of Education, Anhui Collaborative Innovation Centre of Anti-Inflammatory and Immune Medicine, Center of Rheumatoid Arthritis of Anhui Medical University, Hefei 230032, China.
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3
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Distefano R, Ilieva M, Madsen JH, Ishii H, Aikawa M, Rennie S, Uchida S. T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes. Noncoding RNA 2023; 9:30. [PMID: 37218990 PMCID: PMC10204529 DOI: 10.3390/ncrna9030030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Type II diabetes (T2D) is a growing health problem worldwide due to increased levels of obesity and can lead to other life-threatening diseases, such as cardiovascular and kidney diseases. As the number of individuals diagnosed with T2D rises, there is an urgent need to understand the pathogenesis of the disease in order to prevent further harm to the body caused by elevated blood glucose levels. Recent advances in long non-coding RNA (lncRNA) research may provide insights into the pathogenesis of T2D. Although lncRNAs can be readily detected in RNA sequencing (RNA-seq) data, most published datasets of T2D patients compared to healthy donors focus only on protein-coding genes, leaving lncRNAs to be undiscovered and understudied. To address this knowledge gap, we performed a secondary analysis of published RNA-seq data of T2D patients and of patients with related health complications to systematically analyze the expression changes of lncRNA genes in relation to the protein-coding genes. Since immune cells play important roles in T2D, we conducted loss-of-function experiments to provide functional data on the T2D-related lncRNA USP30-AS1, using an in vitro model of pro-inflammatory macrophage activation. To facilitate lncRNA research in T2D, we developed a web application, T2DB, to provide a one-stop-shop for expression profiling of protein-coding and lncRNA genes in T2D patients compared to healthy donors or subjects without T2D.
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Affiliation(s)
- Rebecca Distefano
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
| | - Hideshi Ishii
- Center of Medical Innovation and Translational Research, Department of Medical Data Science, Graduate School of Medicine, Osaka University, Suita 565-0871, Japan;
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Center for Excellence in Vascular Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Rennie
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark;
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.)
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4
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Obaidat D, Giordo R, Kleinbrink EL, Banisad E, Grossman LI, Arshad R, Stark A, Maroun MC, Lipovich L, Fernandez-Madrid F. Non-coding regions of nuclear-DNA-encoded mitochondrial genes and intergenic sequences are targeted by autoantibodies in breast cancer. Front Genet 2023; 13:970619. [PMID: 37082114 PMCID: PMC10111166 DOI: 10.3389/fgene.2022.970619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/15/2022] [Indexed: 03/31/2023] Open
Abstract
Autoantibodies against mitochondrial-derived antigens play a key role in chronic tissue inflammation in autoimmune disorders and cancers. Here, we identify autoreactive nuclear genomic DNA (nDNA)-encoded mitochondrial gene products (GAPDH, PKM2, GSTP1, SPATA5, MFF, TSPOAP1, PHB2, COA4, and HAGH) recognized by breast cancer (BC) patients’ sera as nonself, supporting a direct relationship of mitochondrial autoimmunity to breast carcinogenesis. Autoreactivity of multiple nDNA-encoded mitochondrial gene products was mapped to protein-coding regions, 3’ untranslated regions (UTRs), as well as introns. In addition, autoantibodies in BC sera targeted intergenic sequences that may be parts of long non-coding RNA (lncRNA) genes, including LINC02381 and other putative lncRNA neighbors of the protein-coding genes ERCC4, CXCL13, SOX3, PCDH1, EDDM3B, and GRB2. Increasing evidence indicates that lncRNAs play a key role in carcinogenesis. Consistent with this, our findings suggest that lncRNAs, as well as mRNAs of nDNA-encoded mitochondrial genes, mechanistically contribute to BC progression. This work supports a new paradigm of breast carcinogenesis based on a globally dysfunctional genome with altered function of multiple mitochondrial and non-mitochondrial oncogenic pathways caused by the effects of autoreactivity-induced dysregulation of multiple genes and their products. This autoimmunity-based model of carcinogenesis will open novel avenues for BC treatment.
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Affiliation(s)
- Deya Obaidat
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Roberta Giordo
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Erica L. Kleinbrink
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Emilia Banisad
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Rooshan Arshad
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Azadeh Stark
- Department of Pathology, Henry Ford Health System, Detroit, MI, United States
| | - Marie-Claire Maroun
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Leonard Lipovich
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Shenzhen Huayuan Biotechnology Co. Ltd, Shenzhen Huayuan Biological Science Research Institute, Shenzhen, Guangdong, China
- *Correspondence: Leonard Lipovich, ; Félix Fernandez-Madrid,
| | - Félix Fernandez-Madrid
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
- *Correspondence: Leonard Lipovich, ; Félix Fernandez-Madrid,
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Zhu X, Xu H, Chen B. Inhibition of ox‐LDL‐induced endothelial cell injury by LINC02381 knockdown through the microRNA‐491‐5p/transcription factor 7 axis. Immun Inflamm Dis 2023; 11:e785. [PMID: 36988257 PMCID: PMC10013137 DOI: 10.1002/iid3.785] [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: 10/13/2022] [Revised: 12/26/2022] [Accepted: 01/31/2023] [Indexed: 03/17/2023] Open
Abstract
Atherosclerosis (AS) is a complex multifactorial and chronic inflammatory vascular disease that contributes to the development of cardiovascular diseases. Abnormal cellular proliferation in human umbilical vein endothelial cells (HUVECs) is a crucial element in AS development. In this study, we investigated the potential role of the long noncoding RNA LINC02381/microRNA (miR)‐491‐5p/transcription factor 7 (TCF7) axis in regulating HUVEC injury in 30 participants suffering from AS and 30 healthy control participants. We established an in vitro model of AS in HUVECs using oxidized low‐density lipoprotein (ox‐LDL), and measured cellular mRNA and protein levels of LINC02381, miR‐491‐5p, and TCF7 in serum samples using reverse transcription‐quantitative polymerase chain reaction and Western blotting assays. We evaluated cell viability, apoptosis, and inflammation using Cell Counting Kit‐8, flow cytometry, and enzyme‐linked immunosorbent assays, respectively. Moreover, we analyzed apoptosis‐related protein expression using western blotting analysis and determined the association between miR‐491‐5p and LINC02381 or TCF7 using dual‐luciferase reporter assay, RNA pull‐down, and rescue experiments. We observed that LINC02381 was elevated, while miR‐491‐5p was downregulated in serum samples from participants with AS and in ox‐LDL‐treated HUVECs. LINC02381 knockdown was protective against HUVEC injury via miR‐491‐5p inhibition, which is its downstream target. Rescue experiments further demonstrated that miR‐491‐5p alleviated HUVEC injury by modulating TCF7. Thus, LINC02381 knockdown ameliorated HUVEC injury by regulating the miR‐491‐5p/TCF7 axis, which provides new insights into AS treatment strategies.
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Affiliation(s)
- Xizheng Zhu
- Department of Interventional RadiologyWuhan Asia General HospitalWuhanChina
| | - Hui Xu
- Department of Interventional RadiologyWuhan Asia General HospitalWuhanChina
| | - Beijia Chen
- Department of CardiologyFifth Hospital in WuhanWuhanChina
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LINC02381 suppresses cell proliferation and promotes apoptosis via attenuating IGF1R/PI3K/AKT signaling pathway in breast cancer. Funct Integr Genomics 2023; 23:40. [PMID: 36648607 DOI: 10.1007/s10142-023-00965-w] [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: 10/09/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
Identification of the genes and genetic networks involved in breast cancer development is a major need for prevention and therapy. LINC02381 (lncRNA) has already been introduced as a tumor suppressor in colorectal and gastric cancers. Here, we intended to investigate its potential functional effects on breast cancer. In the analysis performed on RNA-Seq and microarray data, the LINC02381 lncRNA was found to be significantly downregulated in the breast tumors and associated with poor survival of the patients. Then, the differential expression of LINC02381 was confirmed in breast tumor tissues and cancer cell lines using RT-qPCR. Overexpression of LINC02381 resulted in reduced IGF1R and p-AKT expression levels which indicates decreased PI3K pathway activity, detected by RT-qPCR and western blotting. At the cellular level, LINC02381 overexpression was followed by a decreased proliferation rate of transfected breast cell lines, detected by PI flow cytometry, RT-qPCR, colony formation, and MTT assays. Consistently, the results of Annexin-V/PI flow cytometry, RT-qPCR, caspase3/7 activity, and AO/EB-H33342/PI dual staining revealed that LINC02381 overexpression induced apoptosis and cell death. The reduced migration rate of these cells was also verified through wound healing assay and RT-qPCR against the EMT-involved genes. Our data show that LINC02381 exerts its tumor suppressor effect at least partly through attenuation of the IGF1R/PI3K/AKT signaling pathway, which originated from IGF1R downregulation.
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Guo J, Tang C, Shu Z, Guo J, Tang H, Huang P, Ye X, Liang T, Tang K. Single-cell analysis reveals that Jinwu Gutong capsule attenuates the inflammatory activity of synovial cells in osteoarthritis by inhibiting AKR1C3. Front Physiol 2022; 13:1031996. [PMID: 36505054 PMCID: PMC9727177 DOI: 10.3389/fphys.2022.1031996] [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: 08/30/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
Jinwu Gutong capsule (JGC) is a traditional Chinese medicine formula for the treatment of osteoarthritis (OA). Synovitis is a typical pathological change in OA and promotes disease progression. Elucidating the therapeutic mechanism of JGC is crucial for the precise treatment of OA synovitis. In this study, we demonstrate that JGC effectively inhibits hyperproliferation, attenuates inflammation, and promotes apoptosis of synovial cells. Through scRNA-seq data analysis of OA synovitis, we dissected two distinct cell fates that influence disease progression (one fate led to recovery while the other fate resulted in deterioration), which illustrates the principles of fate determination. By intersecting JGC targets with synovitis hub genes and then mimicking picomolar affinity interactions between bioactive compounds and binding pockets, we found that the quercetin-AKR1C3 pair exhibited the best affinity, indicating that this pair constitutes the most promising molecular mechanism. In vitro experiments confirmed that the expression of AKR1C3 in synovial cells was reduced after JGC addition. Further overexpression of AKR1C3 significantly attenuated the therapeutic efficacy of JGC. Thus, we revealed that JGC effectively treats OA synovitis by inhibiting AKR1C3 expression.
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Affiliation(s)
- Junfeng Guo
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Chuyue Tang
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Zhao Shu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Junfeng Guo
- Department of Stomatology, The 970th Hospital of the Joint Logistics Support Force, Yantai, China
| | - Hong Tang
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Pan Huang
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xiao Ye
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Taotao Liang
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China,*Correspondence: Kanglai Tang, ; Taotao Liang,
| | - Kanglai Tang
- State Key Laboratory of Trauma, Burn and Combined Injury, Department of Orthopedics/Sports Medicine Center, Southwest Hospital, Third Military Medical University, Chongqing, China,*Correspondence: Kanglai Tang, ; Taotao Liang,
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8
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Ravaei A, Zimmer-Bensch G, Govoni M, Rubini M. lncRNA-mediated synovitis in rheumatoid arthritis: A perspective for biomarker development. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:103-119. [PMID: 36126801 DOI: 10.1016/j.pbiomolbio.2022.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/28/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) are a regulatory class of noncoding RNAs with a wide range of activities such as transcriptional and post-transcriptional regulations. Emerging evidence has demonstrated that various lncRNAs contribute to the initiation and progression of Rheumatoid Arthritis (RA) through distinctive mechanisms. The present study reviews the recent findings on lncRNA role in RA development. It focuses on the involvement of different lncRNAs in the main steps of RA pathogenesis including T cell activation, cytokine dysregulation, fibroblast-like synoviocyte (FLS) activation and joint destruction. Besides, it discusses the current findings on RA diagnosis and the potential of lncRNAs as diagnostic, prognostic and predictive biomarkers in Rheumatology clinic.
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Affiliation(s)
- Amin Ravaei
- Department of Neurosciences and Rehabilitation, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy.
| | - Geraldine Zimmer-Bensch
- Division of Neuroepigenetics, Institute of Zoology (Biology II), RWTH Aachen University, Aachen, Germany.
| | - Marcello Govoni
- Department of Medical Science, Section of Rheumatology, University of Ferrara, Ferrara, Italy.
| | - Michele Rubini
- Department of Neurosciences and Rehabilitation, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy.
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Jiang SQ, Pan T, Yu JL, Zhang Y, Wang T, Li P, Li F. Thermal and wine processing enhanced Clematidis Radix et Rhizoma ameliorate collagen Ⅱ induced rheumatoid arthritis in rats. JOURNAL OF ETHNOPHARMACOLOGY 2022; 288:114993. [PMID: 35032583 DOI: 10.1016/j.jep.2022.114993] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Clematidis Radix et Rhizoma, a kind of traditional Chinese medicine, is derived from Clematis chinensis Osbeck, Clematis hexapetala Pall. and Clematis manshurica Rupr. This herb shows great effects on expelling wind and dispelling dampness in ancient and it has anti-inflammatory and analgesic activity in modern clinical application. AIM OF THE STUDY This experiment aimed to research anti-rheumatoid arthritis effect of crude and wine processed RC based on glycolysis metabolism to provide new ideas treating RA. MATERIALS AND METHODS Network pharmacology was applied to preliminarily forecast the potential pathways of common targets of RC and RA. RAW264.7 macrophages were induced by LPS, NO production, glucose uptake, lactate production, ROS and MMP were detected as instructions in vitro. ELISA was used to measure the content of HK2, PKM2 and LDHA involving in glycolysis process. Gut microbiota was analyzed by 16S rRNA gene amplicon sequencing in CIA rats. RESULTS Crude and wine processed RC had good anti-inflammatory effect by reducing NO in RAW264.7 macrophages and ameliorating inflammatory infiltration and cartilage surface erosion in CIA rats. Whether in LPS-induced macrophages or CIA rats, crude and wine processed RC could inhibit glycolysis by down-regulating the expression of PKM2, causing less glucose uptake and lactic acid, which lead to less ROS and higher MMP to normal. PI3K-AKT and HIF-1α pathways were deduced to possibly play a crucial part in controlling glycolysis metabolism by network pharmacology analysis. Besides, it was displayed that Firmicutes and Bacteroidetes were prominent gut microbiota in CIA rats feces. CC-H and PZ-H groups could both increase the relative abundance of Firmicutes and decrease Bacteroidetes. These microbiota also played a role in RA pathological process via involving in energy metabolism, carbohydrate metabolism and immune system. CONCLUSION Crude and wine processed RC have a good influence in ameliorating rheumatoid arthritis by inhibiting glycolysis and modulating gut microbiota together.
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Affiliation(s)
- Si-Qi Jiang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ting Pan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Jia-Lin Yu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ying Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China
| | - Ting Wang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Resource, Yunnan University of Chinese Medicine, Kunming, 650000, PR China.
| | - Ping Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China.
| | - Fei Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, 210009, PR China; School of Pharmacy, Xinjiang Medical University, Urumqi, 830011, PR China.
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10
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Yang C, Li D, Teng D, Zhou Y, Zhang L, Zhong Z, Yang GJ. Epigenetic Regulation in the Pathogenesis of Rheumatoid Arthritis. Front Immunol 2022; 13:859400. [PMID: 35401513 PMCID: PMC8989414 DOI: 10.3389/fimmu.2022.859400] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/03/2022] [Indexed: 12/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease. The etiology of RA remains undetermined and the pathogenesis is complex. There remains a paucity of ideal therapeutic drugs and treatment strategies. The epigenetic modifications affect and regulate the function and characteristics of genes through mechanisms, including DNA methylation, histone modification, chromosome remodeling, and RNAi, thereby exerting a significant impact on the living state of the body. Recently, the phenomenon of epigenetic modification in RA has garnered growing research interest. The application of epigenetically modified methods is the frontier field in the research of RA pathogenesis. This review highlights the research on the pathogenesis of RA based on epigenetic modification in the recent five years, thereby suggesting new methods and strategies for the diagnosis and treatment of RA.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, China
| | - Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dehong Teng
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, China
| | - Yueru Zhou
- Department of Chemical Engineering, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Lei Zhang
- Department of Chemical Engineering, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR, China
- *Correspondence: Zhangfeng Zhong, ; Guan-Jun Yang,
| | - Guan-Jun Yang
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, China
- *Correspondence: Zhangfeng Zhong, ; Guan-Jun Yang,
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11
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Yin M, Zhai L, Wang J, Yu Q, Li T, Xu X, Guo X, Mao X, Zhou J, Zhang X. Comprehensive Analysis of RNA-Seq in Endometriosis Reveals Competing Endogenous RNA Network Composed of circRNA, lncRNA and mRNA. Front Genet 2022; 13:828238. [PMID: 35391800 PMCID: PMC8980742 DOI: 10.3389/fgene.2022.828238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/21/2022] [Indexed: 01/01/2023] Open
Abstract
Although long non coding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in the pathogenesis of diseases, endometriosis related lncRNAs and circRNAs are still rarely reported. This study focused on the potential molecular mechanism of endometriosis related competitive endogenous RNA (ceRNA) composed of lncRNAs and circRNAs. We performed high-throughout sequencing of six normal endometria, six eutopic endometria and six ectopic endometria for the first time to describe and analyze the expression profile of lncRNA, circRNA and mRNA. Our results showed that 140 lncRNAs, 107 circRNAs and 1,206 mRNAs were differentially expressed in the ectopic group, compared with the normal and eutopic groups. We established an lncRNA/circRNA-mRNA co-expression network using pearson correlation test. Meanwhile, the results of Gene set enrichment analysis analysis showed that the 569 up-regulated differentially expressed mRNA (DEmRNA) were mainly related to the epithelial-mesenchymal transition, regulation of immune system process and immune effector process. Subsequently, we established a DElncRNA-miRNA and DEcircRNA-miRNA network using the starbase database, identified the common miRNAs and constructed DElncRNA/DEcircRNA-miRNA pairs. miRDB, Targetscan, miRwalk and circRNA/lncRNA-mRNA pairs jointly determined the miRNA-mRNA portion of the circRNA/lncRNA-miRNA-mRNA co-expression network. RT-qPCR results of 15 control samples and 25 ectopic samples confirmed that circGLIS2, circFN1, LINC02381, IGFL2-AS1, CD84, LYPD1 and FAM163A were significantly overexpressed in ectopic tissues. In conclusion, this is the first study to illustrate ceRNA composed of differentially expressed circRNA, lncRNA and mRNA in endometriosis. We also found that lncRNA and circRNA exerted a pivotal function on the pathogenesis of endometriosis, which can provide new insights for further exploring the pathogenesis of endometriosis and identifying new targets.
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Affiliation(s)
- Meichen Yin
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lingyun Zhai
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jianzhang Wang
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qin Yu
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Tiantian Li
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinxin Xu
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinyue Guo
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinqi Mao
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianwei Zhou
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Jianwei Zhou, ; Xinmei Zhang,
| | - Xinmei Zhang
- Department of Obstetrics and Gynecology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jianwei Zhou, ; Xinmei Zhang,
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12
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Long Intergenic Non-Protein Coding RNA 02381 Promotes the Proliferation and Invasion of Ovarian Endometrial Stromal Cells through the miR-27b-3p/CTNNB1 Axis. Genes (Basel) 2022; 13:genes13030433. [PMID: 35327987 PMCID: PMC8955621 DOI: 10.3390/genes13030433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Purpose: Catenin Beta 1 (CTNNB1) is a key regulator of cell proliferation and invasion in endometriosis; however, its upstream factor is not clear. Long noncoding RNAs may participate in endometriosis. The aim of this study was to investigate the mechanism of interaction between LINC02381 and CTNNB1 in endometriosis. Method: Screening and validation of RNAs were completed by whole transcriptional sequencing and qRT-PCR. The subcellular localization of LINC02381 was determined by RNA in situ hybridization and nucleo-cytoplasmic separation. Plasmids were transfected for functional experiments. Luciferase assay was used to verify the binding relationship. Results: The expression of LINC02381 and CTNNB1 was significantly increased in ovarian ectopic endometrial tissues (OSAs) and ectopic endometrial stromal cells (ESCs). When LINC02381 was downregulated in ESCs, the expression of CTNNB1, metallopeptidase 9 (MMP9) and cyclinD1, as well as ESCs invasion and proliferation, decreased. LINC02381 was mainly present in the cytoplasm of ESCs, indicating that it may act as a competitive endogenous RNA. Bioinformatic analysis revealed that microRNA-27b-3p (miR-27b-3p) is a downstream target of LINC02381. miR-27b-3p decreased in OSAs and ESCs. Moreover, when miR-27b-3p was upregulated in ESCs, the expression of CTNNB1, MMP9 and cyclinD1, as well as the invasion and proliferation ability of ESCs, were reduced. Additionally, rescue experiments demonstrated that the expression of CTNNB1, MMP9 and cyclinD1, as well as the invasion and proliferation ability, were significantly increased in the group transfected with both sh-LINC02381 and a miR-27b-3p inhibitor. Conclusion: LINC02381 upregulated CTNNB1 by adsorbing miR-27b-3p, causing increased proliferation and invasion of ESCs.
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Saliani M, Mirzaiebadizi A, Mosaddeghzadeh N, Ahmadian MR. RHO GTPase-Related Long Noncoding RNAs in Human Cancers. Cancers (Basel) 2021; 13:5386. [PMID: 34771549 PMCID: PMC8582479 DOI: 10.3390/cancers13215386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
RHO GTPases are critical signal transducers that regulate cell adhesion, polarity, and migration through multiple signaling pathways. While all these cellular processes are crucial for the maintenance of normal cell homeostasis, disturbances in RHO GTPase-associated signaling pathways contribute to different human diseases, including many malignancies. Several members of the RHO GTPase family are frequently upregulated in human tumors. Abnormal gene regulation confirms the pivotal role of lncRNAs as critical gene regulators, and thus, they could potentially act as oncogenes or tumor suppressors. lncRNAs most likely act as sponges for miRNAs, which are known to be dysregulated in various cancers. In this regard, the significant role of miRNAs targeting RHO GTPases supports the view that the aberrant expression of lncRNAs may reciprocally change the intensity of RHO GTPase-associated signaling pathways. In this review article, we summarize recent advances in lncRNA research, with a specific focus on their sponge effects on RHO GTPase-targeting miRNAs to crucially mediate gene expression in different cancer cell types and tissues. We will focus in particular on five members of the RHO GTPase family, including RHOA, RHOB, RHOC, RAC1, and CDC42, to illustrate the role of lncRNAs in cancer progression. A deeper understanding of the widespread dysregulation of lncRNAs is of fundamental importance for confirmation of their contribution to RHO GTPase-dependent carcinogenesis.
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Affiliation(s)
- Mahsa Saliani
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Amin Mirzaiebadizi
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Mohammad Reza Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
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Priyanka P, Sharma M, Das S, Saxena S. The lncRNA HMS recruits RNA-binding protein HuR to stabilize the 3'-UTR of HOXC10 mRNA. J Biol Chem 2021; 297:100997. [PMID: 34302808 PMCID: PMC8363838 DOI: 10.1016/j.jbc.2021.100997] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to drive key cancer pathways but the functions of majority of lncRNAs are unknown making a case for comprehensive functional evaluation of lncRNAs. With an aim to identify lncRNAs dysregulated in human cancers, we analyzed the cancer patient database of lung adenocarcinoma (LUAD), which revealed an upregulated lncRNA, LINC02381 (renamed HOXC10mRNA stabilizing factor or HMS in this study), whose depletion results in proliferation defects and inhibition of colony formation of human cancer cells. In order to identify the binding targets of HMS, we screened for cis-genes and discovered that HOXC10, an oncogene, is downregulated in the absence of HMS. Depletion of HMS does not affect the HOXC10 promoter activity but inhibits the HOXC10 3′-UTR-linked luciferase reporter activity. Since lncRNAs have been known to associate with RNA-binding proteins (RBPs) to stabilize mRNA transcripts, we screened for different RBPs and discovered that HuR, an ELAV family protein, stabilizes HOXC10 mRNA. Using RNA pull-down and deletion mapping experiments, we show that HuR physically interacts with the cytosine-rich stretch of HMS and HOXC10 3′-UTR to stabilize HOXC10 mRNA. HOXC10 is overexpressed in many human cancers, and our discovery highlights that lncRNA HMS sustains the HOXC10 mRNA levels to maintain the invasive phenotypes of cancer cells.
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Affiliation(s)
- Priyanka Priyanka
- DNA Replication and Cell Cycle Laboratory, National Institute of Immunology, New Delhi, India
| | | | - Sanjeev Das
- DNA Replication and Cell Cycle Laboratory, National Institute of Immunology, New Delhi, India
| | - Sandeep Saxena
- DNA Replication and Cell Cycle Laboratory, National Institute of Immunology, New Delhi, India; Department of Biotechnology, JNU, New Delhi, India.
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15
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Yan YM, Zheng JN, Wu LW, Rao QW, Yang QR, Gao D, Wang Q. Prediction of a Competing Endogenous RNA Co-expression Network by Comprehensive Methods in Systemic Sclerosis-Related Interstitial Lung Disease. Front Genet 2021; 12:633059. [PMID: 34290731 PMCID: PMC8287190 DOI: 10.3389/fgene.2021.633059] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/16/2021] [Indexed: 11/27/2022] Open
Abstract
Systemic sclerosis (SSc) is an immune-mediated connective tissue disease characterized by fibrosis of multi-organs, and SSc-related interstitial lung disease (SSc-ILD) is a leading cause of morbidity and mortality. To explore molecular biological mechanisms of SSc-ILD, we constructed a competing endogenous RNA (ceRNA) network for prediction. Expression profiling data were obtained from the Gene Expression Omnibus (GEO) database, and differential expressed mRNAs and miRNAs analysis was further conducted between normal lung tissue and SSc lung tissue. Also, the interactions of miRNA–lncRNA, miRNA–mRNA, and lncRNA–mRNA were predicted by online databases including starBase, LncBase, miRTarBase, and LncACTdb. The ceRNA network containing 11 lncRNAs, 7 miRNAs, and 20 mRNAs were constructed. Based on hub genes and miRNAs identified by weighted correlation network analysis (WGCNA) method, three core sub-networks—SNHG16, LIN01128, RP11-834C11.4(LINC02381)/hsa-let-7f-5p/IL6, LINC01128/has-miR-21-5p/PTX3, and LINC00665/hsa-miR-155-5p/PLS1—were obtained. Combined with previous studies and enrichment analyses, the lncRNA-mediated network affected LPS-induced inflammatory and immune processes, fibrosis development, and tumor microenvironment variations. The ceRNA network, especially three core sub-networks, may be served as early biomarkers and potential targets for SSc, which also provides further insights into the occurrence, progression, and accurate treatment of SSc at the molecular level.
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Affiliation(s)
- Yue-Mei Yan
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ji-Na Zheng
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Li-Wei Wu
- Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qian-Wen Rao
- Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiao-Rong Yang
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Di Gao
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiang Wang
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
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16
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Chauhan RK, Sharma PK, Srivastava S. Role of signaling pathway in biological cause of Rheumatoid arthritis. Curr Drug Res Rev 2020; 13:130-139. [PMID: 33172384 DOI: 10.2174/2589977512999201109215004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/14/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
Rheumatoid Arthritis is a chronic progressive inflammatory auto-immune disease in which the immune system of the body attacks its cartilage and joints lining. It not only affects synovial joints but also many other sites including heart, blood vessels, and skins. It is more common in females than in males. The exact cause of rheumatoid arthritis is not well established but the hypothesis reported in the literature is that in the development stage of the disease, both genetics and environmental factors can play an inciting role. Along with these factors alteration in the normal physiology of enzymatic action, acts as a trigger to develop this condition. Numerous signaling pathways involved in the pathogenesis of Rheumatoid Arthritis involves activation of mitogen-activated protein kinase, kinases Janus family, P-38 Mitogen-Activated Protein Kinase, Nuclear Factor-kappa B. Interleukin-1 to play a proinflammatory cytokine that plays an important role in inflammation in RA. These are also associated with an increase in neutrophil, macrophage and lymphocytic chemotaxis, mast cell degranulation, activation, maturation and survival of T-cells and B-cells activated. These signaling pathways also show that p38α downregulation in myeloid cells exacerbates the severity of symptoms of arthritis. Thus, present review carters about the detail of different signaling pathways and their role in rheumatoid arthritis.
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Affiliation(s)
- Rakesh Kumar Chauhan
- Department of Pharmacy, School of Medical and Allied Science, Galgotias University, Plot N. 2, Sector 17- A, Yamuna Expressway, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh 201306,. India
| | - Pramod Kumar Sharma
- Department of Pharmacy, School of Medical and Allied Science, Galgotias University, Plot N. 2, Sector 17- A, Yamuna Expressway, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh 201306,. India
| | - Shikha Srivastava
- Department of Pharmacy, School of Medical and Allied Science, Galgotias University, Plot N. 2, Sector 17- A, Yamuna Expressway, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh 201306,. India
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17
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Jafarzadeh M, Soltani BM. Long Noncoding RNA LOC400043 (LINC02381) Inhibits Gastric Cancer Progression Through Regulating Wnt Signaling Pathway. Front Oncol 2020; 10:562253. [PMID: 33194632 PMCID: PMC7645048 DOI: 10.3389/fonc.2020.562253] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is one of the common causes of cancer mortality worldwide, with a low survival rate for the affected people. Recent studies have revealed the key role of long non-coding RNAs (lncRNAs) in the development and progression of many cancers, including gastric cancer. Looking for the potential molecular regulators of gastric cancer incidence and progression, LINC02381 was identified as a downregulated lncRNA in gastric cancer tissues by analysis of available microarray and RNA-seq data and RT-qPCR confirmed this differential expression. MiR-21, miR-590, and miR-27a miRNAs were predicted to be sponged by LINC02381, and dual luciferase assay verified LINC02381 as a competitive endogenous RNA (CeRNA), which binds to them. Furthermore, we found that increased expression of LINC02381 attenuates Wnt pathway activity. Also, functional analysis indicates that LINC02381 arrests cell cycle, increases apoptosis and caspase activity, and reduces cell survival and proliferation rate of the human gastric cancer cell lines AGS and MKN45. Moreover, EMT analysis showed that LINC02381 is involved in gastric cancer progression and inhibits metastasis. Overall, this work for the first time introduces LINC02381 as a CeRNA involved in gastric cancer and provides novel insight into the molecular pathogenesis of gastric cancer.
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Affiliation(s)
| | - Bahram M. Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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