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Miaskowski C, Conley YP, Cooper BA, Paul SM, Smoot BJ, Hammer MJ, Fu M, Levine JD. Identification Of A Higher Risk Lymphedema Phenotype And Associations With Cytokine Gene Polymorphisms. J Pain Symptom Manage 2024; 67:375-383.e3. [PMID: 38307372 DOI: 10.1016/j.jpainsymman.2024.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/04/2024]
Abstract
CONTEXT Breast cancer-related lymphedema (BCRL) is chronic condition that occurs in 5% to 75% of women following treatment for breast cancer. However, little is known about the risk factors and mechanisms associated with a worse BCRL profile. OBJECTIVES Identify distinct BCRL profiles in women with the condition (i.e., lower vs. higher risk phenotype) and evaluate for associations with pro- and anti-inflammatory genes. METHODS Latent class profile analysis (LCPA) was used to identify the BCRL profiles using phenotypic characteristics evaluated prior to surgery. Candidate gene analyses were done to identify cytokine genes associated with the two BCRL profiles. RESULTS Of the 155 patients evaluated, 35.5% (n = 55) were in the Lower and 64.5% (n = 100) were in the Higher Risk classes. Risk factors for membership in the Higher class included: lower functional status, having sentinel lymph node biopsy, axillary lymph node dissection, mastectomy, higher number of positive lymph nodes, and receipt of chemotherapy. Polymorphisms for interleukin (IL)1-beta and IL6 were associated with membership in the Higher Risk class. CONCLUSION The readily available and clinically relevant phenotypic characteristics associated with a worse BCRL profile can be used by clinicians to identify higher risk patients. If confirmed, these characteristics can be tested in predictive risk models. In addition, the candidate gene findings may guide the development of mechanistically-based interventions to decrease the risk of BCRL.
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Affiliation(s)
- Christine Miaskowski
- School of Nursing, University of California, San Francisco, CA, USA; School of Medicine, University of California, San Francisco, CA, USA.
| | | | - Bruce A Cooper
- School of Nursing, University of California, San Francisco, CA, USA
| | - Steven M Paul
- School of Nursing, University of California, San Francisco, CA, USA
| | - Betty J Smoot
- School of Medicine, University of California, San Francisco, CA, USA
| | | | - Mei Fu
- School of Nursing and Health Studies, University of Missouri, Kansas City, MO, USA
| | - Jon D Levine
- School of Medicine, University of California, San Francisco, CA, USA
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Gong B, Li M, Wang Z, Hao G, Sun L, Zhang J, Yuan L. Integrated analysis of circRNA- related ceRNA network targeting neuroinflammation in medial temporal lobe epilepsy. Brain Res Bull 2024; 209:110908. [PMID: 38402995 DOI: 10.1016/j.brainresbull.2024.110908] [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: 08/21/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND medial temporal lobe epilepsy (mTLE) is among the most common types of temporal lobe epilepsy (TLE) ,it is generally resistant to drug treatment, which significantly impacts the quality of life and treatment. Research on novel therapeutic approaches for mTLE has become a current focus. Our study aims to construct and analyze a competing endogenous RNA (ceRNA) network that targets neuroinflammation using publicly available data, which may offer a novel therapeutic approach for mTLE. METHODS we utilized the R package to analyze GSE186334 downloaded from Gene Expression Omnibus database, subsequently constructing and identifying hub network within the ceRNA network using public databases. Lastly, we validated the expressions and interactions of some nodes within the hub ceRNA network in Sombati cell model. RESULTS our transcriptome analysis identified 649 differentially expressed (DE) mRNAs (273 up-regulated, 376 down-regulated) and 36 DE circRNAs (11 up-regulated, 25 down-regulated) among mTLE patients. A total of 23 candidate DE mRNAs associated with neuroinflammation were screened, and two ceRNA networks were constructed. A hub network was further screened which included 3 mRNAs, 22 miRNAs, and 11 circRNAs. Finally, we confirmed the hsa-miR-149-5p is crucial in the regulatory effect of hsa_circ_0005145 on IL - 1α in the hub network. CONCLUSIONS In summary, our study identified a hub ceRNA network and validated a potential circRNA-miRNA-mRNA axis targeting neuroinflammation. The results of our research may serve as a potential therapeutic target for mTLE.
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Affiliation(s)
- Bingzheng Gong
- The Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China
| | - Mian Li
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Ziru Wang
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Gulingyue Hao
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Liang Sun
- College of Artificial Intelligence and Big Data for Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
| | - Jingjun Zhang
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
| | - Liangjie Yuan
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
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Zhang X, Shao R. LncRNA SNHG8 upregulates MUC5B to induce idiopathic pulmonary fibrosis progression by targeting miR-4701-5p. Heliyon 2024; 10:e23233. [PMID: 38163156 PMCID: PMC10756985 DOI: 10.1016/j.heliyon.2023.e23233] [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: 06/28/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play a critical role in idiopathic pulmonary fibrosis (IPF); however, the underlying molecular mechanisms are unclear. Our study demonstrated that lncRNA small nucleolar RNA host gene 8 (SNHG8) was increased in bleomycin (BLM)-induced A549 cells. LncRNA SNHG8 overexpression further elevated fibrosis-related factors monocyte chemotactic protein 1 (MCP1), CC motif chemokine ligand 18 (CCL18), and α-smooth muscle actin (α-SMA), as well as increased collagen type I alpha-1 chain (COL1A1) and collagen type III alpha-1 chain (COL3A1). Meanwhile, lncRNA SNHG8 knockdown exhibited an opposite role in reducing BLM-induced pulmonary fibrosis. With regard to the mechanism, SNHG8 was then revealed to act as a competing endogenous RNA (ceRNA) for microRNA (miR)-4701-5p in regulating Mucin 5B (MUC5B) expression. Furthermore, the interactions between SNHG8 and miR-4701-5p, between miR-4701-5p and MUC5B, and between SNHG8 and MUC5B on the influence of fibrosis-related indicators were confirmed, respectively. In addition, SNHG8 overexpression enhanced the levels of transforming growth factor (TGF)-β1 and phosphorylation Smad2/3 (p-Smad2/3), which was suppressed by SNHG8 knockdown in BLM-induced A549 cells. Moreover, miR-4701-5p inhibitor-induced elevation of TGF-β1 and p-Smad2/3 was significantly suppressed by SNHG8 knockdown. In conclusion, SNHG8 knockdown attenuated pulmonary fibrosis progression by regulating miR-4701-5p/MUC5B axis, which might be associated with the modulation of TGF-β1/Smad2/3 signaling. These findings reveal that lncRNA SNHG8 may become a potential target for the treatment of IPF.
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Affiliation(s)
- Xiaoping Zhang
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
| | - Runxia Shao
- Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450014, China
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Tan Y, Qiao J, Yang S, Wang Q, Liu H, Liu Q, Feng W, Yang B, Li Z, Cui L. ARID5B-mediated LINC01128 epigenetically activated pyroptosis and apoptosis by promoting the formation of the BTF3/STAT3 complex in β2GPI/anti-β2GPI-treated monocytes. Clin Transl Med 2024; 14:e1539. [PMID: 38224186 PMCID: PMC10788880 DOI: 10.1002/ctm2.1539] [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: 09/17/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Alterations of the trimethylation of histone 3 lysine 4 (H3K4me3) mark in monocytes are implicated in the development of autoimmune diseases. Therefore, the purpose of our study was to elucidate the role of H3K4me3-mediated epigenetics in the pathogenesis of antiphospholipid syndrome (APS). METHODS H3K4me3 Cleavage Under Targets and Tagmentation and Assay for Transposase-Accessible Chromatin were performed to determine the epigenetic profiles. Luciferase reporter assay, RNA immunoprecipitation, RNA pull-down, co-immunoprecipitation and chromatin immunoprecipitation were performed for mechanistic studies. Transmission electron microscopy and propidium iodide staining confirmed cell pyroptosis. Primary monocytes from patients with primary APS (PAPS) and healthy donors were utilised to test the levels of key molecules. A mouse model mimicked APS was constructed with beta2-glycoprotein I (β2GPI) injection. Blood velocity was detected using murine Doppler ultrasound. RESULTS H3K4me3 signal and open chromatin at the ARID5B promoter were increased in an in vitro model of APS. The epigenetic factor ARID5B directly activated LINC01128 transcription at its promoter. LINC01128 promoted the formation of the BTF3/STAT3 complex to enhance STAT3 phosphorylation. Activated STAT3 interacted with the NLRP3 promoter and subsequently stimulated pyroptosis and apoptosis. ARID5B or BTF3 depletion compensated for LINC01128-induced pyroptosis and apoptosis by inhibiting STAT3 phosphorylation. In mice with APS, β2GPI exposure elevated the levels of key proteins of pyroptosis and apoptosis pathways in bone marrow-derived monocytes, reduced the blood velocity of the ascending aorta, increased the thrombus size of the carotid artery, and promoted the release of interleukin (IL)-18, IL-1β and tissue factor. Patients with PAPS had the high-expressed ARID5B and LINC01128, especially those with triple positivity for antiphospholipid antibodies. Moreover, there was a positive correlation between ARID5B and LINC01128 expression. CONCLUSION This study indicated that ARID5B/LINC01128 was synergistically upregulated in APS, and they aggravated disease pathogenesis by enhancing the formation of the BTF3/STAT3 complex and boosting p-STAT3-mediated pyroptosis and apoptosis, thereby providing candidate therapeutic targets for APS. HIGHLIGHTS The H3K4me3 mark and chromatin accessibility at the ARID5B promoter are increased in vitro model mimicked APS. ARID5B-mediated LINC01128 induces pyroptosis and apoptosis via p-STAT3 by binding to BTF3. ARID5B is high- expressed in patients with primary APS and positively correlated with LINC01128 expression. OICR-9429 treatment mitigates pyroptosis and related inflammation in vivo and in vitro models mimicked APS.
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Affiliation(s)
- Yuan Tan
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Jiao Qiao
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Shuo Yang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Qingchen Wang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Hongchao Liu
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Qi Liu
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Weimin Feng
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Boxin Yang
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Zhongxin Li
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
| | - Liyan Cui
- Institute of Medical TechnologyPeking University Health Science CenterBeijingChina
- Department of Laboratory MedicinePeking University Third HospitalBeijingChina
- Core Unit of National Clinical Research Center for Laboratory MedicinePeking University Third HospitalBeijingChina
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Fenton CG, Ray MK, Meng W, Paulssen RH. Methylation-Regulated Long Non-Coding RNA Expression in Ulcerative Colitis. Int J Mol Sci 2023; 24:10500. [PMID: 37445676 DOI: 10.3390/ijms241310500] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play a role in the pathogenesis of ulcerative colitis (UC). Although epigenetic processes such as DNA methylation and lncRNA expression are well studied in UC, the importance of the interplay between the two processes has not yet been fully explored. It is, therefore, believed that interactions between environmental factors and epigenetics contribute to disease development. Mucosal biopsies from 11 treatment-naïve UC patients and 13 normal controls were used in this study. From each individual sample, both whole-genome bisulfite sequencing data (WGBS) and lncRNA expression data were analyzed. Correlation analysis between lncRNA expression and upstream differentially methylated regions (DMRs) was used to identify lncRNAs that might be regulated by DMRs. Furthermore, proximal protein-coding genes associated with DMR-regulated lncRNAs were identified by correlating their expression. The study identified UC-associated lncRNAs such as MIR4435-2HG, ZFAS1, IL6-AS1, and Pvt1, which may be regulated by DMRs. Several genes that are involved in inflammatory immune responses were found downstream of DMR-regulated lncRNAs, including SERPINB1, CCL18, and SLC15A4. The interplay between lncRNA expression regulated by DNA methylation in UC might improve our understanding of UC pathogenesis.
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Affiliation(s)
- Christopher G Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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Pan J, Zhan C, Yuan T, Gu W, Wang W, Sun Y, Chen L. Long noncoding RNA signatures in intrauterine infection/inflammation-induced lung injury: an integrative bioinformatics study. BMC Pulm Med 2023; 23:194. [PMID: 37280583 DOI: 10.1186/s12890-023-02505-5] [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: 08/08/2022] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intrauterine infection/inflammation can result in fetal and neonatal lung injury. However, the biological mechanisms of intrauterine infection/inflammation on fetal and neonatal lung injury and development are poorly known. To date, there are no reliable biomarkers for improving intrauterine infection/inflammation-induced lung injury. METHODS An animal model of intrauterine infection/inflammation-induced lung injury was established with pregnant Sprague-Dawley rats inoculated with Escherichia coli suspension. The intrauterine inflammatory status was assessed through the histological examination of the placenta and uterus. A serial of histological examinations of the fetal and neonatal rats lung tissues were performed. The fetal and neonatal rat lung tissues were harvested for next generation sequencing at embryonic day 17 and postnatal day 3, respectively. Differentially expressed mRNAs and lncRNAs were identified by conducting high-throughput sequencing technique. The target genes of identified differentially expressed lncRNAs were analyzed. Homology analyses for important differentially expressed lncRNAs were performed. RESULTS The histopathological results showed inflammatory infiltration, impaired alveolar vesicular structure, less alveolar numbers, and thickened alveolar septa in fetal and neonatal rat lung tissues. Transmission electron micrographs revealed inflammatory cellular swelling associated with diffuse alveolar damage and less surfactant-storing lamellar bodies in alveolar epithelial type II cells. As compared with the control group, there were 432 differentially expressed lncRNAs at embryonic day 17 and 125 differentially expressed lncRNAs at postnatal day 3 in the intrauterine infection group. The distribution, expression level, and function of these lncRNAs were shown in the rat genome. LncRNA TCONS_00009865, lncRNA TCONS_00030049, lncRNA TCONS_00081686, lncRNA TCONS_00091647, lncRNA TCONS_00175309, lncRNA TCONS_00255085, lncRNA TCONS_00277162, and lncRNA TCONS_00157962 may play an important role in intrauterine infection/inflammation-induced lung injury. Fifty homologous sequences in Homo sapiens were also identified. CONCLUSIONS This study provides genome-wide identification of novel lncRNAs which may serve as potential diagnostic biomarkers and therapeutic targets for intrauterine infection/inflammation-induced lung injury.
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Affiliation(s)
- Jiarong Pan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Canyang Zhan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Tianming Yuan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China.
| | - Weizhong Gu
- Zhejiang Key Laboratory for Diagnosis and Therapy of Neonatal Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Weiyan Wang
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Yi Sun
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Lihua Chen
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
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Yi E, Lin B, Zhang Y, Wang X, Zhang J, Liu Y, Jin J, Hong W, Lin Z, Cao W, Mei X, Bai G, Bing Li B, Zhou Y, Ran P. Smad3-mediated lncRNA HSALR1 enhances the non-classic signalling pathway of TGF-β1 in human bronchial fibroblasts by binding to HSP90AB1. Clin Transl Med 2023; 13:e1292. [PMID: 37317677 PMCID: PMC10267427 DOI: 10.1002/ctm2.1292] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/17/2023] [Accepted: 05/27/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is one of the diseases with high mortality and morbidity with complex pathogenesis. Airway remodeling is an unavoidable pathological characteristic. However, the molecular mechanisms of airway remodeling are incompletely defined. METHODS lncRNAs highly correlated with transforming growth factor beta 1(TGF-β1) expression were chosen, the lncRNA ENST00000440406 (named HSP90AB1 Assoicated LncRNA 1, HSALR1) was chosen for further functional experiments. Dual luciferase and ChIP assay were used to detect the upstream of HSALR1, transcriptome sequencing, Cck-8, Edu, cell proliferation, cell cycle assay, and WB detection of pathway levels confirmed the effect of HSALR1 on fibroblast proliferation and phosphorylation levels of related pathways. Mice was infected with adeno-associated virus (AAV) to express HSALR1 by intratracheal instillation under anesthesia and was exposure to cigarette smoke, then mouse lung function was performed and the pathological sections of lung tissues were analyzed. RESULTS Herein, lncRNA HSALR1 was identified as highly correlated with the TGF-β1 and mainly expressed in human lung fibroblasts. HSALR1 was induced by Smad3 and promoted fibroblasts proliferation. Mechanistically, it could directly bind to HSP90AB1 protein, and acted as a scaffold to stabilize the binding between Akt and HSP90AB1 to promote Akt phosphorylation. In vivo, mice expressed HSALR1 by AAV was exposure to cigarette smoke (CS) for COPD modeling. We found that lung function was worse and airway remodeling was more pronounced in HSLAR1 mice compare to wild type (WT) mice. CONCLUSION Our results suggest that lncRNA HSALR1 binds to HSP90AB1 and Akt complex component, and enhances activity of the TGF-β1 smad3-independent pathway. This finding described here suggest that lncRNA can participate in COPD development, and HSLAR1 is a promising molecular target of COPD therapy.
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Affiliation(s)
- Erkang Yi
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Biting Lin
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Yi Zhang
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xiaoyu Wang
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jiahuan Zhang
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Yu Liu
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jing Jin
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Wei Hong
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Zhiwei Lin
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Weitao Cao
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xinyue Mei
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Ge Bai
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Bing Bing Li
- GMU‐GIBH Joint School of Life SciencesGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Yumin Zhou
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
| | - Pixin Ran
- Guangzhou Institute of Respiratory Health & State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease & National Center for Respiratory MedicineThe First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdongChina
- Guangzhou LaboratoryBiolandGuangzhouGuangdongChina
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8
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Small AM, Peloso G, Linefsky J, Aragam J, Galloway A, Tanukonda V, Wang LC, Yu Z, Selvaraj MS, Farber-Eger EH, Baker MT, Setia-Verma S, Lee SSK, Preuss M, Ritchie M, Damrauer SM, Rader DJ, Wells QS, Loos RJF, Lubitz S, Thanassoulis G, Cho K, Wilson PWF, Natarajan P, O’Donnell CJ. Multiancestry Genome-Wide Association Study of Aortic Stenosis Identifies Multiple Novel Loci in the Million Veteran Program. Circulation 2023; 147:942-955. [PMID: 36802703 PMCID: PMC10806851 DOI: 10.1161/circulationaha.122.061451] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/15/2022] [Indexed: 02/22/2023]
Abstract
BACKGROUND Calcific aortic stenosis (CAS) is the most common valvular heart disease in older adults and has no effective preventive therapies. Genome-wide association studies (GWAS) can identify genes influencing disease and may help prioritize therapeutic targets for CAS. METHODS We performed a GWAS and gene association study of 14 451 patients with CAS and 398 544 controls in the Million Veteran Program. Replication was performed in the Million Veteran Program, Penn Medicine Biobank, Mass General Brigham Biobank, BioVU, and BioMe, totaling 12 889 cases and 348 094 controls. Causal genes were prioritized from genome-wide significant variants using polygenic priority score gene localization, expression quantitative trait locus colocalization, and nearest gene methods. CAS genetic architecture was compared with that of atherosclerotic cardiovascular disease. Causal inference for cardiometabolic biomarkers in CAS was performed using Mendelian randomization and genome-wide significant loci were characterized further through phenome-wide association study. RESULTS We identified 23 genome-wide significant lead variants in our GWAS representing 17 unique genomic regions. Of the 23 lead variants, 14 were significant in replication, representing 11 unique genomic regions. Five replicated genomic regions were previously known risk loci for CAS (PALMD, TEX41, IL6, LPA, FADS) and 6 were novel (CEP85L, FTO, SLMAP, CELSR2, MECOM, CDAN1). Two novel lead variants were associated in non-White individuals (P<0.05): rs12740374 (CELSR2) in Black and Hispanic individuals and rs1522387 (SLMAP) in Black individuals. Of the 14 replicated lead variants, only 2 (rs10455872 [LPA], rs12740374 [CELSR2]) were also significant in atherosclerotic cardiovascular disease GWAS. In Mendelian randomization, lipoprotein(a) and low-density lipoprotein cholesterol were both associated with CAS, but the association between low-density lipoprotein cholesterol and CAS was attenuated when adjusting for lipoprotein(a). Phenome-wide association study highlighted varying degrees of pleiotropy, including between CAS and obesity at the FTO locus. However, the FTO locus remained associated with CAS after adjusting for body mass index and maintained a significant independent effect on CAS in mediation analysis. CONCLUSIONS We performed a multiancestry GWAS in CAS and identified 6 novel genomic regions in the disease. Secondary analyses highlighted the roles of lipid metabolism, inflammation, cellular senescence, and adiposity in the pathobiology of CAS and clarified the shared and differential genetic architectures of CAS with atherosclerotic cardiovascular diseases.
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Affiliation(s)
- Aeron M Small
- Department of Cardiology, Boston Veterans Affairs Healthcare System, West Roxbury, MA, USA
- Cardiovascular Medicine Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, MA, USA
| | - Gina Peloso
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs, Boston Healthcare System, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States
| | - Jason Linefsky
- Atlanta Veterans Affairs Medical Center, Decatur, Georgia
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jayashri Aragam
- Department of Cardiology, Boston Veterans Affairs Healthcare System, West Roxbury, MA, USA
| | - Ashley Galloway
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs, Boston Healthcare System, Boston, Massachusetts
| | | | - Lu-Chen Wang
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA, 02114
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA, 02142
| | - Zhi Yu
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA, 02114
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA, 02142
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Margaret Sunitha Selvaraj
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA, 02114
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Eric H Farber-Eger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States, 37232
| | - Michael T Baker
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Shefali Setia-Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon SK Lee
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
| | - Michael Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
| | - Marylyn Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA, 19104
- Corporal Michael Crescenz VA Medical Center, Philadelphia, PA, USA, 19104
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Quinn S Wells
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - Steven Lubitz
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA, 02114
| | - George Thanassoulis
- Department of Medicine, Division of Experimental Medicine, McGill University Health Center, 1001 Decarie Boulevard, Montreal, QC H4A 3J1, Canada
| | - Kelly Cho
- Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), Veterans Affairs, Boston Healthcare System, Boston, Massachusetts
| | - Peter WF Wilson
- Atlanta Veterans Affairs Medical Center, Decatur, Georgia
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | | | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA, 02114
- Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA, 02142
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston
- Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston
| | - Christopher J O’Donnell
- Department of Cardiology, Boston Veterans Affairs Healthcare System, West Roxbury, MA, USA
- Cardiovascular Medicine Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, MA, USA
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9
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Liu R, Lv D, Cao L, Liu Y, Wen X, Jiang Y, Xu J, Qin J, Qin P. The hub genes and their potential regulatory mechanisms in chronic spontaneous urticaria revealed by integrated transcriptional expression analysis. Exp Dermatol 2023. [PMID: 36856573 DOI: 10.1111/exd.14785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 02/26/2023] [Indexed: 03/02/2023]
Abstract
Chronic spontaneous urticaria (CSU) is a recurrent disease characterized by wheals and or angioedema, and its pathogenesis is still unclear. The microarray datasets of skin tissue from CSU patients and healthy controls were integrated and analysed in Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using the NetworkAnalyst tool. Then, the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Subsequently, a protein-protein interaction (PPI) network of DEGs was constructed by STRING and the related hub genes were identified through the MOCDE tool. The potential miRNAs targeting hub genes were predicted based on the intersection of three online databases, namely TargetScanHuman, TargetBase and miRNet. Differentially expressed lncRNAs (DElncRNAs) was performed using the GEO2R tool. The potential miRNAs targeting DElncRNAs were predicted through miRNet. Finally, the shared miRNAs targeting both hub genes and DElncRNAs were used to construct an mRNA/miRNA/lncRNA regulatory network. A total of 296 DEGs were obtained, which were mainly enriched in inflammatory and immune responses. Further, 14 hub genes were identified by the PPI network of DEGs. Clinical correlation analysis showed that the mRNA expressions of S100A7, S100A8, S100A9, S100A12, IL6 and SOCS3 in CSU were positively correlated with the 7-day urticaria activity score (UAS7), and their potential diagnostic value was supported by the receiver operating characteristic curve (ROC) analysis. Five up-regulated lncRNAs in the cytoplasm were obtained by DElncRNAs analysis. The ROC analysis showed that PVT1, SNHG3 and ZBTB20 - AS1 was of potential diagnostic value for CSU. Eight shared miRNAs targeting both hub genes and DElncRNAs were identified and used to construct a competing endogenous RNA (ceRNA) network. It was found that the IL-6/miR - 149 - 5p/ZBTB20 - AS1 axis might play an important role in the activation of mast cells in CSU. IL-6 and its related regulatory molecules may be used as potential diagnostic markers and therapeutic targets for CSU.
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Affiliation(s)
- Runqiu Liu
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Dong Lv
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Lihua Cao
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Yu Liu
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Xiaoting Wen
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Yannan Jiang
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Jiandan Xu
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
| | - Jie Qin
- Department of Pediatrics, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Pediatrics, The First people's Hospital of Yancheng, Yancheng, China
| | - Pingping Qin
- Department of Dermatology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China.,Department of Dermatology, The First people's Hospital of Yancheng, Yancheng, China
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10
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Genetic screening of MMP1 as a potential pathogenic gene in chronic obstructive pulmonary disease. Life Sci 2023; 313:121214. [PMID: 36442527 DOI: 10.1016/j.lfs.2022.121214] [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: 09/15/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Airway inflammation and remodeling are the two key processes involved in COPD pathogenesis. However, the key pathogenic genes driving COPD development have not been revealed. This study aims to identify and validate hub gene(s) underlying COPD development through bioinformatics analysis and experimental validation. METHODS Three lung tissue sequencing datasets of the COPD (including GSE38974, GSE103174, and GSE106986) were analyzed. Further, differentially expressed genes (DEGs) were used to compare patients with COPD with non-COPD individuals, and the Robust Rank Aggregation (RRA) analysis was also performed. Results revealed a series of potential pathogenic genes of COPD. DEGs were subjected to KEGG, GO, and GSEA analyses. The scRNA dataset of human lung tissues (Human Lung Cell Atlas), and human primary airway epithelial cells (GSE134147) were used to identify the cell subtype localization. The qRT-PCR assay was performed in the human lung tissues, COPD mice model, and primary bronchial epithelial cells at the air-liquid interface (ALI) under cigarette smoke extract (CSE) stimulation to verify the expression of the hub genes. LASSO and GLM analysis with the hub genes were performed to identify the most critical gene. RNA-seq was performed after knocking down the critical gene using siRNA in HBECs at ALI. The potential role of the critical gene was confirmed through qRT-PCR, Western blot, and Immunofluorescence (IF) assays. RESULTS A total of 98 genes were significantly and differently expressed in 3 GEO datasets. The KEGG and GO analyses showed that most of these genes are responsible for inflammation, immunity, and cell proliferation. The core gene set including 15 genes was screened out and consequently, the MMP1 was the most likely responsible for the progression of COPD. Moreover, we confirmed that MMP1 is significantly related to inflammatory effects and cilia function in human bronchial epithelial cells cultured at the air-liquid interface (ALI). CONCLUSION In summary, we confirmed that inflammation and cell proliferation are potentially critical processes in COPD occurrence and development. A total of 15 potential hub genes were identified among which MMP1 was the most likely gene responsible for the development of COPD. Therefore, MMP1 is a potential molecular target of COPD therapy.
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11
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Papageorgiou L, Papakonstantinou E, Diakou I, Pierouli K, Dragoumani K, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Semantic and Population Analysis of the Genetic Targets Related to COVID-19 and Its Association with Genes and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:59-78. [PMID: 37525033 DOI: 10.1007/978-3-031-31978-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multifaceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread, and therapeutics are currently under development. Toward this goal, scientific attention is shifting toward variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2-related publications, which yielded a repertoire of SNPs, genes, and disease ontologies. Population data from the 1000 Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts toward precision medicine.
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Affiliation(s)
- Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece.
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece.
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece.
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12
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Song B, Wu S, Ye L, Jing Z, Cao J. Circular RNA 0000157 depletion protects human bronchial epithelioid cells from cigarette smoke extract-induced human bronchial epithelioid cell injury through the microRNA-149-5p/bromodomain containing 4 pathway. Hum Exp Toxicol 2023; 42:9603271231167581. [PMID: 37533154 DOI: 10.1177/09603271231167581] [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] [Indexed: 08/04/2023]
Abstract
BACKGROUND Circular RNA (circRNA) has been reported to regulate respiratory diseases. In the study, we aimed to elucidate the role of circ_0000157 in smoke-related chronic obstructive pulmonary disease (COPD) and the inner mechanism. METHODS COPD-like cell injury was induced by treating human bronchial epithelioid cells (16HBE) with cigarette smoke extract (CSE). The expression of circ_0000157, miR-149-5p, bromodomain containing 4 (BRD4), BCL2-associated x protein (Bax) and B-cell lymphoma-2 (Bcl-2) was analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) or Western blotting. Enzyme-linked immunosorbent assay was performed to detect interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) levels. Malondialdehyde (MDA) production was detected by a lipid peroxidation MDA assay kit. Superoxide dismutase (SOD) activity was analyzed by a SOD activity assay kit. RESULTS Circ_0000157 and BRD4 expression were upregulated, while miR-149-5p expression was downregulated in the blood of smokers with COPD and CSE-induced 16HBE cells compared with control groups. CSE treatment inhibited 16HBE cell proliferation and induced cell apoptosis, inflammation, and oxidative stress; however, these effects were remitted when circ_0000157 expression was decreased. In addition, circ_0000157 acted as a miR-149-5p sponge and regulated CSE-caused 16HBE cell damage by targeting miR-149-5p. The overexpression of BRD4, a target gene of miR-149-5p, attenuated the inhibitory effects of miR-149-5p introduction on CSE-induced cell damage. Further, circ_0000157 modulated BRD4 expression by associating with miR-149-5p in CSE-treated 16HBE cells. CONCLUSION Circ_0000157 knockdown ameliorated CSE-caused 16HBE cell damage by targeting the miR-149-5p/BRD4 pathway, providing a potential therapeutic strategy for clinic intervention in COPD.
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Affiliation(s)
- B Song
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - S Wu
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - L Ye
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Z Jing
- Department of Pharmacy, The Fourth Hospital of Shijiazhuang, Shijiazhuang, China
| | - J Cao
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Liu X, Wang J, Duan L, Zhang Y, Yang D. lncRNAs have special significance in diagnosis and therapy for cancer and inflammation. Cell Biol Toxicol 2022; 38:923-925. [PMID: 36418596 DOI: 10.1007/s10565-022-09781-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Xuanqi Liu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
| | - Jiongyuan Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China
| | - Lian Duan
- Faculty of Pediatrics, the Chinese PLA General Hospital, Beijing, China
| | - Yong Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.
| | - Dong Yang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, China.
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14
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Han H, Hao L. Revealing lncRNA Biomarkers Related to Chronic Obstructive Pulmonary Disease Based on Bioinformatics. Int J Chron Obstruct Pulmon Dis 2022; 17:2487-2515. [PMID: 36217332 PMCID: PMC9547624 DOI: 10.2147/copd.s354634] [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: 12/30/2021] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a common chronic disease of the respiratory tract, with high prevalence, high disability, and poor prognosis. However, the molecular mechanism of COPD needs to be further revealed. Methods We obtained the gene expression profile and miRNA expression profile of COPD patients from Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmis) in COPD were identified. Subsequently, the COPD-related ceRNA network was constructed based on the interaction between lncRNA, miRNA, and mRNA using the lncACTdb database. Finally, the Cytoscape software was used to analyze the network topology and COPD-related lncRNAs. Results Firstly, the 519 DEGs and 17 DEmis were identified from COPD GEO datasets. GO enrichment showed that leukocyte chemotaxis, cell chemotaxis, and myeloid leukocyte migration were upregulated, and muscle and membrane repolarization-related biological progress were downregulated in COPD. KEGG pathway enrichment shows that the p53 pathway was upregulated in COPD. Hallmark enrichment showed that chronic neutrophil inflammation was a sign of the pathogenesis of COPD. Next, a ceRNA network including 93 DEGs, 2 DEmi, 463 lncRNAs, and 1157 DEG-lncRNA, DEmi-lncRNA, and DEmi-DEG interactions were obtained. The hub-lncRNA (the network is ranked in the top 10) as the core marker of COPD, including SNHG12, SLFNL1-AS1, KCNQ1OT1, XIST, EAF1-AS1, FOXD2-AS1, NORAD, PINK1-AS and RP11-69E11.4. And the cytoHubba analysis identified ATM, SMAD7 and HIF1A as hub genes of ceRNA network. Conclusion This study provides a landscape of ceRNA network of COPD, which help to reveal the underlying pathophysiological mechanisms of COPD and shed light on novel therapeutic strategies for COPD.
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Affiliation(s)
- Hui Han
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, People’s Republic of China
| | - Lu Hao
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, People’s Republic of China,Correspondence: Lu Hao, Area B, Department of Respiratory Medicine, Affiliated Hospital of Inner Mongolia Medical University, No. 1 Tongdao North Street, Huimin District, Hohhot, 010010, Inner Mongolia Autonomous Region, People’s Republic of China, Email
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15
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He F, Wang N, Yu X, Zheng Y, Liu Q, Chen Q, Pu J, Li N, Zou W, Li B, Ran P. GATA3/long noncoding RNA MHC-R regulates the immune activity of dendritic cells in chronic obstructive pulmonary disease induced by air pollution particulate matter. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129459. [PMID: 35780733 DOI: 10.1016/j.jhazmat.2022.129459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous illness associated with aberrant inflammatory immune reaction in the lung in response to noxious particles and gases. Our previous epidemiological studies discovered that long-term exposure to air pollution PM was associated with an increase in the incidence of COPD and lung function decline, but the impact of air pollution on the onset of COPD and its pathogenesis remains obscure. In recent years, long noncoding RNAs (lncRNAs) have been documented to have a crucial role in COPD. Our preliminary study found that the expression of lncRNA MHC-R in the lung tissues of rats exposed to air pollution PM was dramatically elevated, and the specific expression was mainly focused on the immune-related MHC I, antigen-presenting, and adaptive immune response. After transcription factor prediction, it was found that GATA3 could be combined with the specific sequence of the lncRNA MHC-R promoter region. Dendritic cells (DCs) are necessary antigen-presenting cells (APCs) with the most potent antigen-presenting function. We proved that GATA3/lncRNA MHC-R might regulate the immune activities of DCs to participate in the pathogenic mechanism of COPD induced by air pollution PM, which opens up a new way for early COPD diagnosis and treatment.
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Affiliation(s)
- Fang He
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China; School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Nian Wang
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Xiaoyuan Yu
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Yufan Zheng
- Zhongshan School of Medical, Sun Yat-sen University//Center for Pain Research, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Qun Liu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, Guangdong 510000, China
| | - Qingzi Chen
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Jinding Pu
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Naijian Li
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Weifeng Zou
- Guangzhou Chest Hospital, Guangzhou, Guangdong 510000, China
| | - Bing Li
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Pixin Ran
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510000, China.
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16
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Zhong Y, Ashley CL, Steain M, Ataide SF. Assessing the suitability of long non-coding RNAs as therapeutic targets and biomarkers in SARS-CoV-2 infection. Front Mol Biosci 2022; 9:975322. [PMID: 36052163 PMCID: PMC9424846 DOI: 10.3389/fmolb.2022.975322] [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: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts that are over 200 nucleotides and rarely encode proteins or peptides. They regulate gene expression and protein activities and are heavily involved in many cellular processes such as cytokine secretion in respond to viral infection. In severe COVID-19 cases, hyperactivation of the immune system may cause an abnormally sharp increase in pro-inflammatory cytokines, known as cytokine release syndrome (CRS), which leads to severe tissue damage or even organ failure, raising COVID-19 mortality rate. In this review, we assessed the correlation between lncRNAs expression and cytokine release syndrome by comparing lncRNA profiles between COVID-19 patients and health controls, as well as between severe and non-severe cases. We also discussed the role of lncRNAs in CRS contributors and showed that the lncRNA profiles display consistency with patients’ clinic symptoms, thus suggesting the potential of lncRNAs as drug targets or biomarkers in COVID-19 treatment.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Caroline L. Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sandro Fernandes Ataide
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Sandro Fernandes Ataide,
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17
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Manevski M, Devadoss D, Long C, Singh SP, Nasser MW, Borchert GM, Nair MN, Rahman I, Sopori M, Chand HS. Increased Expression of LASI lncRNA Regulates the Cigarette Smoke and COPD Associated Airway Inflammation and Mucous Cell Hyperplasia. Front Immunol 2022; 13:803362. [PMID: 35774797 PMCID: PMC9237255 DOI: 10.3389/fimmu.2022.803362] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/09/2022] [Indexed: 12/04/2022] Open
Abstract
Research Impact Cigarette smoke (CS) exposure is strongly associated with chronic obstructive pulmonary disease (COPD). In respiratory airways, CS exposure disrupts airway barrier functions, mucous/phlegm production, and basic immune responses of airway epithelial cells. Based on our recent identification of a specific immunomodulatory long noncoding RNA (lncRNA), we investigated its role in CS-induced responses in bronchial airways of cynomolgus macaque model of CS-induced COPD and in former smokers with and without COPD. The lncRNA was significantly upregulated in CS-induced macaque airways and in COPD airways that exhibited higher mucus expression and goblet cell hyperplasia. Experimental models of cells derived from COPD subjects recapitulated the augmented inflammation and mucus expression following the smoke challenge. Blocking of lncRNA expression in cell culture setting suppressed the smoke-induced and COPD-associated dysregulated mucoinflammatory response suggesting that this airway specific immunomodulatory lncRNA may represent a novel target to mitigate the smoke-mediated inflammation and mucus hyperexpression. Rationale In conducting airways, CS disrupts airway epithelial functions, mucociliary clearances, and innate immune responses that are primarily orchestrated by human bronchial epithelial cells (HBECs). Mucus hypersecretion and dysregulated immune response are the hallmarks of chronic bronchitis (CB) that is often exacerbated by CS. Notably, we recently identified a long noncoding RNA (lncRNA) antisense to ICAM-1 (LASI) that mediates airway epithelial responses. Objective To investigate the role of LASI lncRNA in CS-induced airway inflammation and mucin hyperexpression in an animal model of COPD, and in HBECs and lung tissues from former smokers with and without COPD. To interrogate LASI lncRNA role in CS-mediated airway mucoinflammatory responses by targeted gene editing. Methods Small airway tissue sections from cynomolgus macaques exposed to long-term mainstream CS, and those from former smokers with and without COPD were analyzed. The structured-illumination imaging, RNA fluorescence in-situ hybridization (FISH), and qRT-PCR were used to characterize lncRNA expression and the expression of inflammatory factors and airway mucins in a cell culture model of CS extract (CSE) exposure using HBECs from COPD (CHBEs) in comparison with cells from normal control (NHBEs) subjects. The protein levels of mucin MUC5AC, and inflammatory factors ICAM-1, and IL-6 were determined using specific ELISAs. RNA silencing was used to block LASI lncRNA expression and lentivirus encoding LASI lncRNA was used to achieve LASI overexpression (LASI-OE). Results Compared to controls, LASI lncRNA was upregulated in CS-exposed macaques and in COPD smoker airways, correlating with mucus hyperexpression and mucus cell hyperplasia in severe COPD airways. At baseline, the unstimulated CHBEs showed increased LASI lncRNA expression with higher expression of secretory mucin MUC5AC, and inflammatory factors, ICAM-1, and IL-6 compared to NHBEs. CSE exposure of CHBEs resulted in augmented inflammation and mucus expression compared to controls. While RNA silencing-mediated LASI knockdown suppressed the mucoinflammatory response, cells overexpressing LASI lncRNA showed elevated mRNA levels of inflammatory factors. Conclusions Altogether, LASI lncRNA may represent a novel target to control the smoke-mediated dysregulation in airway responses and COPD exacerbations.
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Affiliation(s)
- Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Christopher Long
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Shashi P. Singh
- Respiratory Immunology Program, Lovelace Respiratory Research Institute, Albuquerque, NM, United States
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL, United States
| | - Madhavan N. Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Mohan Sopori
- Respiratory Immunology Program, Lovelace Respiratory Research Institute, Albuquerque, NM, United States
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
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18
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Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis. Int J Mol Sci 2022; 23:ijms23105801. [PMID: 35628612 PMCID: PMC9146199 DOI: 10.3390/ijms23105801] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 12/07/2022] Open
Abstract
In the last few years, more and more scientists have suggested and confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. This is particularly interesting for a better understanding of processes that occur in the development and progression of various diseases. Appearing on the preclinical stages of diseases, epigenetic aberrations may be prominent biomarkers. Being dynamic and reversible, epigenetic modifications could become targets for a novel option for therapy. Therefore, in this review, we are focusing on histone modifications and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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19
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Lin Y, Qiu T, Wei G, Que Y, Wang W, Kong Y, Xie T, Chen X. Role of Histone Post-Translational Modifications in Inflammatory Diseases. Front Immunol 2022; 13:852272. [PMID: 35280995 PMCID: PMC8908311 DOI: 10.3389/fimmu.2022.852272] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammation is a defensive reaction for external stimuli to the human body and generally accompanied by immune responses, which is associated with multiple diseases such as atherosclerosis, type 2 diabetes, Alzheimer’s disease, psoriasis, asthma, chronic lung diseases, inflammatory bowel disease, and multiple virus-associated diseases. Epigenetic mechanisms have been demonstrated to play a key role in the regulation of inflammation. Common epigenetic regulations are DNA methylation, histone modifications, and non-coding RNA expression; among these, histone modifications embrace various post-modifications including acetylation, methylation, phosphorylation, ubiquitination, and ADP ribosylation. This review focuses on the significant role of histone modifications in the progression of inflammatory diseases, providing the potential target for clinical therapy of inflammation-associated diseases.
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Affiliation(s)
- Yingying Lin
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Ting Qiu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Guifeng Wei
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yueyue Que
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Wenxin Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Department of Pharmacology, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yichao Kong
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xiabin Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
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20
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Liu Q. The emerging roles of exosomal long non-coding RNAs in bladder cancer. J Cell Mol Med 2022; 26:966-976. [PMID: 34981655 PMCID: PMC8831985 DOI: 10.1111/jcmm.17152] [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: 10/08/2021] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs), especially exosomes, have been reported to play essential roles as extracellular messengers by transporting goods in various diseases, while their potential roles in bladder cancer (BC) still remain to be further studied. BC exhibits a high degree of chemoresistance and metastatic ability, which may be affected by cancer‐derived exosomes that carry proteins, lipids and RNA. To date, the most studied exosomal molecular cargo is long non‐coding RNA (lncRNA). Although there is increasing interest in its role and function, there is relatively little knowledge about it compared with other RNA transcripts. Nevertheless, in the past ten years, we have witnessed increasing interest in the role and function of lncRNA. For example, lncRNAs have been studied as potential biomarkers for the diagnosis of BC. They may play a role as a therapeutic target in precision medicine, but they may also be directly involved in the characteristics of tumour progression, such as metastasis, epithelial‐mesenchymal transition and drug resistance. Cancer cells are on chemotherapy acting. The function of lncRNA in various cancer exosomes has not yet been determined. In this review, we summarize the current studies about the prominent roles of exosomal lncRNAs in genome integrity, BC progression and carcinogenic features.
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Affiliation(s)
- Qiang Liu
- Department of Urology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, China
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